http://2011.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=250&target=Gngr2011.igem.org - User contributions [en]2024-03-29T14:19:11ZFrom 2011.igem.orgMediaWiki 1.16.0http://2011.igem.org/Team:METU-BIN_Ankara/ContactTeam:METU-BIN Ankara/Contact2011-11-21T22:57:35Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>Contact Information</h2><br />
<p class="p"><strong>Adress:</strong> İnönü Blvd. METU Informatics Institute B-207, Çankaya, Ankara, 06531, TURKEY</p><br />
<p class="p"><strong>Phone:</strong> +90 312 210 7708<br><br />
<strong>Fax:</strong> +90 312 210 3745<br><br />
<strong>E-mail:</strong> metu-bin [at] ii [dot] metu [dot] edu [dot] tr<br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/FromPressTeam:METU-BIN Ankara/FromPress2011-11-21T22:57:08Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>METU-BIN From Press</h2><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/NextVersionTeam:METU-BIN Ankara/NextVersion2011-11-21T22:56:30Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>Next Version: Future Plans</h2><br />
<h3>NEW FEATURES TO BE INCLUDED in M4B by 2012</h3><br />
<p class="p">Features we would like to introduce in the next version of “Mining for BioBricks” can be listed under two categories.</p><br />
<ul style="list-style:decimal;"><br />
<li><strong>Improvements on our code</strong> that we couldn’t add this year due to limited time for the development of the software.<br />
<ul style="list-style:disc;"><br />
<li>Offering search options for multiple input and output parameters.</li><br />
<li>Including all possible biobrick categories in search algorithm, such as DNA, linker etc. Current vesion of M4B is limited to basic parts, which are promoter, RBS, gene, and terminator.</li><br />
<li>Providing link-outs for gene products to external databases such as NCBI, ENSEMBL.</li><br />
</ul><br />
</li><br />
<li><strong>Improvements to the Parts Registry</strong> that are needed so new information provided can be utilized by our software.<br />
<ul style="list-style:disc;"><br />
<li>In the next version of M4B we are planning to integrate with SBOL. This year we have tried to demonstrate SBOL symbols at least in a limited way, but we faced difficulty in assigning the right categories. For example iGEM classifies biobricks as terminators but in SBOL there are three different subclasses for a terminator and no symbol for a general terminator. Therefore, we suggest that biobricks in the Parts Registry needs to be characterized according to SBOL first, then we can utilize this information to <strong>provide SBOL codes to present and share the composite device results choices M4B suggests.</strong></li><br />
<li><strong>We would like to add safety warnings for the composite devices that contain subparts with potential threats.</strong> In order to integrate this into M4B, Classification of bioparts in the Parts Registry with gene products that are pathogenic, infective or toxic with potential threats to researchers, public health and environment, is needed. When this information is available, the subparts can be tagged within the composite devices presented in query results to warn the users. By this way, users of the Parts Registry will be aware of the potential dangers of any bioparts they are planning to use in their devices.</li><br />
</ul><br />
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</ul><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/CollaborationsTeam:METU-BIN Ankara/Collaborations2011-11-21T22:56:09Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#HIBIT11_Roundtable">HIBIT'11 Roundtable</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#Teknovasyon_2011">Teknovasyon 2011</a></li><br />
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<h2>Collaborations</h2><br />
<p class="p">Our software, <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">M4B: Mining for BioBricks</a>, is available for everyone, you can find us on the Community Page soon!</p><br />
<h3>METU-Ankara</h3><br />
<p class="p">Since M4B contains bioparts from 2011 distribution in its database and we know METU-Ankara Team who are engineering E.Coli to decrease harmful effects of methane gas use 2011 distribution as well, we sent it them.</p><br />
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<p class="p">Their feedback is the following.</p><br />
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<span style="width:250px;height:auto;float:left;margin:0 10px 0 0;"><a href="https://static.igem.org/mediawiki/2011/b/bf/Metu-ankara-ss.png" target="_blank"><img style="border:1px solid #ccc;width:250px;height:auto;" src="https://static.igem.org/mediawiki/2011/b/bf/Metu-ankara-ss.png" /></a><br><small style="color:#ccc;">Click on the image to view larger size.</small></span><br />
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<p class="p">"We are constructing a device that is induced by IPTG and that gives lysis enzymes and GFP as the outputs because, in order to elute methanol we need to kill our modified cells that convert ambient methane to methanol and the reason why we want GFP as one output is to be sure that it works. Our modelled device has promoter induced by IPTG, RBS, gene coding GFP and lysis cassette ending with cell death and we are glad to have it and it's working how we expected. So then, we use M4B to see that if it finds the exact device or the device that can do the same job. Since the software has only one place for output, we queried IPTG as an input and GFP as an output on the software and got corresponding 117 results. These results contain devices exactly what we have one for the same operation. However, we couldn't find the lysozyme output for the IPTG input in the software."</p><br />
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<p class="p">We are pleased to hear the feedback of METU-Ankara Team and it's good the know that their first query on our software was successful. As for the second one, we haven't included DNA, RNA and tags yet. It's one of our future plans and next year, it'll be done. Furthermore, queries with multiple inputs or outputs will be available. So, in one operation, they will be able to get what they want. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/NextVersion">See our future plans on the next version</a>.</p><br />
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<h3>Uppsala-Sweden</h3><br />
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We also collaborated with the team Uppsala-Sweden. Below, you can see their feedback on our project, the software: M4B: Mining for BİoBrick.<br />
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<p class="p">"The METU-BIN_Ankara team provided us their software which they developed for their project to test it if we can use for our Project. We examined the software by searching the parts that have been used during our Project.We used red,blue and green lights as input which activate red sensor(cph8), green sensor(ccaS) and blue sensor(YF1). We are aiming to get three colours as output which are blue output(amilCP), red output(mCherry) and green/yellow output(amilGFP).<br />
<br />
<p class="p">However, we got no result for our specific input - output relations but, the software has some of the inputs and outputs.</p><br />
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<p class="p">This software is very helpful to search the parts and check if the parts are in the standart registry database and decide which parts work effectively with eachother as well.That provides an easy start to constract the parts and give more efficient results.</p><br />
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<p class="p">We appreciate METU-BIN_Ankara team to create that software and believe that it will be a very helpful software which will solve the problems that we or another teams faced up in the beginning.</p><br />
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<p class="p">The software can be improved further by adding more parameters."</p><br />
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<p class="p">We are happy to see that they use and have positive expressions on our software. As we got the information about their project, they are adding some of the bioparts of their modified device newly into the Registry. Because of this, and since our software has 2011 spring distribution in its database, it's normal to get no results for their specific device. However, when they'll add them and our database is updated, finally our software will be able to find that specific result.</p><br />
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<p class="p">At the same time, our team has given a feedback on the Biosafety document of the team Uppsala-Sweden, you can read it <a href="https://2011.igem.org/Team:Uppsala-Sweden/Feedback" target="_blank">on this page</a>.</p><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank">Click to see!</a><br />
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<div class="margin"><h6>Do you care safety?</h6><br />
Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/HumanPracticeTeam:METU-BIN Ankara/HumanPractice2011-11-21T22:55:47Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<p class="p">"Mining for BioBricks" software designs new devices depending on the user defined input and output parameters by searching all biobricks in iGEM 2011 distribution plates. After all possible devices and constructs are listed, a ranking is performed based on the scoring system we have developed in order to suggest the best possible biobrick combination for the job described by the user. The novel scoring system we have developed and implemented this year efficiently characterize and ranks biobricks distributed to the iGEM teams and any possible new devices that can be build from these parts in terms of status,results, quality, and rating.</p><br />
<br />
<p class="p">While M4B is an <strong>innovative approach</strong> to design synthetic devices from biobricks, it also stimulates the <strong>construction of innovative devices</strong>, as it reveals different biobrick combination to achieve same end function with the same starting stimuli. The print out function implemented in the software allows easy recording and <strong>sharing</strong> of the resulting biobrick constructs between researchers or teams. We are planning to integrate an option for <strong>sharing the favorite results image</strong> through a social network such as facebook or tweeter, which will also increase the awareness of public about our research and synthetic biology. </p><br />
<br />
<p class="p">In the results section of the M4B, the author information for each biobrick suggested to be included in a device is provided along with other features and informaiton. We specifically want to point out the <strong>avalibity of ownership information</strong> because citation of the work done previously was important for us to follow the scientific etiquette. While M4B is suggesting novel device combinations, the owners of the each biobrick within the new device is credited with this functionality.</p><br />
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<h3><a name="HIBIT11_Roundtable"></a>HIBIT'11 Roundtable</h3><br />
<p class="p">METU-BIN attended International Symposium on Health Informatics and Bioinformatics (HIBIT) 2011 and a roundtable was organized and moderated by our team.</p><br />
<p class="p">The HIBIT series has been initiated by the Informatics Institute at METU in 2005. HIBIT aims to bring together academicians, researchers and practitioners from the general area of health or medical informatics and bioinformatics or computational biology. Biomathematics, statistics and other related and supporting fields are also welcome and have contributed papers and posters in the past. <a href="http://hibit11.iyte.edu.tr/" target="_blank">Visit official website of HIBIT'11 for more information</a>.</p><br />
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<h4>Applications of Bioinformatics for Synthetic Biology</h4><br />
<h5>Abstract</h5><br />
<p class="p">Synthetic Biology is a discipline that embraces the emerging ability to design and synthesize novel DNA constructs, new genomes and biomimetic systems. Biomimetic systems are human-made processes, substances, devices, or systems that imitate nature. Therefore, we can define synthetic biology as an emerging field which aspire the usage of synthetic technology in order to create novel molecular machines for the good of human beings and bring insight to current biological questions by providing new approaches and methodologies. In addition, synthetic biology contributes to the accumulation of molecular data. Since 2004, Registry of Standard Biological Parts (a.k.a Parts Registry) is the only source for the standardized biobricks, which currently harbors 700 available and 2000 defined parts. Annual iGEM competitions continue to help for the accumulation of new biobricks each year. Due to the exponential growth observed in the number of biobricks, application of bioinformatics techniques is urgently needed for the organization, analysis and association of the data in the Registry of Standard Biological Parts and for the prediction of functional device candidates without using wet laboratory.</p><br />
<br />
<p class="p">In this roundtable a brief introduction to synthetic biology will be given and research areas where bioinformatics applications can be applied in synthetic biology will be presented. Following the introduction to the field, discussions on the current topics of synthetic biology research and how bioinformatics can be utilized to address these issues will be conducted. Major discussion topics will be on how bioinformatics can be utilized to aid in organization and presentation of the Registry of Standard Biological Parts, and solutions that can be offered regarding safety, ethics, and ownership in the emerging field of synthetic biology. Although, synthetic biology has scientific and industrial potential, it is hard to foresee and predict potential misuses and dangers. We will be also discussing potential threats of products and publication of these through web-based databases.</p><br />
<br />
<p class="p">Discussions will be organized in to two major topics. Firstly, current applications of bioinformatics in synthetic biology will be discussed. The major aim of the first session is to bring different disciplines together and create an interdisciplinary environment for information exchange and inspiration. Secondly, possible open questions and major discussion subtopics which regard safety and security, ownership and ethics will be included and potential solutions for major problems by using bioinformatics will be discussed as well.</p><br />
<h5>Topics</h5><br />
<ul><br />
<li>Introduction to the state of the art in Synthetic Biology and current issues of the field.</li><br />
<ul><br />
<li>What are the major literature resources for Synthetic Biology related research? Existing Bioinformatics tools and techniques used in Synthetic Biology.</li><br />
<li>Synthetic Biology Sector in Turkish Industry</li><br />
</ul><br />
<li>Discussion Session &quot;Applications of Bioinformatics for Synthetic Biology&quot;</li><br />
<ul><br />
<li>How would the application of Bioinformatics methods enhance Synthetic Biology in general ?</li><br />
<li>Specific areas of synthetic biology new bioinformatics applications are needed to be developed?</li><br />
<ul><br />
<li>selection and design of BioBrick Parts or Devices specific to problem at hand</li><br />
<li>characterization of BioBrick Parts or Devices</li><br />
<li>the analysis, modeling, and simulation of BioBrick Parts or Devices</li><br />
<li>the sharing of BioBrick Parts or Devices as information via the internet.</li><br />
</ul><br />
<li>Human Practice issues of Synthetic Biology that can be addressed and solutions can be offered by the design and development of new bioinformatics applications. (ownership, sharing, and innovation, safety, security and ethics and others)</li><br />
<li>Language of choice for developing software geared for Synthetic Biology. SBML, SBOL and other choices.</li><br />
<li>As bioinformaticians which other disciplines we need to collaborate while addressing issues for synthetic biology, such as Biological Sciences, Engineering, and Statistics.</li><br />
</ul><br />
</ul><br />
<h5>About the Roundtable Organizers</h5><br />
<p class="p"> This round table will be presented and moderated by the METU-BIN Team, who will be representing METU at iGEM 2011 in Software Category on November 2011.</p><br />
<p class="p"><a href="http://hibit11.iyte.edu.tr/day_1.html" target="_blank">See HIBIT'11 Program</a></p><br />
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<h3><a name="Teknovasyon_2011"></a>Teknovasyon 2011</h3><br />
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<a href="https://static.igem.org/mediawiki/2011/2/23/Teknovasyon.jpg" target="_blank"><img style="float:left;margin-right:15px;margin-bottom:15px;width:300px;height:auto;" src="https://static.igem.org/mediawiki/2011/2/23/Teknovasyon.jpg" /></a><br />
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<p class="p">We have entered a nation-wide project competition organized by Hacettepe University with our project titled "Genetically Engineered MRSA Bıosensor based on Synthetic DNA Technology". We have been placed 5th place and got our first financial support for 2011 iGEM competition.</p><br />
<p class="p">This, our first action as a team, had two focus:</p><br />
<ul><li>Raising funds for the team</li><li>Getting the attention of researchers to synthetic biology applications</li></ul><br />
<p class="p"><a href="http://www.teknovasyon.com.tr/saglik_bilimleri/duyurular_haberler.php?id=1015" target="_blank">Check out the official website of Teknovasyon 2011</a></p><br />
<h3><a name="DNA_School"></a>DNA School</h3><br />
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<img class="dna" src="https://static.igem.org/mediawiki/2011/c/ca/Dna_school_1.JPG" /><br />
<small>DNA School - 1: We have organized an introductory course for pre-school kids on fundamentals of molecular biology which is allowed us to spread seeds of synthetic biology into the young minds of kids continuing to METU College.</small><br />
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<img class="dna" src="https://static.igem.org/mediawiki/2011/e/e4/Dna_school_2.JPG" /><br />
<small>DNA School - 2:The interest was high as our presentation got lots of follow up questions.</small><br />
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<div style="height:321px;" class="dna_box"><br />
<img class="dna" src="https://static.igem.org/mediawiki/2011/4/48/Dna_school_3.JPG" /><br />
<small>DNA School - 3: After how DNA is build up was clear we have put to gather a model of DNA double helix as a whole class. Each kid selected a letter representing one nucleotide and colored it appropriately.</small><br />
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<img class="dna" src="https://static.igem.org/mediawiki/2011/e/e8/Dna_school_4.JPG" /><br />
<small>DNA School - 4: Next was to finding the right spot for their nucleotide on the DNA code.</small><br />
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<div class="dna_box"><br />
<img class="dna" src="https://static.igem.org/mediawiki/2011/e/ee/Dna_school_5.JPG" /><br />
<small>DNA School - 5: After all nucleotide bonds were in place we have talked about the role of DNA in organisms and its applications based on DNA in our daily lifes.</small><br />
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<div class="dna_box"><br />
<img class="dna" src="https://static.igem.org/mediawiki/2011/8/82/Dna_school_6.JPG" /><br />
<small>DNA School - 6: Close up of the DNA double helix model build in classroom Hz-A. We have leave these models as a thank you gift to the classes for their participation, which will continue to stimulate their curiosity about molecular genetics.</small><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank">Click to see!</a><br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
<div class="metu-bin"><a href="https://2011.igem.org/Team:METU-BIN_Ankara" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d6/Metu-bin_logo.png" /></a></div><br />
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<h2>Safety</h2><br />
<p class="p">The aim of this project is to provide a software tool for wet-lab biologists to facilitate the process of choosing the appropriate parts to use in their experiments in minimum amount of time and effort. It is always challenging for wet-lab biologists to pick the right parts to make a working device that satisfies their demand, for solving this issue, our team decided to prepare a software that enables wet-lab biologists to easily pass their desired input and output to this software and observing the predicted pathways which are activated by the input and produce the requested output. Our software can also rank the DNA constructs based on the popularity of BioBricks and the frequency of their usage. By this way, our software proposes a method which can be utilized in pre-experimental step as a supporter DNA design tool.</p><br />
<p class="p">Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. We can safely say that "we are as safe as the Parts Registry database." We do not use any information or part that is not already available in the parts registry database. Whatever new "constructs/devices" Mining for BioBricks (M4B) software generates can also be generated manually by browsing the parts registry. We do not build or test these devices and provide purely "information" to biologists. The Mining for BioBricks (M4B) software we are developing is only intended to use for research purposes and no clinical or military application is supported by METU-BIN Team. </p><br />
<br />
<ul style="list-style-image:none;list-style-type:decimal;"><br />
<br />
<li><strong>Would the materials used in your project and/or your final product pose:<br><br />
a. Risks to the safety and health of team members or others in the lab?<br><br />
b. Risks to the safety and health of the general public if released by design or accident?<br><br />
c. Risks to environmental quality if released by design or accident?<br><br />
d. Risks to security through malicious misuse by individuals, groups or states?</strong><br />
<p class="p">As a pure software team we are, our materials used for project or final products are not in any biohazard classification. Middle East Technical University complies with all regulations about office health and safety as required by Turkish Office of Safety and Health at Work (OSHA). Safety and health issues that might be a concern for METU-BIN Team members can be addressed with general precautions for office workers, such as not working long hours in front of the computer screen, taking frequent, short breaks, using ergonomic equipment, changing position and posture to ease the pressure on certain joints and adding an exercise routine into their breaks to strengthen their posture.<br><strong>Specifically, are any parts or devices in your project associated with (or known to cause):</p><br />
<ul style="list-style:disc;"><br />
<li>pathogenicity, infectivity, or toxicity?</li><br />
<li>threats to environmental quality?</li><br />
<li>security concerns?</li><br />
</ul></strong><br />
<p class="p">All answers to these questions are “no”. as we are a software team, we are not using BioBricks/devices physically. Therefore, our project is associated with none of the above.</p><br />
</li> <br />
<br />
<li><strong>If your response to any of the questions above is yes:<br><br />
a. Explain how you addressed these issues in project design and while conducting laboratory work.<br><br />
b. Describe and document safety, security, health and/or environmental issues as you submit your parts to the Registry.</strong><br />
<p class="p">The standard questions in the questionnaire about safety are not applicable to "software" projects as our project doesn't require any biological laboratory work and we won't be submitting any parts to the Registry.</p></li><br />
<br />
<li><strong>Under what biosafety provisions will / do you operate?</strong><br><br />
<p class="p">METU-BIN Team is supported by the Bioinformatics Program at METU Informatics Institute. Even though we are not a biological or natural sciences department we are doing our best to act within the national biosafety regulations our university has to comply with, which can be found on <a href="http://www.ttb.org.tr/mevzuat/index.php?option=com_content&view=article&id=753:bogenl-kanunu&catid=1:yasa&Itemid=28" target="_blank">this page</a> and also <a href="http://www.tbbdm.gov.tr/en/Home.aspx" target="_blank">this page.</a></p></li><br />
<br />
<li><strong>Do you have other ideas on how to deal with safety or security issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</strong><br />
<p class="p">Our software tool, Mining for BioBricks (M4B), will be providing in-silico blueprints for new devices that can be built by using DNA constructs in iGEM's 2011 plate distributions. Even though we won't be physically providing the constructs to researchers, we have been brainstorming on how to make Parts Registry safer and secure, which in return can minimize the unintended use of the software we have been developing for efficient use of the parts database.</p></li></ul><br />
<p class="p">Classification of BioBricks in the Parts Registry with gene products that are pathogenic, infective or toxic with potential threats to researchers, public health and environment are some of our main suggestions. When this information is available it can be integrated into the database search tools and users of the Parts Registry will be aware of the potential dangers of any biobrick they are planning to use in their devices. Some might argue that this classification might point to the candidate biobricks for misuse, but as METU-BIN Team we support that the researchers should be informed about the potential threats of the parts and this information should be easy to access so that they can take precautions for their designs.</p><br />
<br />
<p class="p">Any information needs to turn into action to become an actual threat as in garage bioterrorism. But one would need to physically access to the biobricks distributed through iGEM's Parts Registry, so increased security measures to control, screen and follow the laboratories, which requests biobricks and registering users, is a natural start point for a more safer Parts Registry. As an initial precaution to make our software, M4B, safer we will be following the users of our software by their IPs and if needed we can restrict access to our software website to academic users or to only iGEM registered laboratories. If a list of high risk IPs is provided to us by iGEM we can cross-check our users in real time and inform iGEM about these suspicious activities. In addition, if the biobricks in the registry are classified by iGEM, we can keep the list of users whose search involves high risk biobricks or the search results with devices which includes potentially hazardous subparts and track the access of these users to our server site to inform iGEM.</p><br />
<p class="p">At the same time, we are aware of the fact that iGEM's biobrick distributions are not the only source of devices that are built with synthetic biology techniques. Most molecular biology laboratories would have the capability of building biobricks and devices as in the Parts Registry. So, any new security measure on access to the Parts Registry and to our server site to use M4B should not be a restrain on researchers, should support the creative side of the synthetic biology, aiding to the new innovations in the field.</p><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank">Click to see!</a><br />
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<div class="margin"><h6>Do you care safety?</h6><br />
Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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<a href="http://www.facebook.com/METUBIN" target="_blank"><img src="https://static.igem.org/mediawiki/2011/5/55/Facebook.png" /></a><br />
<a href="http://www.twitter.com/METUBIN" target="_blank"><img src="https://static.igem.org/mediawiki/2011/f/f7/Twitter.png" /></a><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/NotebookTeam:METU-BIN Ankara/Notebook2011-11-21T22:54:23Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>Notebook</h2><br />
<h3>March 2011</h3><br />
<p class="p"><strong>Kick-Off of METU-BIN iGEM Software Team:</strong> As new members from different disciplines joined, our team got more powerful. Then, we started to know more about each other to understand how to determine our strategy to be successful in iGEM competition.</p><br />
<p class="p"><strong>Reaching out to our Potential Sponsors:</strong> The content and organization of our sponsorship package is discussed and all information is pulled together into one package for easy presentation. Also, we have practiced on how to present our project to specific companies and thus worked hard on basics of synthetic biology.<br />
In order to raise some funds for the team, we have entered into the Hacettepe Technopolis Innovation Project Competition “Teknovasyon 2011” with a scientific project on synthetic biology. Our project was about MRSA biosensor modified by synthetic DNA technology. </p><br />
<p class="p">All team members prepared presentations on iGEM and synthetic biology and these presentations helped us to open up the communication between the team members coming from different fields and educated us on different aspects of iGEM competition, synthetic biology and software development. As a software field, we had to have a good understanding of molecular biology, genetics, synthetic biology and computer sciences. Thus, we created an environment where people in every field, could provide useful and innovative advice.</p><br />
<p class="p"><strong>Towards the end of March 2011, we got a little more into the competition, and Yener who was a competitor at iGEM 2010 talked about his experiences and explained the Registry of Standard Biological Parts. This was the key moments because, as a software team programming a software that integrates the Registry, we should know and understand the Registry completely.</strong></p><br />
<br />
<h3>April 2011</h3><br />
<p class="p">In Turkey, synthetic biology and the opportunities it presents is not a well-known even within the academia. We, as an iGEM team, had the responsibility to spread the word and introduce the field of synthetic biology. Thus, we decided to organize a roundtable discussion at HIBIT’11 conference and inform researchers whose domain is mainly bioinformatics about the synthetic biology, iGEM competition, and the Parts Registry as a new field for translational research.</p><br />
<br />
<p class="p">HIBIT is an annual international symposium on Health Informatics and Bioinformatics which aims to bring together academicians, researchers and practitioners from the general area of health or medical informatics and bioinformatics or computational biology. All poster, workshop and roundtable applications are peer reviewed before acceptance and we were invited to hold our roundtable during HIBIT 11 on 3rd of April 2011, you can find more details on our <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#HIBIT11_Roundtable" target="_blank">human practice page</a>.</p><br />
<br />
<p class="p">During the month of April our effort to find sponsorships continued and we have visited few companies in Ankara, Turkey.</p><br />
<br />
<h3>May 2011</h3><br />
<p class="p">Our first potential sponsor was the METU-Technopolis, who have promised to cover the team registration fees for the competition.</p><br />
<br />
<p class="p">METU-BIN registered iGEM 2011 as a software team.</p><br />
<br />
<p class="p">We have been placed 5th place at nation-wide project competition organized by Hacettepe University with our project titled "GENETICALLY ENGINEERED MRSA BIOSENSOR BASED ON SYNTHETIC DNA TECHNOLOGY" and got our first financial support for 2011 İGEM competition. We have been placed 5th place and got our first financial support for 2011 iGEM competition. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#Teknovasyon_2011" target="_blank">See more</a>.</p><br />
<br />
<p class="p">We have been accepted to organize a roundtable at HIBIT’11 about synthetic biology, iGEM and Parts Registry. Our topic was “Applications of Bioinformatics for Synthetic Biology”. In the roundtable we firstly explained what is synthetic biology, its importance to humankind and in which fields it can be used. Then we informed audience about iGEM and Parts Registry and discussed such topics as safety, security, ethics, or ownership, sharing, and innovation.</p><br />
<br />
<p class="p">To work more effectively on our Project and to improve our knowledge we started to read articles and discuss them at our weekly meetings.</p><br />
<ul style="list-style:none;"><br />
<li>M. T. Cooling, V. Rouilly, G. Misirli, J. Lawson, T. Yu,J. Hallinan,A. Wipat.Standard virtual biological parts: a repository of modular modeling components for synthetic biology, Bioinformatics, 2010</li><br />
<br />
<li>Anthony D. Hill, Jonathan R. Tomshine, Emma M. B. Weeding, Vassilios<br />
Sotiropoulos, Yiannis N. Kaznessis, Yiannis N. Kaznessis. SynBioSS: the synthetic biology modeling suite. Bioinformatics, 2008</li><br />
<br />
<li>Ernesto Andrianantoandro, Subhayu Basu,David K Karig, Ron Weiss. Synthetic biology: new engineering rules for an emerging discipline. Bioinformatics. 2006</li><br />
<br />
<li>Priscilla E. M. Purnick, Ron Weiss. The second wave of synthetic biology: from modules to systems. Nature. 2009</li><br />
<br />
<li>Raik Grunberg, Luis Serrano. Strategies for protein synthetic biology. Nucleic Acid Research, 2010</li><br />
<br />
<li>Sean C. Sleight, Bryan A. Bartley, Jane A. Lieviant, Herbert M. Sauro. In-Fusion BioBrick assembly and re-engineering, 2010</li><br />
<br />
<li>Yizhi Cai, Mandy L. Wilson, Jean Peccoud. GenoCAD for iGEM: a grammatical approach to<br />
the design of standard-compliant constructs. NAR, 2010</li><br />
<br />
<li>Barry Canton, Anna Labno, Drew Endy. Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology, 2008</li><br />
<br />
<li>Tom Ellis, Xiao Wang, James J Collins. Diversity-based, model-guided construction of synthetic gene networks with predicted functions, Nature Biotechnology, 2009</li><br />
<br />
<li>Kurt W Kohn and Mirit I Aladjem. Circuit diagrams for biological networks, Molecular Systems Biology, 2006</li><br />
<br />
<li>Yong-Jun Shin, Mehrdad Nourani.Statecharts for Gene Network Modeling, PLoS ONE, 2009</li><br />
<br />
<li>Christopher A Voigt. Genetic parts to program bacteria, Current Opinion in Biotechnology, 2006</li><br />
</ul><br />
<p class="p">We looked into last years software teams and discussed their projects.</p><br />
<br />
<h3>June 2011</h3><br />
<br />
<p class="p">We all had final exams on the first two weeks.</p><br />
<br />
<p class="p">Between June 9th -10th we have celebrated the 15th Anniversary of METU Informatics Institute with Informatics Science Festival 2011. We all attended to the symposiums in this festival. The speakers were:</p><br />
<ul style="list-style:disc;"><br />
<li>Prof. Charles DELISI: Dean Emeritus, College of Engineering, Boston <br />
University </li><br />
<li>Prof. Charles CANTOR: Chairman of Sequenom, Inc’s Scientific Advisory </li><br />
<li>Board and Chief Scientific Officer, Boston University </li><br />
<li>Prof. Aravind JOSHI: University of Pennsylvania </li><br />
<li>Prof. Selim ÜNLÜ: Associate Dean for Research and Graduate Programs, <br />
Boston University </li><br />
<li>Prof.Asuman ÖZDAĞLAR ACEMOĞLU: Electrical Engineering and Computer Science Department, MIT</li><br />
</ul><br />
<p class="p">We talked to Prof.Charles CANTOR and took his advices about our project and iGEM.</p><br />
<p class="p">Kick off Of Summer Meetings (14th June) : We are starting to work on our project again.</p><br />
<p class="p">In our first meeting in summer we have discussed how our program will work, how to categorize the algorithm, how to extract information from Parts Registry 2011 distribution, how our GUI should look like, and decide a few options about it and we have have made the distribution of tasks (parts database translation, database search algorithm, software and GUI, website design and presentation, sponsorship).</p><br />
<p class="p">All individual teams are working now. We will meet again by the early July. Biologists started to find input-output relationships. They are using a simple program developed by one of our advisors ,Sassan, with an interface for entering parts relation in a tab delimited text files. These files are processed by our team developer to be in used in our main program.</p><br />
<p class="p">Software developers are discussing how they will design the algorithm's first part.</p><br />
<br />
<h3>July 2011</h3><br />
<p class="p">Biologists are revealing the connections between bioparts one by one for all the plates in iGEM 2011 distribution. The relations between bioparts, subparts and subdevices are investigated to form a connection database that is used for M4B to find pathways. The input-output datas in the plates is shared with the software developers. They are planning to complete this job in the middle of the July.</p><br />
<br />
<p class="p">Developers continue improving the algorithm's first part. They are also working on a database where all the XML information of 2011 distribution will be locally downloaded for easy access.</p><br />
<br />
<p class="p">12th June: We test the algorithm for the first time.</p><br />
<br />
<p class="p">We discussed different program names and at last we decided on Mining For Biobricks (M4B). Our design team is now working on our team and program logo. They are offering us different alternatives. We began to discuss our wiki design.</p><br />
<br />
<br />
<h3>August 2011</h3><br />
<p class="p">Our software developers worked on scoring and GUI. We decided how our GUI should look like. We brainstormed about the scoring of the constructed devices and we discussed which information is more important for scoring.</p><br />
<br />
<p class="p">A national news channel is interested in our team and iGEM competition so we gave an interview about our project and iGEM competition on live news for Haberturk channel. We sent our documents to a news agency and some national newspapers made news about us. A video is made that introduce our team and project for BBC Horizon.</p><br />
<br />
<p class="p">All this media attention helped to secure a big fund from by Akgun Yazılım in August 2011.</p><br />
<br />
<p class="p">We continue looking for sponsors. We applied for a scholarship that is given by TUBITAK for international project competitions. We send e-mails to potential sponsors. We are visiting some companies, foundations and associations that give financial supports for education in Turkey.</p><br />
<br />
<p class="p">We have fulfilled the requirement of Regional Jamboree Registration. Discussed on the safety issue and share our thoughts by answering all safety and security questions that iGEM asked.</p><br />
<br />
<br />
<h3>September 2011</h3><br />
<p class="p">Developers continue working on scoring and final the GUI design.</p><br />
<br />
<p class="p">10th September: Our software is moved to web.</p><br />
<br />
<p class="p">We have published and shared code and other material on GitHub.</p><br />
<br />
<p class="p">We began to design our iGEM wiki. We shared the work and we all are working on our wiki content.</p><br />
<br />
<p class="p">We gave a presentation for “Synthetic Biology Turkey 1.0 Activity and Meeting of The iGEM Turkey Teams” that was organized by Synthetic Biology Association. We asked other Turkey teams for collabration during this presentation.</p><br />
<br />
<p class="p">We also asked the other iGEM teams for collabration.</p> <br />
<br />
<p class="p">We have collaborated with the teams Uppsala-Sweden and METU-Ankara.</p><br />
<br />
<p class="p">19th September: This week we are now finalizing our wiki page and software video tutorial before the freeze. M4B’s GUI is almost done. Next we will tackle the presentation and the poster.</p><br />
<br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>Project</h2><br />
<br />
<h3><a name="Introduction"></a>Introduction</h3><br />
<p class="p">While the interest to the field of synthetic biology is uprising, iGEM and Parts Registry is getting more important for researchers interested working in the field of synthetic biology. As the number of attendees and teams to iGEM competition increases each year, number of BioBricks submitted to the Parts Registry are increasing too. As we all know, Parts Registry is an inimitable library for synthetic biologists. Although it is an important source of information and tool for biologists, the parts are not organized very well. Therefore, while constructing devices, synthetic biologists usually faces following difficulties at the pre-experimental stage:</p><br />
<ul><br />
<li>Searching through the Parts</li><br />
<li>Deciding if the parts needed are already in the database or not</li><br />
<li>Deciding which BioBrick will work effectively with which</li><br />
<li>Finding the most accurate combination between the parts</li><br />
<li>Constructing the most effectively working devices</li><br />
</ul><br />
<p class="p">Figuring out all these answers is time consuming and takes too much effort. Our main goal as 2011 METU-BIN iGEM Software team was to provide a web based tool that helps synthetic biologists at the pre-experimental step to search the Part Registry with input and output keywords and to design their genetic constructs using the biobricks provided in the 2011 distribution of DNA constructs.</p><br />
<br />
<p class="p"><strong>M4B: Mining for Biobricks</strong> is developed to aid synthetic biologist. Our software proposes a method which can be utilized in pre-experimental step as a supporter data mining tool. Following the user defined input and output parameters, M4B lists all possible composite devices and ranks them according to the novel scoring measurement developed by METU-BIN.</p><br />
<br />
<h4>Aim</h4><br />
<p class="p">Main goal of our 2011 project is to provide a web based tool that helps synthetic biologists at the pre-experimental step to design their genetic constructs according to their input and output parameters.</p><br />
<ul><br />
<li>A network of all bioparts in 2011 distribution will be generated, which describes the functional relations between the subatomic bioparts.</li><br />
<li>A search algorithm will be developed to reveal all possible device combinations for the user defined input and output within bioparts of 2011 distribution.</li><br />
<li>Visualization tools will be applied for graphical representation of the results.</li><br />
<li>A web-based user interface will be provided for the developed software.</li><br />
</ul><br />
<h3><a name="Algorithm"></a>Algorithm</h3><br />
<p class="p">M4B is developed using Java Web Technologies. Web programming enables user- and PC-friendly products. Users do not need to install any program on their PC, and so they do not need to waste PC resources for programs. A web application can easily be reached using a simple web-browser from any PC and from anywhere in the world . It is the most important property of M4B.</p><br />
<h4>Flowcharts for the Algorithms</h4><br />
<div><br />
<a href="https://static.igem.org/mediawiki/2011/b/bb/Search_algorithm3.png" target="_blank"><img style="width:290px;margin-right:10px;" src="https://static.igem.org/mediawiki/2011/b/bb/Search_algorithm3.png" /></a><a href="https://static.igem.org/mediawiki/2011/a/a4/Scoring_algorithm.png" target="_blank"><img style="width:290px;margin-right:10px;" src="https://static.igem.org/mediawiki/2011/a/a4/Scoring_algorithm.png" /></a><br />
</div><br />
<p class="p">In detail, we have used Java Applet to serve M4B on the net. And to store data of M4B, we have used an instance of MySQL database. We've created tables for all XML files of PartsRegistry. For example, they contain part info, deep subparts and specific subparts info, scars info, etc. In addition we've added a few more tables to implement algorithm. They are for interaction relations between parts, scores of main parts, scores of edges, etc.</p> <br />
<p class="p">For the implementation of M4B, a huge biobrick network is constructed using information in the PartsRegistry database. With information of interactions between edges, we are creating a part network. It is a hashtable of hashtables. By the use of hashtables, we can easily find the input part on network to start searching. All useful information about a part is stored in a type of Part. It has following fields.</p><br />
<br />
<ul><br />
<li>partID</li><li>partType</li><li>promoterType</li><li>output</li><li>terminator</li><li>nextParts</li></ul><br />
<br />
<p class="p">After constructing the network, we are making a search for the list of all possible composite devices beginning with given input and output parameters. To traverse whole graph, we are using a customized version of the famous graph traversal algorithm, <strong>DFS (Depth First Search)</strong>. In DFS, it is making a search on one way until the leaf node, then if it cannot find it goes back to last disjoint point and goes on searching until next leaf node.</p><br />
<br />
<img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/2/26/Algorithm_img.gif" /><br />
<br />
<p class="p">Using the quick access property of hashtable we are finding the input part on network. If the given input is found on the graph once, we go over all the descendant nodes until finding the expected output. While searching an output node, all nodes traversed are being recorded. When the output is found, the recorded path is added to the “results list”. Else, it is discarded until the last disjoint point, and a new path is searched continuing from that point. After all possible paths are found, the list of paths is shown on the GUI.</p><br />
<br />
<p class="p">One can also search for the devices starting with a constitutive promoter. To do this, user shouldn't enter the input parameter. By this empty input information, algorithm looks for constitutive promoters to start as an input point. "$" sign is used as symbolic input for constitutive promoters.</p><br />
<br />
<p class="p">When we are searching for the expected output, we may find different outputs. If that output continues with a Promoter as an Input, it means that we are starting to add the parts of next device. A composite part can have more than one device. So we've added an input field to specify the maximum device count of results. User can change the number of device count using this field.</p><br />
<br />
<p class="p">Let's talk about visualization of the graph. If user selects an input from the list, it parses all parts from selected device and looks for it is type from network. Then, it creates a node of that type. We are using icons of Parts Registry for the types of parts. And we are using yFiles for visualization.</p><br />
<br />
<p class="p">If user selects a node in the graph, it queries the information about that part from tables created using XML files of Parts Registry.</p><br />
<br />
<p class="p">Quick search when typing the input name is the user friendly property of M4B. No need for a “Find” button.</p><br />
<br />
<p class="p">The other feature of the program is printing the results. Most of users wants to save their results. It enables saving.</p><br />
<br />
<h3><a name="Construction_of_Relational_Database"></a>Extraction of Relations of Bioparts and Construction of Relational Database</h3><br />
<br />
<p class="p">Parts Registry contains various types of biobricks and connections in between parts. In our software, we aimed to develop an algorithm which goes over the devices and finds connections between biobricks to present users all possible constructed devices. However, it was very difficult to go over biobricks and find the relations in not very well organized Parts Registry. For that reason, we have decided to form a ”Part Connections Database” by examining all the bilateral relations between biobricks which will be used by our program, M4B. By this way, the complex information in Parts Registry will be simplified and our algorithm will work faster and more effectively.</p><br />
<br />
<p class="p">The biology group focused on all of the four 384 well plates of 2011 distribution and extracted information between connections and devices in a standard way. This information is stored into a relational database and enables queries from remote computer programs.</p><br />
<br />
<p class="p">Our software group developed a toolbox to help biology group in storing the part relations into the new database of connections between biobricks. Using this tool, we were able to minimize the possibility of mistakes while entering bilateral relations manually. More importantly, this organized the database entries in a standardized way, according to the requirements of Mining for BioBricks to run the searching algorithm easily.</p><br />
<br />
<img style="margin-bottom:5px;display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/a/ab/Input-output-gadget.png" /><br />
<small>Figure 1: The toolbox which was used while building the “Part Connections Database” by our biology group.</small><br />
<img style="margin-bottom:5px;display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/7/7e/Input-output-relations.png" /><br />
<small>Figure 2: A screen shot from our temporary file of “relational database”</small><br />
<p class="p">As there are various types of biobricks in the Parts Registry, we set up rules to organize the “relational database” in an appropriate way.</p><br />
<br />
<br />
<h4>Rules</h4><br />
<p class="p">The most important rule is “A constructed device formed by combination of promoter-ribosome binding site-gene-terminator, respectively, is the minimal functional device.”</p><br />
<br />
<p class="p">This is the major rule, because without these 4 major biobrick types, a device cannot work. In addition to this, without knowing the description of “basic device” it is impossible for us to present accurate results to users.<br />
Although Parts Registry contains various types of biobricks, in our database there are 4 basic biobricks which are promoters, ribosome binding sites, genes, and terminators. This helped us to simplify the complex information in the Parts Registry in our initial attempt of mining.</p><br />
<br />
<p class="p">In addition to 4 basic biobrick types, there are inputs and outputs which are our software’s parameters. Inputs are chosen according to promoters. Both activators and inhibitors of promoters were listed in our database. Main source of activators and inhibitors was the information from the Parts Registry. The reason of listing inhibitors was to filter out constructed devices which do not produce the required outputs. When a constructed device is formed by multiple devices, although the input activates first device’s promoter, it may inhibit other promoters of following devices. Outputs were chosen according to the genes, the product they synthesize. Although, most of the time, input and output information was extracted from Parts Registry, sometimes external sources were used as well because of the uninformative part descriptions at Parts Registry. External sources such as NCBI, PubMed and wiki of the team who submitted the biobrick to iGEM were used.</p><br />
<br />
<p class="p">Constitutive promoters are entered without any input, but especially their “constitutiveness” is recorded as a property in our relations database.</p><br />
<br />
<p class="p">In our software, after constructing a device by combining biobricks to construct multiple devices, combination between devices is formed according to this rule: “Output of the first gene will be the input of the following promoter(s)”</p><br />
<br />
<p class="p">According to this rule, first promoter will be activated by given Input and the product of first gene will be used as activator of the following promoters. By activation of the promoters, genes will synthesize the output. By this way, the constructed complex is expected to work effectively.</p><br />
<br />
<p class="p">In Parts Registry, there are composite parts, translation units, generators, reporters, inverters, intermediate devices, and signaling devices. As Parts Registry 2011 distribution was being examined in detail, to simplify these parts, their connection information was simplified to promoter-ribosome binding site-gene-terminator relation by our biological knowledge. This rule is explained with details as seen below:</p><br />
<br />
<ul><br />
<li>Reporters<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/2/27/Reporter-img.png" /><br />
<p class="p">The biobricks which synthesize fluorescent proteins are classified as “reporters” as they give out light to report something. We accepted these parts as “genes” because they are synthesizing proteins.</p></li><br />
<br />
<br />
<li>Translational Units<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/4/48/Translational-units-img.png" /><br />
<p class="p">Combination of ribosome binding site and gene is classified as “translational units”. We accepted this as two biobricks rather than one. Therefore the bilateral relation between ribosome binding site and gene was entered in our database.</p></li><br />
<br />
<br />
<li>Inverters<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/c/c0/Inverters-img.png" /><br />
<p class="p">Inverters were challenging parts; they are formed from more than 2 biobricks. Rather than accepting this as one biobrick, we accepted this part as a combination of four biobricks. Therefore, we entered bilateral relations between each biobricks as ribosome binding site-gene, gene-terminator, and terminator- promoter. We also entered gene-output and input-promoter connections.</p></li><br />
<br />
<li>Composites<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/b/bc/Composites_img.png" /></li><br />
<br />
<li>Generators<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/b/b1/Generators-img.png" /></li><br />
<br />
<li>Signalling Devices<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/7/7d/Signalling_img.png" /></li><br />
<br />
<li>Intermediate Devices<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/8/84/Intermediate-parts-img.png" /><br />
<br />
<p class="p">Composite parts, generators, signaling devices, and intermediate devices were also challenging parts like inverters. They don’t have a specific rule about how many and which types of biobricks they consist of. However, we accepted them as complex subdevices and entered bilateral relation between each connected biobricks.</p><br />
</li><br />
</ul><br />
<p class="p">In METU-BIN 2011 project, our main priority was to focus on (minimal) Functional devices. Therefore we named DNAs, RNAs, and Tags as “accessories” because they are not vital for a device to work. However, we know that using these accessories during construction helps devices work more effectively by adding some extra features. For that reason, it’s in on future plan to form a database for these accessories and present them to our users in their query results.</p><br />
<br />
<br />
<br />
<h3><a name="Scoring"></a>EDGE-SUM Scoring</h3><br />
<p class="p">In order to provide the biologists a reliability measure about the<br />
M4B suggested composite devices, we devised a scoring mechanism.<br />
Composite devices found by M4B could be ranked by simple measures such<br />
as device count, path length, or whether a specific part is included<br />
in the device or not. Instead of these simple scoring mechanisms, we<br />
decided to propose a more eloborate scoring algorithm that takes into<br />
account status, rating, quality, and results of a device available in<br />
the Parts Registry. Such a scoring mechanim makes use of information<br />
provided by the community and it will be useful to decide which<br />
devices are more “valuable” than others if a set of alternative<br />
devices are available for a given input-output pair.</p><br />
<br />
<p class="p">To compute a score for a novel composite device, we first calculate a<br />
score for each edge in the composite device. To compute an edge score,<br />
we find all the existing devices in the Parts Registry that contain<br />
that specific edge and compute an accumulated score for that edge by<br />
summing up the scores of these existing Parts Registry devices that<br />
contain the edge. All the edge scores are normalized to the interval<br />
[0,1] by a sigmoid function. After finding the scores of all edges in<br />
a novel composite device found by M4B, we sum the logarithms of these<br />
edge scores which is equal to logarithm of the multiplication of<br />
scores. If we cannot compute a score for an edge (when the edge is completely<br />
new for example) we use a small number for that edge, similar to the idea of<br />
pseudocounts in profile HMMs. Since, this logarithm is a negative number we raise it to the<br />
power of e again to report the final score between 0.0 and 1.0. Values<br />
close to 1.0 indicate more reliable devices. EDGE-SUM SCORES are categorized into three classes according to their numeric range only. Gold-silver and bronze categories are assigned just for easy visualization of the results.</p><br />
<br />
<p class="p">To calculate the score of an existing Parts Registry device, we use<br />
the following features of devices. In addition, we give a relative<br />
importance to each of these features as suggested by our biologist<br />
team members. These relative importance weights is just a heuristic<br />
and can be optimized in future versions of M4B.</p><br />
<br />
<p class="p"><br />
<table width="625" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_status</th><br />
<th>Available</th><br />
<th>Planning</th><br />
<th>Missing</th><br />
<th>Deleted</th><br />
<th>Unavailable</th><br />
<th>Informational</th><br />
</tr><br />
<tr><br />
<td>1.0</td><br />
<td>0.1</td><br />
<td>0.0</td><br />
<td>0.0</td><br />
<td>0.0</td><br />
<td>0.2</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="650" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">best_quality</th><br />
<th>Partially Confirmed</th><br />
<th>None</th><br />
<th>Confirmed</th><br />
<th>Long Part</th><br />
<th>Questionable</th><br />
<th>Bad Sequencing</th><br />
</tr><br />
<tr><br />
<td>0.5</td><br />
<td>0.0</td><br />
<td>1.0</td><br />
<td>0.2</td><br />
<td>0.1</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="200" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_rating </th><br />
<th>1</th><br />
<th>NULL</th><br />
</tr><br />
<tr><br />
<td>1.0</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="500" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_results</th><br />
<th>None</th><br />
<th>Works</th><br />
<th>Fails</th><br />
<th>Issues</th><br />
<th>NULL</th><br />
</tr><br />
<tr><br />
<td>0.0</td><br />
<td>1.0</td><br />
<td>0.0</td><br />
<td>0.2</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p">For example, if a device is Available, Partially Confirmed and Works,<br />
its score will be "1.0+0.5+1.0 = 2.5". And, if an edge is included in<br />
this device, that edge is going to inherit the score of 2.5 and all<br />
these inherited scores from other devices that contain the edge is<br />
accumulated to compute the raw (unnormalized) score of that edge.</p><br />
<br />
<h3><a name="Results"></a>Results</h3><br />
<p class="p">Our software, M4B: Mining for BioBricks, provides many features saving of time, money and effort for scientists. With this software, scientists don't need to do long-term research and have expensive lab tools.</p><br />
<p class="p">Since it's online and can be used via any updated browser, users don't need to install it and carry it with themselves in order to use it on another computer. With this feature, they can use our software on all the computers having updated system. Also, they don't have to provide any place in their storage device.</p><br />
<br />
<br />
<h3><a name="System_Specifications"></a>Recommended Minimum System Specifications</h3><br />
<ul><br />
<li>Intel Pentium 2Ghz</li><br />
<li>512 MB Ram</li><br />
<li>Java Runtime Environment 1.6</li><br />
<li>128K Internet Speed</li><br />
<li>Supported web browsers: Firefox, Chrome, Safari, Internet Explorer</li><br />
</ul><br />
<br />
</div><br />
<div id="sidebar"><br />
<!-- SAME AREA STARTS --><br />
<br />
<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank">Click to see!</a><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/TeamTeam:METU-BIN Ankara/Team2011-11-21T22:53:27Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
<div class="metu-bin"><a href="https://2011.igem.org/Team:METU-BIN_Ankara" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d6/Metu-bin_logo.png" /></a></div><br />
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<h2>Team: <span class="cont">Attribution and Contributions</span></h2><br />
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<p class="p">METU-BIN is an interdisciplinary research team whose main focus is on the intersection of Systems Biology approaches and Synthetic Biology applications. For this aim METU-BIN team is composed of 12 students and 2 advisors from different disciplines such as Biology, Molecular Biology, Electronics, Computer Science, Mathematics, Statistics and Bioinformatics.</p><br />
<p class="p"><iframe src="http://player.vimeo.com/video/29401573?title=0&amp;byline=0&amp;portrait=0" width="400" height="220" frameborder="0" webkitAllowFullScreen allowFullScreen></iframe></p><br />
<h3>Students</h3><br />
<div class="sections"><br />
<img class="secimg" src="https://static.igem.org/mediawiki/2011/d/dd/Gokce.png" /><br />
<span class="sectext"><br />
<h4>Gökçe OĞUZ</h4><br />
<p class="p">Hi, I’m Gökçe :) I graduated with a degree in Biology and currently I’m taking lectures to start the Bioinformatics graduate program at Middle East Technical University. After learning there is a huge unknown world of Syntehic Biology, I became more curious about synthetic Biology. This is my first year in iGEM. When I heard igem, I directly jumped into because this is a great opportunity for me to get knowledge about Synthetic biology, meet new people and have fun at the same time :) <span class="cont">In this team, as a biologist, I am the bridge in between the partsregistry and software team. I am working on a database which contains bilateral relations between biobricks in Partsregistry.</span></p><br />
</span><br />
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<div class="sections"><br />
<img class="secimg" src="https://static.igem.org/mediawiki/2011/b/b2/Burcu.png" /><br />
<span class="sectext"><br />
<h4>Burcu YALDIZ</h4><br />
<p class="p">Hi, I'm Burcu. I'm a mathematician and I am taking scientific preparation courses for Graduate Program of Bioinformatics at Middle East Technical University. I like biology more than mathematics and bioinformatics give me a chance to use my mathematician skills in biology. This is my first year in iGEM. When I heard that two teams from METU got medals in iGEM 2010 I thought that “I must be in these teams” and now I'm a member of METU-BIN. I think Synthetic Biology is an extreme subject and it's an exciting experience for me being a part of this team. <span class="cont">In the team I am responsible for editorial issues and organizing the sponsorship application.</span></p><br />
</span><br />
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<div class="sections"><br />
<img class="secimg" src="https://static.igem.org/mediawiki/2011/c/c6/Ismail.png" /><br />
<span class="sectext"><br />
<h4>İsmail ASLANER</h4><br />
<p class="p">I have just graduated from Hacettepe University Electrical and Electronics Engineering department and a fresh new student at METU Bioinformatics Msc. Program. I also have Moleculer Biology background which is the real motivation for me in this project. I would like to work more on systems biology and i believe that working on modelling and data analysis in this project is a good start for me.</p><br />
</span><br />
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<img class="secimg" src="https://static.igem.org/mediawiki/2011/b/b5/Ogun.png" /><br />
<span class="sectext"><br />
<h4>Ogün ADEBALİ</h4><br />
<p class="p">Hello! I am Ogün Adebali, a fresh graduate from the 'Molecular Biology & Genetics' department of METU. Currently I am a PhD student in the program called 'Genome Science and Technology' in University of Tennessee. <span class="cont">My mission in this team is to support our synthetic biology approach by representing it on various platforms. We organized synthetic biology round table in HIBIT2011 and participated in 'Teknovasyon' competition with our synthetic biology project.</span> As a geneticist, I believe that it is good to be here to keep up with the developments of synthetic biology, which is one of the up-and-coming fields in my interest. </p><br />
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<img class="secimg" src="https://static.igem.org/mediawiki/2011/d/da/Saygin.png" /><br />
<span class="sectext"><br />
<h4>Saygın KARAASLAN</h4><br />
<p class="p">Hi there, I am a senior in Biology Department at METU and about to launch my own scientific animation company focusing on developing a Virtual Lab application. After graduation I would like to continue my studies on medical informatics, and 3D molecular animations. <span class="cont">I was a part of the design and mutimedia group of METU-BIN and have produced METU-BIN's introductory video for BBC, logos, animation for M4B and designed the team-wear.</span></span></p><br />
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<h4>Ebru ŞAHİN</h4><br />
<p class="p">Hi, I’m Ebru. My major is Statistics and Computer Sciences. I’m studying Master of Science in Bioinformatics program in Middle East Technical University. I got really excited when I heard iGEM, synthetic biology and the idea of constructing artificial biological systems. This is the first time participating to iGEM and <span class="cont">I’m on the editorial board.</span></span></p><br />
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<div class="sections"><br />
<img class="secimg" src="https://static.igem.org/mediawiki/2011/6/6a/Gokhan.png" /><br />
<span class="sectext"><br />
<h4>Gökhan ERSOY</h4><br />
<p class="p">Hi, I am Gökhan. :) I am a Computer Engineer. And this year, I will start studying the scientific preperation class in Bioinformatics Department of Middle East Technical University, as a graduate student. This is my first year in genetics science and iGEM. Although I'm a computer scientist; I always like genetics and working in the lab environment. I think iGEM is a perfect way to improve my knowledge on genetics. <span class="cont">In our team, I am responsible of software development. I've coded search and scoring algorithms. And I've developed GUI with the assistance of Güngör. And i've added some extra tables to the database created by Seyedsasan. Other than software development, I've helped on finding sponsorships and talked about our project in a seminar with Gökçe, for human practice. And finally with my friends, I made an interview for live news on TV. That's all.</span> :) I would like to thank my teachers, advisors and friends for their hardwork. Good luck for all teams! :)</p><br />
<p>Contact: goksoy66 [at] gmail [dot] com</p></span><br />
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<img class="secimg" src="https://static.igem.org/mediawiki/2011/d/d1/Gungor.png" /><br />
<span class="sectext"><br />
<h4>Güngör BUDAK</h4><br />
<p class="p">Hi, I'm Güngör. I'm one of the undergraduate students in the iGEM team METU-BIN and studying Biology major at Middle East Technical University (METU). So I'm learning the great science, Biology but at the same time, my deep interest in computer sciences takes me to that area as well. When I was taking some advice on Bioinformatics, which is the application of computer science and information technology to the field of biology and medicine, by Assoc. Prof. Yeşim AYDIN SON, she told me about the competition and the field synthetic biology. After a quick search on the Internet, I found this area amazing, and eventually I was one of the member of the METU-BIN. <span class="cont">In the team, my contributions were to get the relational data of bioparts in PartsRegistry and store it in a standard way for computer engineers to use it. Then, I coded and designed the wiki page using HTML and CSS, and also I designed the team logo and logo of M4B. At the same time, I provided the content of wiki, with the help of my friends Burcu, Gökçe, Gökhan.</span></p><br />
<p>Contact: gngrbdk [at] gmail [dot] com</p><br />
</span><br />
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<h3>Advisors</h3><br />
<div class="sections"><br />
<img class="secimg" src="https://static.igem.org/mediawiki/2011/7/7a/Sasan.png" /><br />
<span class="sectext"><br />
<h4>Seyedsasan HASHEMIKHABIR</h4><br />
<p class="p">My name is Sasan. I'm studying Master of Science in computer engineering program in Middle East Technical University and participated in this team as an Advisor. <span class="cont">I designed all the algorithms and the database in the team and also deployed the database on MySQL. In addition, I tried to motivate the rest of the team members as much as I can and to be like a chain for connecting biology subteam and our team developer, Gokhan.</span></p><br />
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<span class="sectext"><br />
<h4>Yener TUNCEL</h4><br />
<p class="p">I am a graduate of METU Molecular Biology and Genetics Program and currently studying towards my M.Sc. degree on Bioinformatics at METU. This is my second year in the iGEM competition and I am one of the advisors of the METU-BIN Software team. Synthetic biology is very promising and attractive field. Although it is a new scientific field, it holds so many opportunities for biotechnology as well as human health. <span class="cont">My major mission is to organize and manage the team. I have also contributed to Human Practice issue for iGEM by joining innovative project competitions and scientific platforms in order to disseminate and introduce Synthetic Biology concept in Turkey.</span></p><br />
<p class="p">I am very deeply interested in systems biology and its applications in the sub-fields of Molecular Biology because I believe the holistic approach is required in all aspects of molecular biology and serves as the key factor for the understanding of entire cell behaviour, its overall mechanism and its dynamics.</p><br />
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<h3>Instructors</h3><br />
<br />
<div class="sections"><br />
<img class="secimg" src="https://static.igem.org/mediawiki/2011/7/7b/Yesim.png" /><br />
<span class="sectext"><br />
<h4>Yeşim AYDIN SON</h4><br />
<p class="p">Yeşim, is a medical scientist with M.D from HÜTF, Ankara and a Ph.D from University of TN, Knoxville on Genome Science and Technology. She currently holds a faculty position as an Assistant Professor of Medical Informatics at METU Informatics Institute and also the acting coordinator of the Bioinformatics Graduate Program in METU. Main focus of her research is Genomic Biomarker discovery and applications of biomarker research in Personalized Medicine. Her research group recently developed an integrated desktop application the "METU-SNP" for genome wide association of SNP biomarkers and discovery of genes and pathways related to diseases. She is also interested in translational medicine and integrative bioinformatics working on developing genomic diagnostics for prediction, diagnosis and maintenance of drug therapies in complex diseases.</p><br />
</span><br />
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<br />
<div class="sections"><br />
<img class="secimg" src="https://static.igem.org/mediawiki/2011/0/06/Tolga.png" /><br />
<span class="sectext"><br />
<h4>Tolga CAN</h4><br />
<p class="p">Tolga Can received his PhD in Computer Science at the University of California at Santa Barbara in 2004. He is currently an Assistant Professor of the Department of Computer Engineering, Middle East Technical University, Ankara, Turkey. His main research interests are in bioinformatics, especially prediction and analysis of protein-protein interaction networks, and statistical methods such as graphical models and kernel methods.</p><br />
</span><br />
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</div><br />
<br />
<br />
</div><br />
<div id="sidebar"><br />
<!-- SAME AREA STARTS --><br />
<br />
<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank">Click to see!</a><br />
<div class="clearfixed"></div><br />
</div><br />
<br />
<div class="social margin"><h6>Find us on</h6><br />
<a href="http://www.facebook.com/METUBIN" target="_blank"><img src="https://static.igem.org/mediawiki/2011/5/55/Facebook.png" /></a><br />
<a href="http://www.twitter.com/METUBIN" target="_blank"><img src="https://static.igem.org/mediawiki/2011/f/f7/Twitter.png" /></a><br />
<a href="http://vimeo.com/user8040359" target="_blank"><img src="https://static.igem.org/mediawiki/2011/5/51/Vimeo.png" /></a><br />
<a href="http://picasaweb.google.com/105434043475546846942" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d4/Picasa.png" /></a><br />
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<div id="gallery"><h6>Some photos during summer</h6><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_AnkaraTeam:METU-BIN Ankara2011-11-21T22:52:46Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h3 class="boxheader m4btab">M4B: Mining for BioBricks</h3><br />
<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank"><img class="boximage imgm4b" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a><br />
<span class="boxtext">It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">See our software, it's online!</a></span><br />
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<span class="boxtext">Our project aims to provide a software tool to facilitate selection process of the right parts for their experiments in minimum amount of time and effort. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project">Read more</a>.</span><br />
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<h3 class="boxheader collaborationtab">Collaborations</h3><br />
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<span class="boxtext">It's very important that on projects or even a little work people should collaborate always to reach the best! Thus, we consider it as a key factor to succeed. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Collaborations">See it</a>.</span><br />
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<span class="boxtext">Science and technology are not only for students, academicians but they are also for children and people with other interests. Thus, we've been with them together. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice">See</a>.</span><br />
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<h3 class="boxheader safetytab">Safety</h3><br />
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<span class="boxtext">Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Safety">Read more</a>.</span><br />
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<h3 class="boxheader teamtab">Team</h3><br />
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<span class="boxtext">METU-BIN team with Prof. Dr. Charles Cantor at Informatics Science Festival 2011 at METU. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Team">Meet the team</a>.</span><br />
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<h3 class="boxheader notebooktab">Notebook</h3><br />
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<span class="boxtext">We want to inform you about our adventures when getting ready for the iGEM competition. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Notebook">Take a look</a>.</span><br />
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<div class="margin"><h6>Why do you need M4B?</h6><br />
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<div class="margin"><h6>Do you care safety?</h6><br />
Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/M4BTeam:METU-BIN Ankara/M4B2011-11-21T13:20:23Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
<div class="metu-bin"><a href="https://2011.igem.org/Team:METU-BIN_Ankara" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d6/Metu-bin_logo.png" /></a></div><br />
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<h2>M4B: Mining for BioBricks</h2><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/M4BTeam:METU-BIN Ankara/M4B2011-11-18T22:06:33Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>M4B: Mining for BioBricks</h2><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/M4BTeam:METU-BIN Ankara/M4B2011-11-17T20:59:46Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
<div class="metu-bin"><a href="https://2011.igem.org/Team:METU-BIN_Ankara" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d6/Metu-bin_logo.png" /></a></div><br />
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<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Instructions" target="_blank">Instructions</a></li><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_AnkaraTeam:METU-BIN Ankara2011-11-17T20:58:49Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
<div class="metu-bin"><a href="https://2011.igem.org/Team:METU-BIN_Ankara" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d6/Metu-bin_logo.png" /></a></div><br />
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<h3 class="boxheader m4btab">M4B: Mining for BioBricks</h3><br />
<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img class="boximage imgm4b" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a><br />
<span class="boxtext">It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">See our software, it's online!</a></span><br />
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<h3 class="boxheader projecttab">Project</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/0/06/Metu-bin-project.png" /><br />
<span class="boxtext">Our project aims to provide a software tool to facilitate selection process of the right parts for their experiments in minimum amount of time and effort. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project">Read more</a>.</span><br />
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<h3 class="boxheader collaborationtab">Collaborations</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/1/1c/Metu-bin-collaboration.png" /><br />
<span class="boxtext">It's very important that on projects or even a little work people should collaborate always to reach the best! Thus, we consider it as a key factor to succeed. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Collaborations">See it</a>.</span><br />
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<span class="boxtext">Science and technology are not only for students, academicians but they are also for children and people with other interests. Thus, we've been with them together. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice">See</a>.</span><br />
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<h3 class="boxheader safetytab">Safety</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/ec/Metu-bin-safety.png" /><br />
<span class="boxtext">Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Safety">Read more</a>.</span><br />
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<h3 class="boxheader teamtab">Team</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/e5/Metu-bin-team.png" /><br />
<span class="boxtext">METU-BIN team with Prof. Dr. Charles Cantor at Informatics Science Festival 2011 at METU. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Team">Meet the team</a>.</span><br />
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<h3 class="boxheader notebooktab">Notebook</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/c/cd/Metu-bin-notebook.png" /><br />
<span class="boxtext">We want to inform you about our adventures when getting ready for the iGEM competition. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Notebook">Take a look</a>.</span><br />
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<div class="margin"><h6>Do you care safety?</h6><br />
Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
<div class="metu-bin"><a href="https://2011.igem.org/Team:METU-BIN_Ankara" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d6/Metu-bin_logo.png" /></a></div><br />
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<h2>M4B: Mining for BioBricks</h2><br />
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<applet code="http://dayhoff.ii.metu.edu.tr:8080/m4b/igem_applet.M4BApplet"><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/InstructionsTeam:METU-BIN Ankara/Instructions2011-10-27T17:47:50Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
<div class="metu-bin"><a href="https://2011.igem.org/Team:METU-BIN_Ankara" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d6/Metu-bin_logo.png" /></a></div><br />
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<h2>Instructions: How to use M4B?</h2><br />
<h3>Usage</h3><br />
<p class="p"><iframe width="425" height="349" src="http://www.youtube.com/embed/F-0k4FWm83A?hl=en&fs=1" frameborder="0" allowfullscreen></iframe></p><br />
<p class="p">M4B: Mining for BioBricks is a software that scans the parts on the database we created by the relational data of 2011 distribution and shows the combination of parts which starts with a specific promoter and a specific gene, of course after gene there is always terminator.</p><br />
<br />
<p class="p">The specifity is determined by users. Our software provides two textfields for input of the desired device and output of it. By these parameters, users select those and with the other options, hit the search button and take results of possible desired devices.</p><br />
<br />
<p class="p">In the results area, possible devices are shown by the specific order of parts' ID's given by PartsRegistry. So you can know which parts a resulted device is composed of. When a result is clicked, it's composition is shown graphically with exact PartsRegistry images just above the results field.</p><br />
<br />
<p class="p">At the left of the software, you'll see the information field for the parts. When you click on a part in the field of graphical results, its all the information available in XML database of PartsRegistry will appear.</p><br />
<br />
<br />
<h3>README file for the team METU-BIN_Ankara iGEM 2011</h3><br />
<br />
<p class="p">Developed Software: M4B: Mining for BioBricks</p><br />
<br />
<p class="p">M4B is a java applet that can find novel composite devices for a user specified input and output based on the parts connection graph that we constructed using the information in Parts Registry.</p><br />
<br />
<p class="p">The applet is available at <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">http://dayhoff.ii.metu.edu.tr:8080/m4b/</a></p><br />
<br />
<p class="p">The applet contains code that remotely access a MySQL database; therefore, it had to be signed with a security certificate. The users should accept the certificate when prompted with "The application's digital signature cannot be verified. Do you want to run the application?" by choosing the "Run" option at the bottom of the notification window.</p><br />
<br />
<p class="p">In order to compile the source code provided at GitHub:</p><br />
<ul style="list-style:decimal;"><br />
<li>The developer should install and create a MySQL database. The "database" directory contains a dump of the current database tables used by M4B. These dump files contain SQL statements that can be executed under MySQL to create the corresponding database locally.</li><br />
<br />
<li>The developer should download the Connector/J library which is a java library for connection to MySQL databases. Documentation and download links can be found at: <a href="http://dev.mysql.com/usingmysql/java/ and http://dev.mysql.com/downloads/connector/j/" target="_blank">http://dev.mysql.com/usingmysql/java/ and http://dev.mysql.com/downloads/connector/j/</a></li><br />
<br />
<li>The developer should get the yFiles, graph visualization library. METU-BIN_Ankara purchased a single developer license. Hence, we cannot make the licensed library available at GitHub. An evaluation copy of "yFiles for Java" can be obtained from: <a href="http://www.yworks.com/en/downloads.html" target="_blank">http://www.yworks.com/en/downloads.html</a>. The current version of yFiles for Java is 2.8.0.3 as of September 18, 2011.</li><br />
<br />
<li>The developer should get the JSch - Java Secure Channel library. The library is an implementation of SSH2 for java and allows our applet to connect to sshd servers. The library can be downloaded from: <a href="http://www.jcraft.com/jsch/" target="_blank">http://www.jcraft.com/jsch/</a></li><br />
<br />
<li>The developer should modify the MySQL database user information hardcoded inside the java source file: IIConnection.java before compilation.</li><br />
<br />
<li>The java source files are defined under the package igem_applet and can be compiled using "javac igem_applet/<file name>" in the src directory.</li><br />
</ul><br />
<br />
<p class="p">The source code under the directory "src/igem_applet" is composed of 7 .java files. </p><br />
<br />
<p class="p">M4BApplet.java is the main applet and GUI code.</p><br />
<br />
<p class="p">PathwayFinder.java is the main code for finding composite devices in the parts registry graph. The source code is modified from the original version to hide some user/password information required for remote database access. The original passwords are replaced with "******".</p><br />
<br />
<p class="p">Util.java contains some utility code.</p><br />
<br />
<p class="p">Part.java contains the class description for a Part object.</p><br />
<br />
<p class="p">GraphConstructor.java contains code for generating a visual description of the composite device found.</p><br />
<br />
<p class="p">MysqlTunnelSession.java contains code for database access via JDBC.</p><br />
<br />
<p class="p">IIConnection.java contains code to establish database connection to our Part Connections database at the Informatics Institute. The original passwords are replaced with "*****". The developer should replace them with their own user/passwords before compilation.</p><br />
<br />
<p class="p">More information can be found on our <a href="http://github.com/igemsoftware/METU-BIN_Ankara_2011" target="_blank">GitHub account.</a></p><br />
<br />
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<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank">Click to see!</a><br />
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<h2>Contact Information</h2><br />
<p class="p"><strong>Adress:</strong> İnönü Blvd. METU Informatics Institute B-207, Çankaya, Ankara, 06531, TURKEY</p><br />
<p class="p"><strong>Phone:</strong> +90 312 210 7708<br><br />
<strong>Fax:</strong> +90 312 210 3745<br><br />
<strong>E-mail:</strong> metu-bin [at] ii [dot] metu [dot] edu [dot] tr<br />
</p><br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>METU-BIN From Press</h2><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank">Click to see!</a><br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>Next Version: Future Plans</h2><br />
<h3>NEW FEATURES TO BE INCLUDED in M4B by 2012</h3><br />
<p class="p">Features we would like to introduce in the next version of “Mining for BioBricks” can be listed under two categories.</p><br />
<ul style="list-style:decimal;"><br />
<li><strong>Improvements on our code</strong> that we couldn’t add this year due to limited time for the development of the software.<br />
<ul style="list-style:disc;"><br />
<li>Offering search options for multiple input and output parameters.</li><br />
<li>Including all possible biobrick categories in search algorithm, such as DNA, linker etc. Current vesion of M4B is limited to basic parts, which are promoter, RBS, gene, and terminator.</li><br />
<li>Providing link-outs for gene products to external databases such as NCBI, ENSEMBL.</li><br />
</ul><br />
</li><br />
<li><strong>Improvements to the Parts Registry</strong> that are needed so new information provided can be utilized by our software.<br />
<ul style="list-style:disc;"><br />
<li>In the next version of M4B we are planning to integrate with SBOL. This year we have tried to demonstrate SBOL symbols at least in a limited way, but we faced difficulty in assigning the right categories. For example iGEM classifies biobricks as terminators but in SBOL there are three different subclasses for a terminator and no symbol for a general terminator. Therefore, we suggest that biobricks in the Parts Registry needs to be characterized according to SBOL first, then we can utilize this information to <strong>provide SBOL codes to present and share the composite device results choices M4B suggests.</strong></li><br />
<li><strong>We would like to add safety warnings for the composite devices that contain subparts with potential threats.</strong> In order to integrate this into M4B, Classification of bioparts in the Parts Registry with gene products that are pathogenic, infective or toxic with potential threats to researchers, public health and environment, is needed. When this information is available, the subparts can be tagged within the composite devices presented in query results to warn the users. By this way, users of the Parts Registry will be aware of the potential dangers of any bioparts they are planning to use in their devices.</li><br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>Collaborations</h2><br />
<p class="p">Our software, <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">M4B: Mining for BioBricks</a>, is available for everyone, you can find us on the Community Page soon!</p><br />
<h3>METU-Ankara</h3><br />
<p class="p">Since M4B contains bioparts from 2011 distribution in its database and we know METU-Ankara Team who are engineering E.Coli to decrease harmful effects of methane gas use 2011 distribution as well, we sent it them.</p><br />
<br />
<p class="p">Their feedback is the following.</p><br />
<br />
<span style="width:250px;height:auto;float:left;margin:0 10px 0 0;"><a href="https://static.igem.org/mediawiki/2011/b/bf/Metu-ankara-ss.png" target="_blank"><img style="border:1px solid #ccc;width:250px;height:auto;" src="https://static.igem.org/mediawiki/2011/b/bf/Metu-ankara-ss.png" /></a><br><small style="color:#ccc;">Click on the image to view larger size.</small></span><br />
<br />
<p class="p">"We are constructing a device that is induced by IPTG and that gives lysis enzymes and GFP as the outputs because, in order to elute methanol we need to kill our modified cells that convert ambient methane to methanol and the reason why we want GFP as one output is to be sure that it works. Our modelled device has promoter induced by IPTG, RBS, gene coding GFP and lysis cassette ending with cell death and we are glad to have it and it's working how we expected. So then, we use M4B to see that if it finds the exact device or the device that can do the same job. Since the software has only one place for output, we queried IPTG as an input and GFP as an output on the software and got corresponding 117 results. These results contain devices exactly what we have one for the same operation. However, we couldn't find the lysozyme output for the IPTG input in the software."</p><br />
<br />
<p class="p">We are pleased to hear the feedback of METU-Ankara Team and it's good the know that their first query on our software was successful. As for the second one, we haven't included DNA, RNA and tags yet. It's one of our future plans and next year, it'll be done. Furthermore, queries with multiple inputs or outputs will be available. So, in one operation, they will be able to get what they want. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/NextVersion">See our future plans on the next version</a>.</p><br />
<br />
<br />
<h3>Uppsala-Sweden</h3><br />
<br />
We also collaborated with the team Uppsala-Sweden. Below, you can see their feedback on our project, the software: M4B: Mining for BİoBrick.<br />
<br />
<p class="p">"The METU-BIN_Ankara team provided us their software which they developed for their project to test it if we can use for our Project. We examined the software by searching the parts that have been used during our Project.We used red,blue and green lights as input which activate red sensor(cph8), green sensor(ccaS) and blue sensor(YF1). We are aiming to get three colours as output which are blue output(amilCP), red output(mCherry) and green/yellow output(amilGFP).<br />
<br />
<p class="p">However, we got no result for our specific input - output relations but, the software has some of the inputs and outputs.</p><br />
<br />
<p class="p">This software is very helpful to search the parts and check if the parts are in the standart registry database and decide which parts work effectively with eachother as well.That provides an easy start to constract the parts and give more efficient results.</p><br />
<br />
<p class="p">We appreciate METU-BIN_Ankara team to create that software and believe that it will be a very helpful software which will solve the problems that we or another teams faced up in the beginning.</p><br />
<br />
<p class="p">The software can be improved further by adding more parameters."</p><br />
<br />
<p class="p">We are happy to see that they use and have positive expressions on our software. As we got the information about their project, they are adding some of the bioparts of their modified device newly into the Registry. Because of this, and since our software has 2011 spring distribution in its database, it's normal to get no results for their specific device. However, when they'll add them and our database is updated, finally our software will be able to find that specific result.</p><br />
<br />
<p class="p">At the same time, our team has given a feedback on the Biosafety document of the team Uppsala-Sweden, you can read it <a href="https://2011.igem.org/Team:Uppsala-Sweden/Feedback" target="_blank">on this page</a>.</p><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank">Click to see!</a><br />
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<div class="margin"><h6>Do you care safety?</h6><br />
Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>Human Practice</h2><br />
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<p class="p">"Mining for BioBricks" software designs new devices depending on the user defined input and output parameters by searching all biobricks in iGEM 2011 distribution plates. After all possible devices and constructs are listed, a ranking is performed based on the scoring system we have developed in order to suggest the best possible biobrick combination for the job described by the user. The novel scoring system we have developed and implemented this year efficiently characterize and ranks biobricks distributed to the iGEM teams and any possible new devices that can be build from these parts in terms of status,results, quality, and rating.</p><br />
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<p class="p">While M4B is an <strong>innovative approach</strong> to design synthetic devices from biobricks, it also stimulates the <strong>construction of innovative devices</strong>, as it reveals different biobrick combination to achieve same end function with the same starting stimuli. The print out function implemented in the software allows easy recording and <strong>sharing</strong> of the resulting biobrick constructs between researchers or teams. We are planning to integrate an option for <strong>sharing the favorite results image</strong> through a social network such as facebook or tweeter, which will also increase the awareness of public about our research and synthetic biology. </p><br />
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<p class="p">In the results section of the M4B, the author information for each biobrick suggested to be included in a device is provided along with other features and informaiton. We specifically want to point out the <strong>avalibity of ownership information</strong> because citation of the work done previously was important for us to follow the scientific etiquette. While M4B is suggesting novel device combinations, the owners of the each biobrick within the new device is credited with this functionality.</p><br />
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<h3><a name="HIBIT11_Roundtable"></a>HIBIT'11 Roundtable</h3><br />
<p class="p">METU-BIN attended International Symposium on Health Informatics and Bioinformatics (HIBIT) 2011 and a roundtable was organized and moderated by our team.</p><br />
<p class="p">The HIBIT series has been initiated by the Informatics Institute at METU in 2005. HIBIT aims to bring together academicians, researchers and practitioners from the general area of health or medical informatics and bioinformatics or computational biology. Biomathematics, statistics and other related and supporting fields are also welcome and have contributed papers and posters in the past. <a href="http://hibit11.iyte.edu.tr/" target="_blank">Visit official website of HIBIT'11 for more information</a>.</p><br />
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<h4>Applications of Bioinformatics for Synthetic Biology</h4><br />
<h5>Abstract</h5><br />
<p class="p">Synthetic Biology is a discipline that embraces the emerging ability to design and synthesize novel DNA constructs, new genomes and biomimetic systems. Biomimetic systems are human-made processes, substances, devices, or systems that imitate nature. Therefore, we can define synthetic biology as an emerging field which aspire the usage of synthetic technology in order to create novel molecular machines for the good of human beings and bring insight to current biological questions by providing new approaches and methodologies. In addition, synthetic biology contributes to the accumulation of molecular data. Since 2004, Registry of Standard Biological Parts (a.k.a Parts Registry) is the only source for the standardized biobricks, which currently harbors 700 available and 2000 defined parts. Annual iGEM competitions continue to help for the accumulation of new biobricks each year. Due to the exponential growth observed in the number of biobricks, application of bioinformatics techniques is urgently needed for the organization, analysis and association of the data in the Registry of Standard Biological Parts and for the prediction of functional device candidates without using wet laboratory.</p><br />
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<p class="p">In this roundtable a brief introduction to synthetic biology will be given and research areas where bioinformatics applications can be applied in synthetic biology will be presented. Following the introduction to the field, discussions on the current topics of synthetic biology research and how bioinformatics can be utilized to address these issues will be conducted. Major discussion topics will be on how bioinformatics can be utilized to aid in organization and presentation of the Registry of Standard Biological Parts, and solutions that can be offered regarding safety, ethics, and ownership in the emerging field of synthetic biology. Although, synthetic biology has scientific and industrial potential, it is hard to foresee and predict potential misuses and dangers. We will be also discussing potential threats of products and publication of these through web-based databases.</p><br />
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<p class="p">Discussions will be organized in to two major topics. Firstly, current applications of bioinformatics in synthetic biology will be discussed. The major aim of the first session is to bring different disciplines together and create an interdisciplinary environment for information exchange and inspiration. Secondly, possible open questions and major discussion subtopics which regard safety and security, ownership and ethics will be included and potential solutions for major problems by using bioinformatics will be discussed as well.</p><br />
<h5>Topics</h5><br />
<ul><br />
<li>Introduction to the state of the art in Synthetic Biology and current issues of the field.</li><br />
<ul><br />
<li>What are the major literature resources for Synthetic Biology related research? Existing Bioinformatics tools and techniques used in Synthetic Biology.</li><br />
<li>Synthetic Biology Sector in Turkish Industry</li><br />
</ul><br />
<li>Discussion Session &quot;Applications of Bioinformatics for Synthetic Biology&quot;</li><br />
<ul><br />
<li>How would the application of Bioinformatics methods enhance Synthetic Biology in general ?</li><br />
<li>Specific areas of synthetic biology new bioinformatics applications are needed to be developed?</li><br />
<ul><br />
<li>selection and design of BioBrick Parts or Devices specific to problem at hand</li><br />
<li>characterization of BioBrick Parts or Devices</li><br />
<li>the analysis, modeling, and simulation of BioBrick Parts or Devices</li><br />
<li>the sharing of BioBrick Parts or Devices as information via the internet.</li><br />
</ul><br />
<li>Human Practice issues of Synthetic Biology that can be addressed and solutions can be offered by the design and development of new bioinformatics applications. (ownership, sharing, and innovation, safety, security and ethics and others)</li><br />
<li>Language of choice for developing software geared for Synthetic Biology. SBML, SBOL and other choices.</li><br />
<li>As bioinformaticians which other disciplines we need to collaborate while addressing issues for synthetic biology, such as Biological Sciences, Engineering, and Statistics.</li><br />
</ul><br />
</ul><br />
<h5>About the Roundtable Organizers</h5><br />
<p class="p"> This round table will be presented and moderated by the METU-BIN Team, who will be representing METU at iGEM 2011 in Software Category on November 2011.</p><br />
<p class="p"><a href="http://hibit11.iyte.edu.tr/day_1.html" target="_blank">See HIBIT'11 Program</a></p><br />
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<h3><a name="Teknovasyon_2011"></a>Teknovasyon 2011</h3><br />
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<p class="p">We have entered a nation-wide project competition organized by Hacettepe University with our project titled "Genetically Engineered MRSA Bıosensor based on Synthetic DNA Technology". We have been placed 5th place and got our first financial support for 2011 iGEM competition.</p><br />
<p class="p">This, our first action as a team, had two focus:</p><br />
<ul><li>Raising funds for the team</li><li>Getting the attention of researchers to synthetic biology applications</li></ul><br />
<p class="p"><a href="http://www.teknovasyon.com.tr/saglik_bilimleri/duyurular_haberler.php?id=1015" target="_blank">Check out the official website of Teknovasyon 2011</a></p><br />
<h3><a name="DNA_School"></a>DNA School</h3><br />
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<small>DNA School - 1: We have organized an introductory course for pre-school kids on fundamentals of molecular biology which is allowed us to spread seeds of synthetic biology into the young minds of kids continuing to METU College.</small><br />
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<small>DNA School - 2:The interest was high as our presentation got lots of follow up questions.</small><br />
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<img class="dna" src="https://static.igem.org/mediawiki/2011/4/48/Dna_school_3.JPG" /><br />
<small>DNA School - 3: After how DNA is build up was clear we have put to gather a model of DNA double helix as a whole class. Each kid selected a letter representing one nucleotide and colored it appropriately.</small><br />
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<small>DNA School - 4: Next was to finding the right spot for their nucleotide on the DNA code.</small><br />
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<img class="dna" src="https://static.igem.org/mediawiki/2011/e/ee/Dna_school_5.JPG" /><br />
<small>DNA School - 5: After all nucleotide bonds were in place we have talked about the role of DNA in organisms and its applications based on DNA in our daily lifes.</small><br />
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<small>DNA School - 6: Close up of the DNA double helix model build in classroom Hz-A. We have leave these models as a thank you gift to the classes for their participation, which will continue to stimulate their curiosity about molecular genetics.</small><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank">Click to see!</a><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/SafetyTeam:METU-BIN Ankara/Safety2011-10-27T17:45:11Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>Safety</h2><br />
<p class="p">The aim of this project is to provide a software tool for wet-lab biologists to facilitate the process of choosing the appropriate parts to use in their experiments in minimum amount of time and effort. It is always challenging for wet-lab biologists to pick the right parts to make a working device that satisfies their demand, for solving this issue, our team decided to prepare a software that enables wet-lab biologists to easily pass their desired input and output to this software and observing the predicted pathways which are activated by the input and produce the requested output. Our software can also rank the DNA constructs based on the popularity of BioBricks and the frequency of their usage. By this way, our software proposes a method which can be utilized in pre-experimental step as a supporter DNA design tool.</p><br />
<p class="p">Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. We can safely say that "we are as safe as the Parts Registry database." We do not use any information or part that is not already available in the parts registry database. Whatever new "constructs/devices" Mining for BioBricks (M4B) software generates can also be generated manually by browsing the parts registry. We do not build or test these devices and provide purely "information" to biologists. The Mining for BioBricks (M4B) software we are developing is only intended to use for research purposes and no clinical or military application is supported by METU-BIN Team. </p><br />
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<ul style="list-style-image:none;list-style-type:decimal;"><br />
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<li><strong>Would the materials used in your project and/or your final product pose:<br><br />
a. Risks to the safety and health of team members or others in the lab?<br><br />
b. Risks to the safety and health of the general public if released by design or accident?<br><br />
c. Risks to environmental quality if released by design or accident?<br><br />
d. Risks to security through malicious misuse by individuals, groups or states?</strong><br />
<p class="p">As a pure software team we are, our materials used for project or final products are not in any biohazard classification. Middle East Technical University complies with all regulations about office health and safety as required by Turkish Office of Safety and Health at Work (OSHA). Safety and health issues that might be a concern for METU-BIN Team members can be addressed with general precautions for office workers, such as not working long hours in front of the computer screen, taking frequent, short breaks, using ergonomic equipment, changing position and posture to ease the pressure on certain joints and adding an exercise routine into their breaks to strengthen their posture.<br><strong>Specifically, are any parts or devices in your project associated with (or known to cause):</p><br />
<ul style="list-style:disc;"><br />
<li>pathogenicity, infectivity, or toxicity?</li><br />
<li>threats to environmental quality?</li><br />
<li>security concerns?</li><br />
</ul></strong><br />
<p class="p">All answers to these questions are “no”. as we are a software team, we are not using BioBricks/devices physically. Therefore, our project is associated with none of the above.</p><br />
</li> <br />
<br />
<li><strong>If your response to any of the questions above is yes:<br><br />
a. Explain how you addressed these issues in project design and while conducting laboratory work.<br><br />
b. Describe and document safety, security, health and/or environmental issues as you submit your parts to the Registry.</strong><br />
<p class="p">The standard questions in the questionnaire about safety are not applicable to "software" projects as our project doesn't require any biological laboratory work and we won't be submitting any parts to the Registry.</p></li><br />
<br />
<li><strong>Under what biosafety provisions will / do you operate?</strong><br><br />
<p class="p">METU-BIN Team is supported by the Bioinformatics Program at METU Informatics Institute. Even though we are not a biological or natural sciences department we are doing our best to act within the national biosafety regulations our university has to comply with, which can be found on <a href="http://www.ttb.org.tr/mevzuat/index.php?option=com_content&view=article&id=753:bogenl-kanunu&catid=1:yasa&Itemid=28" target="_blank">this page</a> and also <a href="http://www.tbbdm.gov.tr/en/Home.aspx" target="_blank">this page.</a></p></li><br />
<br />
<li><strong>Do you have other ideas on how to deal with safety or security issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</strong><br />
<p class="p">Our software tool, Mining for BioBricks (M4B), will be providing in-silico blueprints for new devices that can be built by using DNA constructs in iGEM's 2011 plate distributions. Even though we won't be physically providing the constructs to researchers, we have been brainstorming on how to make Parts Registry safer and secure, which in return can minimize the unintended use of the software we have been developing for efficient use of the parts database.</p></li></ul><br />
<p class="p">Classification of BioBricks in the Parts Registry with gene products that are pathogenic, infective or toxic with potential threats to researchers, public health and environment are some of our main suggestions. When this information is available it can be integrated into the database search tools and users of the Parts Registry will be aware of the potential dangers of any biobrick they are planning to use in their devices. Some might argue that this classification might point to the candidate biobricks for misuse, but as METU-BIN Team we support that the researchers should be informed about the potential threats of the parts and this information should be easy to access so that they can take precautions for their designs.</p><br />
<br />
<p class="p">Any information needs to turn into action to become an actual threat as in garage bioterrorism. But one would need to physically access to the biobricks distributed through iGEM's Parts Registry, so increased security measures to control, screen and follow the laboratories, which requests biobricks and registering users, is a natural start point for a more safer Parts Registry. As an initial precaution to make our software, M4B, safer we will be following the users of our software by their IPs and if needed we can restrict access to our software website to academic users or to only iGEM registered laboratories. If a list of high risk IPs is provided to us by iGEM we can cross-check our users in real time and inform iGEM about these suspicious activities. In addition, if the biobricks in the registry are classified by iGEM, we can keep the list of users whose search involves high risk biobricks or the search results with devices which includes potentially hazardous subparts and track the access of these users to our server site to inform iGEM.</p><br />
<p class="p">At the same time, we are aware of the fact that iGEM's biobrick distributions are not the only source of devices that are built with synthetic biology techniques. Most molecular biology laboratories would have the capability of building biobricks and devices as in the Parts Registry. So, any new security measure on access to the Parts Registry and to our server site to use M4B should not be a restrain on researchers, should support the creative side of the synthetic biology, aiding to the new innovations in the field.</p><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>Notebook</h2><br />
<h3>March 2011</h3><br />
<p class="p"><strong>Kick-Off of METU-BIN iGEM Software Team:</strong> As new members from different disciplines joined, our team got more powerful. Then, we started to know more about each other to understand how to determine our strategy to be successful in iGEM competition.</p><br />
<p class="p"><strong>Reaching out to our Potential Sponsors:</strong> The content and organization of our sponsorship package is discussed and all information is pulled together into one package for easy presentation. Also, we have practiced on how to present our project to specific companies and thus worked hard on basics of synthetic biology.<br />
In order to raise some funds for the team, we have entered into the Hacettepe Technopolis Innovation Project Competition “Teknovasyon 2011” with a scientific project on synthetic biology. Our project was about MRSA biosensor modified by synthetic DNA technology. </p><br />
<p class="p">All team members prepared presentations on iGEM and synthetic biology and these presentations helped us to open up the communication between the team members coming from different fields and educated us on different aspects of iGEM competition, synthetic biology and software development. As a software field, we had to have a good understanding of molecular biology, genetics, synthetic biology and computer sciences. Thus, we created an environment where people in every field, could provide useful and innovative advice.</p><br />
<p class="p"><strong>Towards the end of March 2011, we got a little more into the competition, and Yener who was a competitor at iGEM 2010 talked about his experiences and explained the Registry of Standard Biological Parts. This was the key moments because, as a software team programming a software that integrates the Registry, we should know and understand the Registry completely.</strong></p><br />
<br />
<h3>April 2011</h3><br />
<p class="p">In Turkey, synthetic biology and the opportunities it presents is not a well-known even within the academia. We, as an iGEM team, had the responsibility to spread the word and introduce the field of synthetic biology. Thus, we decided to organize a roundtable discussion at HIBIT’11 conference and inform researchers whose domain is mainly bioinformatics about the synthetic biology, iGEM competition, and the Parts Registry as a new field for translational research.</p><br />
<br />
<p class="p">HIBIT is an annual international symposium on Health Informatics and Bioinformatics which aims to bring together academicians, researchers and practitioners from the general area of health or medical informatics and bioinformatics or computational biology. All poster, workshop and roundtable applications are peer reviewed before acceptance and we were invited to hold our roundtable during HIBIT 11 on 3rd of April 2011, you can find more details on our <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#HIBIT11_Roundtable" target="_blank">human practice page</a>.</p><br />
<br />
<p class="p">During the month of April our effort to find sponsorships continued and we have visited few companies in Ankara, Turkey.</p><br />
<br />
<h3>May 2011</h3><br />
<p class="p">Our first potential sponsor was the METU-Technopolis, who have promised to cover the team registration fees for the competition.</p><br />
<br />
<p class="p">METU-BIN registered iGEM 2011 as a software team.</p><br />
<br />
<p class="p">We have been placed 5th place at nation-wide project competition organized by Hacettepe University with our project titled "GENETICALLY ENGINEERED MRSA BIOSENSOR BASED ON SYNTHETIC DNA TECHNOLOGY" and got our first financial support for 2011 İGEM competition. We have been placed 5th place and got our first financial support for 2011 iGEM competition. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#Teknovasyon_2011" target="_blank">See more</a>.</p><br />
<br />
<p class="p">We have been accepted to organize a roundtable at HIBIT’11 about synthetic biology, iGEM and Parts Registry. Our topic was “Applications of Bioinformatics for Synthetic Biology”. In the roundtable we firstly explained what is synthetic biology, its importance to humankind and in which fields it can be used. Then we informed audience about iGEM and Parts Registry and discussed such topics as safety, security, ethics, or ownership, sharing, and innovation.</p><br />
<br />
<p class="p">To work more effectively on our Project and to improve our knowledge we started to read articles and discuss them at our weekly meetings.</p><br />
<ul style="list-style:none;"><br />
<li>M. T. Cooling, V. Rouilly, G. Misirli, J. Lawson, T. Yu,J. Hallinan,A. Wipat.Standard virtual biological parts: a repository of modular modeling components for synthetic biology, Bioinformatics, 2010</li><br />
<br />
<li>Anthony D. Hill, Jonathan R. Tomshine, Emma M. B. Weeding, Vassilios<br />
Sotiropoulos, Yiannis N. Kaznessis, Yiannis N. Kaznessis. SynBioSS: the synthetic biology modeling suite. Bioinformatics, 2008</li><br />
<br />
<li>Ernesto Andrianantoandro, Subhayu Basu,David K Karig, Ron Weiss. Synthetic biology: new engineering rules for an emerging discipline. Bioinformatics. 2006</li><br />
<br />
<li>Priscilla E. M. Purnick, Ron Weiss. The second wave of synthetic biology: from modules to systems. Nature. 2009</li><br />
<br />
<li>Raik Grunberg, Luis Serrano. Strategies for protein synthetic biology. Nucleic Acid Research, 2010</li><br />
<br />
<li>Sean C. Sleight, Bryan A. Bartley, Jane A. Lieviant, Herbert M. Sauro. In-Fusion BioBrick assembly and re-engineering, 2010</li><br />
<br />
<li>Yizhi Cai, Mandy L. Wilson, Jean Peccoud. GenoCAD for iGEM: a grammatical approach to<br />
the design of standard-compliant constructs. NAR, 2010</li><br />
<br />
<li>Barry Canton, Anna Labno, Drew Endy. Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology, 2008</li><br />
<br />
<li>Tom Ellis, Xiao Wang, James J Collins. Diversity-based, model-guided construction of synthetic gene networks with predicted functions, Nature Biotechnology, 2009</li><br />
<br />
<li>Kurt W Kohn and Mirit I Aladjem. Circuit diagrams for biological networks, Molecular Systems Biology, 2006</li><br />
<br />
<li>Yong-Jun Shin, Mehrdad Nourani.Statecharts for Gene Network Modeling, PLoS ONE, 2009</li><br />
<br />
<li>Christopher A Voigt. Genetic parts to program bacteria, Current Opinion in Biotechnology, 2006</li><br />
</ul><br />
<p class="p">We looked into last years software teams and discussed their projects.</p><br />
<br />
<h3>June 2011</h3><br />
<br />
<p class="p">We all had final exams on the first two weeks.</p><br />
<br />
<p class="p">Between June 9th -10th we have celebrated the 15th Anniversary of METU Informatics Institute with Informatics Science Festival 2011. We all attended to the symposiums in this festival. The speakers were:</p><br />
<ul style="list-style:disc;"><br />
<li>Prof. Charles DELISI: Dean Emeritus, College of Engineering, Boston <br />
University </li><br />
<li>Prof. Charles CANTOR: Chairman of Sequenom, Inc’s Scientific Advisory </li><br />
<li>Board and Chief Scientific Officer, Boston University </li><br />
<li>Prof. Aravind JOSHI: University of Pennsylvania </li><br />
<li>Prof. Selim ÜNLÜ: Associate Dean for Research and Graduate Programs, <br />
Boston University </li><br />
<li>Prof.Asuman ÖZDAĞLAR ACEMOĞLU: Electrical Engineering and Computer Science Department, MIT</li><br />
</ul><br />
<p class="p">We talked to Prof.Charles CANTOR and took his advices about our project and iGEM.</p><br />
<p class="p">Kick off Of Summer Meetings (14th June) : We are starting to work on our project again.</p><br />
<p class="p">In our first meeting in summer we have discussed how our program will work, how to categorize the algorithm, how to extract information from Parts Registry 2011 distribution, how our GUI should look like, and decide a few options about it and we have have made the distribution of tasks (parts database translation, database search algorithm, software and GUI, website design and presentation, sponsorship).</p><br />
<p class="p">All individual teams are working now. We will meet again by the early July. Biologists started to find input-output relationships. They are using a simple program developed by one of our advisors ,Sassan, with an interface for entering parts relation in a tab delimited text files. These files are processed by our team developer to be in used in our main program.</p><br />
<p class="p">Software developers are discussing how they will design the algorithm's first part.</p><br />
<br />
<h3>July 2011</h3><br />
<p class="p">Biologists are revealing the connections between bioparts one by one for all the plates in iGEM 2011 distribution. The relations between bioparts, subparts and subdevices are investigated to form a connection database that is used for M4B to find pathways. The input-output datas in the plates is shared with the software developers. They are planning to complete this job in the middle of the July.</p><br />
<br />
<p class="p">Developers continue improving the algorithm's first part. They are also working on a database where all the XML information of 2011 distribution will be locally downloaded for easy access.</p><br />
<br />
<p class="p">12th June: We test the algorithm for the first time.</p><br />
<br />
<p class="p">We discussed different program names and at last we decided on Mining For Biobricks (M4B). Our design team is now working on our team and program logo. They are offering us different alternatives. We began to discuss our wiki design.</p><br />
<br />
<br />
<h3>August 2011</h3><br />
<p class="p">Our software developers worked on scoring and GUI. We decided how our GUI should look like. We brainstormed about the scoring of the constructed devices and we discussed which information is more important for scoring.</p><br />
<br />
<p class="p">A national news channel is interested in our team and iGEM competition so we gave an interview about our project and iGEM competition on live news for Haberturk channel. We sent our documents to a news agency and some national newspapers made news about us. A video is made that introduce our team and project for BBC Horizon.</p><br />
<br />
<p class="p">All this media attention helped to secure a big fund from by Akgun Yazılım in August 2011.</p><br />
<br />
<p class="p">We continue looking for sponsors. We applied for a scholarship that is given by TUBITAK for international project competitions. We send e-mails to potential sponsors. We are visiting some companies, foundations and associations that give financial supports for education in Turkey.</p><br />
<br />
<p class="p">We have fulfilled the requirement of Regional Jamboree Registration. Discussed on the safety issue and share our thoughts by answering all safety and security questions that iGEM asked.</p><br />
<br />
<br />
<h3>September 2011</h3><br />
<p class="p">Developers continue working on scoring and final the GUI design.</p><br />
<br />
<p class="p">10th September: Our software is moved to web.</p><br />
<br />
<p class="p">We have published and shared code and other material on GitHub.</p><br />
<br />
<p class="p">We began to design our iGEM wiki. We shared the work and we all are working on our wiki content.</p><br />
<br />
<p class="p">We gave a presentation for “Synthetic Biology Turkey 1.0 Activity and Meeting of The iGEM Turkey Teams” that was organized by Synthetic Biology Association. We asked other Turkey teams for collabration during this presentation.</p><br />
<br />
<p class="p">We also asked the other iGEM teams for collabration.</p> <br />
<br />
<p class="p">We have collaborated with the teams Uppsala-Sweden and METU-Ankara.</p><br />
<br />
<p class="p">19th September: This week we are now finalizing our wiki page and software video tutorial before the freeze. M4B’s GUI is almost done. Next we will tackle the presentation and the poster.</p><br />
<br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank">Click to see!</a><br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/NextVersion" class="versionLink">Next Version</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/FromPress" class="pressLink">From Press</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Contact" class="contactLink">Contact</a></li><br />
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<h2>Project</h2><br />
<br />
<h3><a name="Introduction"></a>Introduction</h3><br />
<p class="p">While the interest to the field of synthetic biology is uprising, iGEM and Parts Registry is getting more important for researchers interested working in the field of synthetic biology. As the number of attendees and teams to iGEM competition increases each year, number of BioBricks submitted to the Parts Registry are increasing too. As we all know, Parts Registry is an inimitable library for synthetic biologists. Although it is an important source of information and tool for biologists, the parts are not organized very well. Therefore, while constructing devices, synthetic biologists usually faces following difficulties at the pre-experimental stage:</p><br />
<ul><br />
<li>Searching through the Parts</li><br />
<li>Deciding if the parts needed are already in the database or not</li><br />
<li>Deciding which BioBrick will work effectively with which</li><br />
<li>Finding the most accurate combination between the parts</li><br />
<li>Constructing the most effectively working devices</li><br />
</ul><br />
<p class="p">Figuring out all these answers is time consuming and takes too much effort. Our main goal as 2011 METU-BIN iGEM Software team was to provide a web based tool that helps synthetic biologists at the pre-experimental step to search the Part Registry with input and output keywords and to design their genetic constructs using the biobricks provided in the 2011 distribution of DNA constructs.</p><br />
<br />
<p class="p"><strong>M4B: Mining for Biobricks</strong> is developed to aid synthetic biologist. Our software proposes a method which can be utilized in pre-experimental step as a supporter data mining tool. Following the user defined input and output parameters, M4B lists all possible composite devices and ranks them according to the novel scoring measurement developed by METU-BIN.</p><br />
<br />
<h4>Aim</h4><br />
<p class="p">Main goal of our 2011 project is to provide a web based tool that helps synthetic biologists at the pre-experimental step to design their genetic constructs according to their input and output parameters.</p><br />
<ul><br />
<li>A network of all bioparts in 2011 distribution will be generated, which describes the functional relations between the subatomic bioparts.</li><br />
<li>A search algorithm will be developed to reveal all possible device combinations for the user defined input and output within bioparts of 2011 distribution.</li><br />
<li>Visualization tools will be applied for graphical representation of the results.</li><br />
<li>A web-based user interface will be provided for the developed software.</li><br />
</ul><br />
<h3><a name="Algorithm"></a>Algorithm</h3><br />
<p class="p">M4B is developed using Java Web Technologies. Web programming enables user- and PC-friendly products. Users do not need to install any program on their PC, and so they do not need to waste PC resources for programs. A web application can easily be reached using a simple web-browser from any PC and from anywhere in the world . It is the most important property of M4B.</p><br />
<h4>Flowcharts for the Algorithms</h4><br />
<div><br />
<a href="https://static.igem.org/mediawiki/2011/b/bb/Search_algorithm3.png" target="_blank"><img style="width:290px;margin-right:10px;" src="https://static.igem.org/mediawiki/2011/b/bb/Search_algorithm3.png" /></a><a href="https://static.igem.org/mediawiki/2011/a/a4/Scoring_algorithm.png" target="_blank"><img style="width:290px;margin-right:10px;" src="https://static.igem.org/mediawiki/2011/a/a4/Scoring_algorithm.png" /></a><br />
</div><br />
<p class="p">In detail, we have used Java Applet to serve M4B on the net. And to store data of M4B, we have used an instance of MySQL database. We've created tables for all XML files of PartsRegistry. For example, they contain part info, deep subparts and specific subparts info, scars info, etc. In addition we've added a few more tables to implement algorithm. They are for interaction relations between parts, scores of main parts, scores of edges, etc.</p> <br />
<p class="p">For the implementation of M4B, a huge biobrick network is constructed using information in the PartsRegistry database. With information of interactions between edges, we are creating a part network. It is a hashtable of hashtables. By the use of hashtables, we can easily find the input part on network to start searching. All useful information about a part is stored in a type of Part. It has following fields.</p><br />
<br />
<ul><br />
<li>partID</li><li>partType</li><li>promoterType</li><li>output</li><li>terminator</li><li>nextParts</li></ul><br />
<br />
<p class="p">After constructing the network, we are making a search for the list of all possible composite devices beginning with given input and output parameters. To traverse whole graph, we are using a customized version of the famous graph traversal algorithm, <strong>DFS (Depth First Search)</strong>. In DFS, it is making a search on one way until the leaf node, then if it cannot find it goes back to last disjoint point and goes on searching until next leaf node.</p><br />
<br />
<img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/2/26/Algorithm_img.gif" /><br />
<br />
<p class="p">Using the quick access property of hashtable we are finding the input part on network. If the given input is found on the graph once, we go over all the descendant nodes until finding the expected output. While searching an output node, all nodes traversed are being recorded. When the output is found, the recorded path is added to the “results list”. Else, it is discarded until the last disjoint point, and a new path is searched continuing from that point. After all possible paths are found, the list of paths is shown on the GUI.</p><br />
<br />
<p class="p">One can also search for the devices starting with a constitutive promoter. To do this, user shouldn't enter the input parameter. By this empty input information, algorithm looks for constitutive promoters to start as an input point. "$" sign is used as symbolic input for constitutive promoters.</p><br />
<br />
<p class="p">When we are searching for the expected output, we may find different outputs. If that output continues with a Promoter as an Input, it means that we are starting to add the parts of next device. A composite part can have more than one device. So we've added an input field to specify the maximum device count of results. User can change the number of device count using this field.</p><br />
<br />
<p class="p">Let's talk about visualization of the graph. If user selects an input from the list, it parses all parts from selected device and looks for it is type from network. Then, it creates a node of that type. We are using icons of Parts Registry for the types of parts. And we are using yFiles for visualization.</p><br />
<br />
<p class="p">If user selects a node in the graph, it queries the information about that part from tables created using XML files of Parts Registry.</p><br />
<br />
<p class="p">Quick search when typing the input name is the user friendly property of M4B. No need for a “Find” button.</p><br />
<br />
<p class="p">The other feature of the program is printing the results. Most of users wants to save their results. It enables saving.</p><br />
<br />
<h3><a name="Construction_of_Relational_Database"></a>Extraction of Relations of Bioparts and Construction of Relational Database</h3><br />
<br />
<p class="p">Parts Registry contains various types of biobricks and connections in between parts. In our software, we aimed to develop an algorithm which goes over the devices and finds connections between biobricks to present users all possible constructed devices. However, it was very difficult to go over biobricks and find the relations in not very well organized Parts Registry. For that reason, we have decided to form a ”Part Connections Database” by examining all the bilateral relations between biobricks which will be used by our program, M4B. By this way, the complex information in Parts Registry will be simplified and our algorithm will work faster and more effectively.</p><br />
<br />
<p class="p">The biology group focused on all of the four 384 well plates of 2011 distribution and extracted information between connections and devices in a standard way. This information is stored into a relational database and enables queries from remote computer programs.</p><br />
<br />
<p class="p">Our software group developed a toolbox to help biology group in storing the part relations into the new database of connections between biobricks. Using this tool, we were able to minimize the possibility of mistakes while entering bilateral relations manually. More importantly, this organized the database entries in a standardized way, according to the requirements of Mining for BioBricks to run the searching algorithm easily.</p><br />
<br />
<img style="margin-bottom:5px;display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/a/ab/Input-output-gadget.png" /><br />
<small>Figure 1: The toolbox which was used while building the “Part Connections Database” by our biology group.</small><br />
<img style="margin-bottom:5px;display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/7/7e/Input-output-relations.png" /><br />
<small>Figure 2: A screen shot from our temporary file of “relational database”</small><br />
<p class="p">As there are various types of biobricks in the Parts Registry, we set up rules to organize the “relational database” in an appropriate way.</p><br />
<br />
<br />
<h4>Rules</h4><br />
<p class="p">The most important rule is “A constructed device formed by combination of promoter-ribosome binding site-gene-terminator, respectively, is the minimal functional device.”</p><br />
<br />
<p class="p">This is the major rule, because without these 4 major biobrick types, a device cannot work. In addition to this, without knowing the description of “basic device” it is impossible for us to present accurate results to users.<br />
Although Parts Registry contains various types of biobricks, in our database there are 4 basic biobricks which are promoters, ribosome binding sites, genes, and terminators. This helped us to simplify the complex information in the Parts Registry in our initial attempt of mining.</p><br />
<br />
<p class="p">In addition to 4 basic biobrick types, there are inputs and outputs which are our software’s parameters. Inputs are chosen according to promoters. Both activators and inhibitors of promoters were listed in our database. Main source of activators and inhibitors was the information from the Parts Registry. The reason of listing inhibitors was to filter out constructed devices which do not produce the required outputs. When a constructed device is formed by multiple devices, although the input activates first device’s promoter, it may inhibit other promoters of following devices. Outputs were chosen according to the genes, the product they synthesize. Although, most of the time, input and output information was extracted from Parts Registry, sometimes external sources were used as well because of the uninformative part descriptions at Parts Registry. External sources such as NCBI, PubMed and wiki of the team who submitted the biobrick to iGEM were used.</p><br />
<br />
<p class="p">Constitutive promoters are entered without any input, but especially their “constitutiveness” is recorded as a property in our relations database.</p><br />
<br />
<p class="p">In our software, after constructing a device by combining biobricks to construct multiple devices, combination between devices is formed according to this rule: “Output of the first gene will be the input of the following promoter(s)”</p><br />
<br />
<p class="p">According to this rule, first promoter will be activated by given Input and the product of first gene will be used as activator of the following promoters. By activation of the promoters, genes will synthesize the output. By this way, the constructed complex is expected to work effectively.</p><br />
<br />
<p class="p">In Parts Registry, there are composite parts, translation units, generators, reporters, inverters, intermediate devices, and signaling devices. As Parts Registry 2011 distribution was being examined in detail, to simplify these parts, their connection information was simplified to promoter-ribosome binding site-gene-terminator relation by our biological knowledge. This rule is explained with details as seen below:</p><br />
<br />
<ul><br />
<li>Reporters<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/2/27/Reporter-img.png" /><br />
<p class="p">The biobricks which synthesize fluorescent proteins are classified as “reporters” as they give out light to report something. We accepted these parts as “genes” because they are synthesizing proteins.</p></li><br />
<br />
<br />
<li>Translational Units<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/4/48/Translational-units-img.png" /><br />
<p class="p">Combination of ribosome binding site and gene is classified as “translational units”. We accepted this as two biobricks rather than one. Therefore the bilateral relation between ribosome binding site and gene was entered in our database.</p></li><br />
<br />
<br />
<li>Inverters<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/c/c0/Inverters-img.png" /><br />
<p class="p">Inverters were challenging parts; they are formed from more than 2 biobricks. Rather than accepting this as one biobrick, we accepted this part as a combination of four biobricks. Therefore, we entered bilateral relations between each biobricks as ribosome binding site-gene, gene-terminator, and terminator- promoter. We also entered gene-output and input-promoter connections.</p></li><br />
<br />
<li>Composites<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/b/bc/Composites_img.png" /></li><br />
<br />
<li>Generators<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/b/b1/Generators-img.png" /></li><br />
<br />
<li>Signalling Devices<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/7/7d/Signalling_img.png" /></li><br />
<br />
<li>Intermediate Devices<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/8/84/Intermediate-parts-img.png" /><br />
<br />
<p class="p">Composite parts, generators, signaling devices, and intermediate devices were also challenging parts like inverters. They don’t have a specific rule about how many and which types of biobricks they consist of. However, we accepted them as complex subdevices and entered bilateral relation between each connected biobricks.</p><br />
</li><br />
</ul><br />
<p class="p">In METU-BIN 2011 project, our main priority was to focus on (minimal) Functional devices. Therefore we named DNAs, RNAs, and Tags as “accessories” because they are not vital for a device to work. However, we know that using these accessories during construction helps devices work more effectively by adding some extra features. For that reason, it’s in on future plan to form a database for these accessories and present them to our users in their query results.</p><br />
<br />
<br />
<br />
<h3><a name="Scoring"></a>EDGE-SUM Scoring</h3><br />
<p class="p">In order to provide the biologists a reliability measure about the<br />
M4B suggested composite devices, we devised a scoring mechanism.<br />
Composite devices found by M4B could be ranked by simple measures such<br />
as device count, path length, or whether a specific part is included<br />
in the device or not. Instead of these simple scoring mechanisms, we<br />
decided to propose a more eloborate scoring algorithm that takes into<br />
account status, rating, quality, and results of a device available in<br />
the Parts Registry. Such a scoring mechanim makes use of information<br />
provided by the community and it will be useful to decide which<br />
devices are more “valuable” than others if a set of alternative<br />
devices are available for a given input-output pair.</p><br />
<br />
<p class="p">To compute a score for a novel composite device, we first calculate a<br />
score for each edge in the composite device. To compute an edge score,<br />
we find all the existing devices in the Parts Registry that contain<br />
that specific edge and compute an accumulated score for that edge by<br />
summing up the scores of these existing Parts Registry devices that<br />
contain the edge. All the edge scores are normalized to the interval<br />
[0,1] by a sigmoid function. After finding the scores of all edges in<br />
a novel composite device found by M4B, we sum the logarithms of these<br />
edge scores which is equal to logarithm of the multiplication of<br />
scores. If we cannot compute a score for an edge (when the edge is completely<br />
new for example) we use a small number for that edge, similar to the idea of<br />
pseudocounts in profile HMMs. Since, this logarithm is a negative number we raise it to the<br />
power of e again to report the final score between 0.0 and 1.0. Values<br />
close to 1.0 indicate more reliable devices. EDGE-SUM SCORES are categorized into three classes according to their numeric range only. Gold-silver and bronze categories are assigned just for easy visualization of the results.</p><br />
<br />
<p class="p">To calculate the score of an existing Parts Registry device, we use<br />
the following features of devices. In addition, we give a relative<br />
importance to each of these features as suggested by our biologist<br />
team members. These relative importance weights is just a heuristic<br />
and can be optimized in future versions of M4B.</p><br />
<br />
<p class="p"><br />
<table width="625" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_status</th><br />
<th>Available</th><br />
<th>Planning</th><br />
<th>Missing</th><br />
<th>Deleted</th><br />
<th>Unavailable</th><br />
<th>Informational</th><br />
</tr><br />
<tr><br />
<td>1.0</td><br />
<td>0.1</td><br />
<td>0.0</td><br />
<td>0.0</td><br />
<td>0.0</td><br />
<td>0.2</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="650" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">best_quality</th><br />
<th>Partially Confirmed</th><br />
<th>None</th><br />
<th>Confirmed</th><br />
<th>Long Part</th><br />
<th>Questionable</th><br />
<th>Bad Sequencing</th><br />
</tr><br />
<tr><br />
<td>0.5</td><br />
<td>0.0</td><br />
<td>1.0</td><br />
<td>0.2</td><br />
<td>0.1</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="200" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_rating </th><br />
<th>1</th><br />
<th>NULL</th><br />
</tr><br />
<tr><br />
<td>1.0</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="500" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_results</th><br />
<th>None</th><br />
<th>Works</th><br />
<th>Fails</th><br />
<th>Issues</th><br />
<th>NULL</th><br />
</tr><br />
<tr><br />
<td>0.0</td><br />
<td>1.0</td><br />
<td>0.0</td><br />
<td>0.2</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p">For example, if a device is Available, Partially Confirmed and Works,<br />
its score will be "1.0+0.5+1.0 = 2.5". And, if an edge is included in<br />
this device, that edge is going to inherit the score of 2.5 and all<br />
these inherited scores from other devices that contain the edge is<br />
accumulated to compute the raw (unnormalized) score of that edge.</p><br />
<br />
<h3><a name="Results"></a>Results</h3><br />
<p class="p">Our software, M4B: Mining for BioBricks, provides many features saving of time, money and effort for scientists. With this software, scientists don't need to do long-term research and have expensive lab tools.</p><br />
<p class="p">Since it's online and can be used via any updated browser, users don't need to install it and carry it with themselves in order to use it on another computer. With this feature, they can use our software on all the computers having updated system. Also, they don't have to provide any place in their storage device.</p><br />
<br />
<br />
<h3><a name="System_Specifications"></a>Recommended Minimum System Specifications</h3><br />
<ul><br />
<li>Intel Pentium 2Ghz</li><br />
<li>512 MB Ram</li><br />
<li>Java Runtime Environment 1.6</li><br />
<li>128K Internet Speed</li><br />
<li>Supported web browsers: Firefox, Chrome, Safari, Internet Explorer</li><br />
</ul><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank">Click to see!</a><br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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</li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Notebook" class="notebookLink">Notebook</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Safety" class="safetyLink">Safety</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice" class="practiceLink">Human Practice</a><br />
<ul class="practice"><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#HIBIT11_Roundtable">HIBIT'11 Roundtable</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#Teknovasyon_2011">Teknovasyon 2011</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#DNA_School">DNA School</a></li><br />
</ul></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Collaborations" class="collaborationsLink">Collaborations</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/NextVersion" class="versionLink">Next Version</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/FromPress" class="pressLink">From Press</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Contact" class="contactLink">Contact</a></li><br />
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<h2>Team: <span class="cont">Attribution and Contributions</span></h2><br />
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<p class="p">METU-BIN is an interdisciplinary research team whose main focus is on the intersection of Systems Biology approaches and Synthetic Biology applications. For this aim METU-BIN team is composed of 12 students and 2 advisors from different disciplines such as Biology, Molecular Biology, Electronics, Computer Science, Mathematics, Statistics and Bioinformatics.</p><br />
<p class="p"><iframe src="http://player.vimeo.com/video/29401573?title=0&amp;byline=0&amp;portrait=0" width="400" height="220" frameborder="0" webkitAllowFullScreen allowFullScreen></iframe></p><br />
<h3>Students</h3><br />
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<h4>Gökçe OĞUZ</h4><br />
<p class="p">Hi, I’m Gökçe :) I graduated with a degree in Biology and currently I’m taking lectures to start the Bioinformatics graduate program at Middle East Technical University. After learning there is a huge unknown world of Syntehic Biology, I became more curious about synthetic Biology. This is my first year in iGEM. When I heard igem, I directly jumped into because this is a great opportunity for me to get knowledge about Synthetic biology, meet new people and have fun at the same time :) <span class="cont">In this team, as a biologist, I am the bridge in between the partsregistry and software team. I am working on a database which contains bilateral relations between biobricks in Partsregistry.</span></p><br />
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<h4>Burcu YALDIZ</h4><br />
<p class="p">Hi, I'm Burcu. I'm a mathematician and I am taking scientific preparation courses for Graduate Program of Bioinformatics at Middle East Technical University. I like biology more than mathematics and bioinformatics give me a chance to use my mathematician skills in biology. This is my first year in iGEM. When I heard that two teams from METU got medals in iGEM 2010 I thought that “I must be in these teams” and now I'm a member of METU-BIN. I think Synthetic Biology is an extreme subject and it's an exciting experience for me being a part of this team. <span class="cont">In the team I am responsible for editorial issues and organizing the sponsorship application.</span></p><br />
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<h4>İsmail ASLANER</h4><br />
<p class="p">I have just graduated from Hacettepe University Electrical and Electronics Engineering department and a fresh new student at METU Bioinformatics Msc. Program. I also have Moleculer Biology background which is the real motivation for me in this project. I would like to work more on systems biology and i believe that working on modelling and data analysis in this project is a good start for me.</p><br />
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<h4>Ogün ADEBALİ</h4><br />
<p class="p">Hello! I am Ogün Adebali, a fresh graduate from the 'Molecular Biology & Genetics' department of METU. Currently I am a PhD student in the program called 'Genome Science and Technology' in University of Tennessee. <span class="cont">My mission in this team is to support our synthetic biology approach by representing it on various platforms. We organized synthetic biology round table in HIBIT2011 and participated in 'Teknovasyon' competition with our synthetic biology project.</span> As a geneticist, I believe that it is good to be here to keep up with the developments of synthetic biology, which is one of the up-and-coming fields in my interest. </p><br />
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<h4>Saygın KARAASLAN</h4><br />
<p class="p">Hi there, I am a senior in Biology Department at METU and about to launch my own scientific animation company focusing on developing a Virtual Lab application. After graduation I would like to continue my studies on medical informatics, and 3D molecular animations. <span class="cont">I was a part of the design and mutimedia group of METU-BIN and have produced METU-BIN's introductory video for BBC, logos, animation for M4B and designed the team-wear.</span></span></p><br />
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<h4>Ebru ŞAHİN</h4><br />
<p class="p">Hi, I’m Ebru. My major is Statistics and Computer Sciences. I’m studying Master of Science in Bioinformatics program in Middle East Technical University. I got really excited when I heard iGEM, synthetic biology and the idea of constructing artificial biological systems. This is the first time participating to iGEM and <span class="cont">I’m on the editorial board.</span></span></p><br />
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<h4>Gökhan ERSOY</h4><br />
<p class="p">Hi, I am Gökhan. :) I am a Computer Engineer. And this year, I will start studying the scientific preperation class in Bioinformatics Department of Middle East Technical University, as a graduate student. This is my first year in genetics science and iGEM. Although I'm a computer scientist; I always like genetics and working in the lab environment. I think iGEM is a perfect way to improve my knowledge on genetics. <span class="cont">In our team, I am responsible of software development. I've coded search and scoring algorithms. And I've developed GUI with the assistance of Güngör. And i've added some extra tables to the database created by Seyedsasan. Other than software development, I've helped on finding sponsorships and talked about our project in a seminar with Gökçe, for human practice. And finally with my friends, I made an interview for live news on TV. That's all.</span> :) I would like to thank my teachers, advisors and friends for their hardwork. Good luck for all teams! :)</p><br />
<p>Contact: goksoy66 [at] gmail [dot] com</p></span><br />
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<h4>Güngör BUDAK</h4><br />
<p class="p">Hi, I'm Güngör. I'm one of the undergraduate students in the iGEM team METU-BIN and studying Biology major at Middle East Technical University (METU). So I'm learning the great science, Biology but at the same time, my deep interest in computer sciences takes me to that area as well. When I was taking some advice on Bioinformatics, which is the application of computer science and information technology to the field of biology and medicine, by Assoc. Prof. Yeşim AYDIN SON, she told me about the competition and the field synthetic biology. After a quick search on the Internet, I found this area amazing, and eventually I was one of the member of the METU-BIN. <span class="cont">In the team, my contributions were to get the relational data of bioparts in PartsRegistry and store it in a standard way for computer engineers to use it. Then, I coded and designed the wiki page using HTML and CSS, and also I designed the team logo and logo of M4B. At the same time, I provided the content of wiki, with the help of my friends Burcu, Gökçe, Gökhan.</span></p><br />
<p>Contact: gngrbdk [at] gmail [dot] com</p><br />
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<h3>Advisors</h3><br />
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<h4>Seyedsasan HASHEMIKHABIR</h4><br />
<p class="p">My name is Sasan. I'm studying Master of Science in computer engineering program in Middle East Technical University and participated in this team as an Advisor. <span class="cont">I designed all the algorithms and the database in the team and also deployed the database on MySQL. In addition, I tried to motivate the rest of the team members as much as I can and to be like a chain for connecting biology subteam and our team developer, Gokhan.</span></p><br />
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<h4>Yener TUNCEL</h4><br />
<p class="p">I am a graduate of METU Molecular Biology and Genetics Program and currently studying towards my M.Sc. degree on Bioinformatics at METU. This is my second year in the iGEM competition and I am one of the advisors of the METU-BIN Software team. Synthetic biology is very promising and attractive field. Although it is a new scientific field, it holds so many opportunities for biotechnology as well as human health. <span class="cont">My major mission is to organize and manage the team. I have also contributed to Human Practice issue for iGEM by joining innovative project competitions and scientific platforms in order to disseminate and introduce Synthetic Biology concept in Turkey.</span></p><br />
<p class="p">I am very deeply interested in systems biology and its applications in the sub-fields of Molecular Biology because I believe the holistic approach is required in all aspects of molecular biology and serves as the key factor for the understanding of entire cell behaviour, its overall mechanism and its dynamics.</p><br />
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<h3>Instructors</h3><br />
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<img class="secimg" src="https://static.igem.org/mediawiki/2011/7/7b/Yesim.png" /><br />
<span class="sectext"><br />
<h4>Yeşim AYDIN SON</h4><br />
<p class="p">Yeşim, is a medical scientist with M.D from HÜTF, Ankara and a Ph.D from University of TN, Knoxville on Genome Science and Technology. She currently holds a faculty position as an Assistant Professor of Medical Informatics at METU Informatics Institute and also the acting coordinator of the Bioinformatics Graduate Program in METU. Main focus of her research is Genomic Biomarker discovery and applications of biomarker research in Personalized Medicine. Her research group recently developed an integrated desktop application the "METU-SNP" for genome wide association of SNP biomarkers and discovery of genes and pathways related to diseases. She is also interested in translational medicine and integrative bioinformatics working on developing genomic diagnostics for prediction, diagnosis and maintenance of drug therapies in complex diseases.</p><br />
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<h4>Tolga CAN</h4><br />
<p class="p">Tolga Can received his PhD in Computer Science at the University of California at Santa Barbara in 2004. He is currently an Assistant Professor of the Department of Computer Engineering, Middle East Technical University, Ankara, Turkey. His main research interests are in bioinformatics, especially prediction and analysis of protein-protein interaction networks, and statistical methods such as graphical models and kernel methods.</p><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank">Click to see!</a><br />
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<div class="social margin"><h6>Find us on</h6><br />
<a href="http://www.facebook.com/METUBIN" target="_blank"><img src="https://static.igem.org/mediawiki/2011/5/55/Facebook.png" /></a><br />
<a href="http://www.twitter.com/METUBIN" target="_blank"><img src="https://static.igem.org/mediawiki/2011/f/f7/Twitter.png" /></a><br />
<a href="http://vimeo.com/user8040359" target="_blank"><img src="https://static.igem.org/mediawiki/2011/5/51/Vimeo.png" /></a><br />
<a href="http://picasaweb.google.com/105434043475546846942" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d4/Picasa.png" /></a><br />
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<div id="gallery"><h6>Some photos during summer</h6><br />
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<a href="https://static.igem.org/mediawiki/2011/b/b3/Summer-img2.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/b/b3/Summer-img2.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/1/1b/Summer-img3.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/1/1b/Summer-img3.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/3/34/Summer-img4.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/3/34/Summer-img4.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/4/4e/Summer-img5.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/4/4e/Summer-img5.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/f/f2/Summer-img6.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/f/f2/Summer-img6.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/a/ac/Summer-img7.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/a/ac/Summer-img7.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/6/6e/Summer-img8.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/6/6e/Summer-img8.jpg" /></a><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/TeamTeam:METU-BIN Ankara/Team2011-10-27T17:42:19Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
<div class="metu-bin"><a href="https://2011.igem.org/Team:METU-BIN_Ankara" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d6/Metu-bin_logo.png" /></a></div><br />
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<h2>Team: <span class="cont">Attribution and Contributions</span></h2><br />
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<p class="p">METU-BIN is an interdisciplinary research team whose main focus is on the intersection of Systems Biology approaches and Synthetic Biology applications. For this aim METU-BIN team is composed of 12 students and 2 advisors from different disciplines such as Biology, Molecular Biology, Electronics, Computer Science, Mathematics, Statistics and Bioinformatics.</p><br />
<p class="p"><iframe src="http://player.vimeo.com/video/29401573?title=0&amp;byline=0&amp;portrait=0" width="400" height="220" frameborder="0" webkitAllowFullScreen allowFullScreen></iframe></p><br />
<h3>Students</h3><br />
<div class="sections"><br />
<img class="secimg" src="https://static.igem.org/mediawiki/2011/d/dd/Gokce.png" /><br />
<span class="sectext"><br />
<h4>Gökçe OĞUZ</h4><br />
<p class="p">Hi, I’m Gökçe :) I graduated with a degree in Biology and currently I’m taking lectures to start the Bioinformatics graduate program at Middle East Technical University. After learning there is a huge unknown world of Syntehic Biology, I became more curious about synthetic Biology. This is my first year in iGEM. When I heard igem, I directly jumped into because this is a great opportunity for me to get knowledge about Synthetic biology, meet new people and have fun at the same time :) <span class="cont">In this team, as a biologist, I am the bridge in between the partsregistry and software team. I am working on a database which contains bilateral relations between biobricks in Partsregistry.</span></p><br />
</span><br />
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<div class="sections"><br />
<img class="secimg" src="https://static.igem.org/mediawiki/2011/b/b2/Burcu.png" /><br />
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<h4>Burcu YALDIZ</h4><br />
<p class="p">Hi, I'm Burcu. I'm a mathematician and I am taking scientific preparation courses for Graduate Program of Bioinformatics at Middle East Technical University. I like biology more than mathematics and bioinformatics give me a chance to use my mathematician skills in biology. This is my first year in iGEM. When I heard that two teams from METU got medals in iGEM 2010 I thought that “I must be in these teams” and now I'm a member of METU-BIN. I think Synthetic Biology is an extreme subject and it's an exciting experience for me being a part of this team. <span class="cont">In the team I am responsible for editorial issues and organizing the sponsorship application.</span></p><br />
</span><br />
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</div><br />
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<div class="sections"><br />
<img class="secimg" src="https://static.igem.org/mediawiki/2011/c/c6/Ismail.png" /><br />
<span class="sectext"><br />
<h4>İsmail ASLANER</h4><br />
<p class="p">I have just graduated from Hacettepe University Electrical and Electronics Engineering department and a fresh new student at METU Bioinformatics Msc. Program. I also have Moleculer Biology background which is the real motivation for me in this project. I would like to work more on systems biology and i believe that working on modelling and data analysis in this project is a good start for me.</p><br />
</span><br />
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<img class="secimg" src="https://static.igem.org/mediawiki/2011/b/b5/Ogun.png" /><br />
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<h4>Ogün ADEBALİ</h4><br />
<p class="p">Hello! I am Ogün Adebali, a fresh graduate from the 'Molecular Biology & Genetics' department of METU. Currently I am a PhD student in the program called 'Genome Science and Technology' in University of Tennessee. <span class="cont">My mission in this team is to support our synthetic biology approach by representing it on various platforms. We organized synthetic biology round table in HIBIT2011 and participated in 'Teknovasyon' competition with our synthetic biology project.</span> As a geneticist, I believe that it is good to be here to keep up with the developments of synthetic biology, which is one of the up-and-coming fields in my interest. </p><br />
</span><br />
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<h4>Saygın KARAASLAN</h4><br />
<p class="p">Hi there, I am a senior in Biology Department at METU and about to launch my own scientific animation company focusing on developing a Virtual Lab application. After graduation I would like to continue my studies on medical informatics, and 3D molecular animations. <span class="cont">I was a part of the design and mutimedia group of METU-BIN and have produced METU-BIN's introductory video for BBC, logos, animation for M4B and designed the team-wear.</span></span></p><br />
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<h4>Ebru ŞAHİN</h4><br />
<p class="p">Hi, I’m Ebru. My major is Statistics and Computer Sciences. I’m studying Master of Science in Bioinformatics program in Middle East Technical University. I got really excited when I heard iGEM, synthetic biology and the idea of constructing artificial biological systems. This is the first time participating to iGEM and <span class="cont">I’m on the editorial board.</span></span></p><br />
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<h4>Gökhan ERSOY</h4><br />
<p class="p">Hi, I am Gökhan. :) I am a Computer Engineer. And this year, I will start studying the scientific preperation class in Bioinformatics Department of Middle East Technical University, as a graduate student. This is my first year in genetics science and iGEM. Although I'm a computer scientist; I always like genetics and working in the lab environment. I think iGEM is a perfect way to improve my knowledge on genetics. <span class="cont">In our team, I am responsible of software development. I've coded search and scoring algorithms. And I've developed GUI with the assistance of Güngör. And i've added some extra tables to the database created by Seyedsasan. Other than software development, I've helped on finding sponsorships and talked about our project in a seminar with Gökçe, for human practice. And finally with my friends, I made an interview for live news on TV. That's all.</span> :) I would like to thank my teachers, advisors and friends for their hardwork. Good luck for all teams! :)</p><br />
<p>Contact: goksoy66 [at] gmail [dot] com</p></span><br />
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<h4>Güngör BUDAK</h4><br />
<p class="p">Hi, I'm Güngör. I'm one of the undergraduate students in the iGEM team METU-BIN and studying Biology major at Middle East Technical University (METU). So I'm learning the great science, Biology but at the same time, my deep interest in computer sciences takes me to that area as well. When I was taking some advice on Bioinformatics, which is the application of computer science and information technology to the field of biology and medicine, by Assoc. Prof. Yeşim AYDIN SON, she told me about the competition and the field synthetic biology. After a quick search on the Internet, I found this area amazing, and eventually I was one of the member of the METU-BIN. <span class="cont">In the team, my contributions were to get the relational data of bioparts in PartsRegistry and store it in a standard way for computer engineers to use it. Then, I coded and designed the wiki page using HTML and CSS, and also I designed the team logo and logo of M4B. At the same time, I provided the content of wiki, with the help of my friends Burcu, Gökçe, Gökhan.</span></p><br />
<p>Contact: gngrbdk [at] gmail [dot] com</p><br />
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<h3>Advisors</h3><br />
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<h4>Seyedsasan HASHEMIKHABIR</h4><br />
<p class="p">My name is Sasan. I'm studying Master of Science in computer engineering program in Middle East Technical University and participated in this team as an Advisor. <span class="cont">I designed all the algorithms and the database in the team and also deployed the database on MySQL. In addition, I tried to motivate the rest of the team members as much as I can and to be like a chain for connecting biology subteam and our team developer, Gokhan.</span></p><br />
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<h4>Yener TUNCEL</h4><br />
<p class="p">I am a graduate of METU Molecular Biology and Genetics Program and currently studying towards my M.Sc. degree on Bioinformatics at METU. This is my second year in the iGEM competition and I am one of the advisors of the METU-BIN Software team. Synthetic biology is very promising and attractive field. Although it is a new scientific field, it holds so many opportunities for biotechnology as well as human health. <span class="cont">My major mission is to organize and manage the team. I have also contributed to Human Practice issue for iGEM by joining innovative project competitions and scientific platforms in order to disseminate and introduce Synthetic Biology concept in Turkey.</span></p><br />
<p class="p">I am very deeply interested in systems biology and its applications in the sub-fields of Molecular Biology because I believe the holistic approach is required in all aspects of molecular biology and serves as the key factor for the understanding of entire cell behaviour, its overall mechanism and its dynamics.</p><br />
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<h3>Instructors</h3><br />
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<h4>Yeşim AYDIN SON</h4><br />
<p class="p">Yeşim, is a medical scientist with M.D from HÜTF, Ankara and a Ph.D from University of TN, Knoxville on Genome Science and Technology. She currently holds a faculty position as an Assistant Professor of Medical Informatics at METU Informatics Institute and also the acting coordinator of the Bioinformatics Graduate Program in METU. Main focus of her research is Genomic Biomarker discovery and applications of biomarker research in Personalized Medicine. Her research group recently developed an integrated desktop application the "METU-SNP" for genome wide association of SNP biomarkers and discovery of genes and pathways related to diseases. She is also interested in translational medicine and integrative bioinformatics working on developing genomic diagnostics for prediction, diagnosis and maintenance of drug therapies in complex diseases.</p><br />
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<h4>Tolga CAN</h4><br />
<p class="p">Tolga Can received his PhD in Computer Science at the University of California at Santa Barbara in 2004. He is currently an Assistant Professor of the Department of Computer Engineering, Middle East Technical University, Ankara, Turkey. His main research interests are in bioinformatics, especially prediction and analysis of protein-protein interaction networks, and statistical methods such as graphical models and kernel methods.</p><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img style="width: 276px;margin:0;" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank">Click to see</a>!<br />
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<div class="social margin"><h6>Find us on</h6><br />
<a href="http://www.facebook.com/METUBIN" target="_blank"><img src="https://static.igem.org/mediawiki/2011/5/55/Facebook.png" /></a><br />
<a href="http://www.twitter.com/METUBIN" target="_blank"><img src="https://static.igem.org/mediawiki/2011/f/f7/Twitter.png" /></a><br />
<a href="http://vimeo.com/user8040359" target="_blank"><img src="https://static.igem.org/mediawiki/2011/5/51/Vimeo.png" /></a><br />
<a href="http://picasaweb.google.com/105434043475546846942" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d4/Picasa.png" /></a><br />
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<div id="gallery"><h6>Some photos during summer</h6><br />
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<a href="https://static.igem.org/mediawiki/2011/b/b3/Summer-img2.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/b/b3/Summer-img2.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/1/1b/Summer-img3.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/1/1b/Summer-img3.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/3/34/Summer-img4.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/3/34/Summer-img4.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/4/4e/Summer-img5.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/4/4e/Summer-img5.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/f/f2/Summer-img6.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/f/f2/Summer-img6.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/a/ac/Summer-img7.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/a/ac/Summer-img7.jpg" /></a><br />
<a href="https://static.igem.org/mediawiki/2011/6/6e/Summer-img8.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2011/6/6e/Summer-img8.jpg" /></a><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/TeamTeam:METU-BIN Ankara/Team2011-10-27T17:40:19Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
<div class="metu-bin"><a href="https://2011.igem.org/Team:METU-BIN_Ankara" target="_blank"><img src="https://static.igem.org/mediawiki/2011/d/d6/Metu-bin_logo.png" /></a></div><br />
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<h2>Team: <span class="cont">Attribution and Contributions</span></h2><br />
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<p class="p">METU-BIN is an interdisciplinary research team whose main focus is on the intersection of Systems Biology approaches and Synthetic Biology applications. For this aim METU-BIN team is composed of 12 students and 2 advisors from different disciplines such as Biology, Molecular Biology, Electronics, Computer Science, Mathematics, Statistics and Bioinformatics.</p><br />
<p class="p"><iframe src="http://player.vimeo.com/video/29401573?title=0&amp;byline=0&amp;portrait=0" width="400" height="220" frameborder="0" webkitAllowFullScreen allowFullScreen></iframe></p><br />
<h3>Students</h3><br />
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<img class="secimg" src="https://static.igem.org/mediawiki/2011/d/dd/Gokce.png" /><br />
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<h4>Gökçe OĞUZ</h4><br />
<p class="p">Hi, I’m Gökçe :) I graduated with a degree in Biology and currently I’m taking lectures to start the Bioinformatics graduate program at Middle East Technical University. After learning there is a huge unknown world of Syntehic Biology, I became more curious about synthetic Biology. This is my first year in iGEM. When I heard igem, I directly jumped into because this is a great opportunity for me to get knowledge about Synthetic biology, meet new people and have fun at the same time :) <span class="cont">In this team, as a biologist, I am the bridge in between the partsregistry and software team. I am working on a database which contains bilateral relations between biobricks in Partsregistry.</span></p><br />
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<h4>Burcu YALDIZ</h4><br />
<p class="p">Hi, I'm Burcu. I'm a mathematician and I am taking scientific preparation courses for Graduate Program of Bioinformatics at Middle East Technical University. I like biology more than mathematics and bioinformatics give me a chance to use my mathematician skills in biology. This is my first year in iGEM. When I heard that two teams from METU got medals in iGEM 2010 I thought that “I must be in these teams” and now I'm a member of METU-BIN. I think Synthetic Biology is an extreme subject and it's an exciting experience for me being a part of this team. <span class="cont">In the team I am responsible for editorial issues and organizing the sponsorship application.</span></p><br />
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<h4>İsmail ASLANER</h4><br />
<p class="p">I have just graduated from Hacettepe University Electrical and Electronics Engineering department and a fresh new student at METU Bioinformatics Msc. Program. I also have Moleculer Biology background which is the real motivation for me in this project. I would like to work more on systems biology and i believe that working on modelling and data analysis in this project is a good start for me.</p><br />
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<h4>Ogün ADEBALİ</h4><br />
<p class="p">Hello! I am Ogün Adebali, a fresh graduate from the 'Molecular Biology & Genetics' department of METU. Currently I am a PhD student in the program called 'Genome Science and Technology' in University of Tennessee. <span class="cont">My mission in this team is to support our synthetic biology approach by representing it on various platforms. We organized synthetic biology round table in HIBIT2011 and participated in 'Teknovasyon' competition with our synthetic biology project.</span> As a geneticist, I believe that it is good to be here to keep up with the developments of synthetic biology, which is one of the up-and-coming fields in my interest. </p><br />
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<h4>Saygın KARAASLAN</h4><br />
<p class="p">Hi there, I am a senior in Biology Department at METU and about to launch my own scientific animation company focusing on developing a Virtual Lab application. After graduation I would like to continue my studies on medical informatics, and 3D molecular animations. <span class="cont">I was a part of the design and mutimedia group of METU-BIN and have produced METU-BIN's introductory video for BBC, logos, animation for M4B and designed the team-wear.</span></span></p><br />
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<h4>Ebru ŞAHİN</h4><br />
<p class="p">Hi, I’m Ebru. My major is Statistics and Computer Sciences. I’m studying Master of Science in Bioinformatics program in Middle East Technical University. I got really excited when I heard iGEM, synthetic biology and the idea of constructing artificial biological systems. This is the first time participating to iGEM and <span class="cont">I’m on the editorial board.</span></span></p><br />
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<h4>Gökhan ERSOY</h4><br />
<p class="p">Hi, I am Gökhan. :) I am a Computer Engineer. And this year, I will start studying the scientific preperation class in Bioinformatics Department of Middle East Technical University, as a graduate student. This is my first year in genetics science and iGEM. Although I'm a computer scientist; I always like genetics and working in the lab environment. I think iGEM is a perfect way to improve my knowledge on genetics. <span class="cont">In our team, I am responsible of software development. I've coded search and scoring algorithms. And I've developed GUI with the assistance of Güngör. And i've added some extra tables to the database created by Seyedsasan. Other than software development, I've helped on finding sponsorships and talked about our project in a seminar with Gökçe, for human practice. And finally with my friends, I made an interview for live news on TV. That's all.</span> :) I would like to thank my teachers, advisors and friends for their hardwork. Good luck for all teams! :)</p><br />
<p>Contact: goksoy66 [at] gmail [dot] com</p></span><br />
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<h4>Güngör BUDAK</h4><br />
<p class="p">Hi, I'm Güngör. I'm one of the undergraduate students in the iGEM team METU-BIN and studying Biology major at Middle East Technical University (METU). So I'm learning the great science, Biology but at the same time, my deep interest in computer sciences takes me to that area as well. When I was taking some advice on Bioinformatics, which is the application of computer science and information technology to the field of biology and medicine, by Assoc. Prof. Yeşim AYDIN SON, she told me about the competition and the field synthetic biology. After a quick search on the Internet, I found this area amazing, and eventually I was one of the member of the METU-BIN. <span class="cont">In the team, my contributions were to get the relational data of bioparts in PartsRegistry and store it in a standard way for computer engineers to use it. Then, I coded and designed the wiki page using HTML and CSS, and also I designed the team logo and logo of M4B. At the same time, I provided the content of wiki, with the help of my friends Burcu, Gökçe, Gökhan.</span></p><br />
<p>Contact: gngrbdk [at] gmail [dot] com</p><br />
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<h3>Advisors</h3><br />
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<h4>Seyedsasan HASHEMIKHABIR</h4><br />
<p class="p">My name is Sasan. I'm studying Master of Science in computer engineering program in Middle East Technical University and participated in this team as an Advisor. <span class="cont">I designed all the algorithms and the database in the team and also deployed the database on MySQL. In addition, I tried to motivate the rest of the team members as much as I can and to be like a chain for connecting biology subteam and our team developer, Gokhan.</span></p><br />
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<h4>Yener TUNCEL</h4><br />
<p class="p">I am a graduate of METU Molecular Biology and Genetics Program and currently studying towards my M.Sc. degree on Bioinformatics at METU. This is my second year in the iGEM competition and I am one of the advisors of the METU-BIN Software team. Synthetic biology is very promising and attractive field. Although it is a new scientific field, it holds so many opportunities for biotechnology as well as human health. <span class="cont">My major mission is to organize and manage the team. I have also contributed to Human Practice issue for iGEM by joining innovative project competitions and scientific platforms in order to disseminate and introduce Synthetic Biology concept in Turkey.</span></p><br />
<p class="p">I am very deeply interested in systems biology and its applications in the sub-fields of Molecular Biology because I believe the holistic approach is required in all aspects of molecular biology and serves as the key factor for the understanding of entire cell behaviour, its overall mechanism and its dynamics.</p><br />
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<h3>Instructors</h3><br />
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<span class="sectext"><br />
<h4>Yeşim AYDIN SON</h4><br />
<p class="p">Yeşim, is a medical scientist with M.D from HÜTF, Ankara and a Ph.D from University of TN, Knoxville on Genome Science and Technology. She currently holds a faculty position as an Assistant Professor of Medical Informatics at METU Informatics Institute and also the acting coordinator of the Bioinformatics Graduate Program in METU. Main focus of her research is Genomic Biomarker discovery and applications of biomarker research in Personalized Medicine. Her research group recently developed an integrated desktop application the "METU-SNP" for genome wide association of SNP biomarkers and discovery of genes and pathways related to diseases. She is also interested in translational medicine and integrative bioinformatics working on developing genomic diagnostics for prediction, diagnosis and maintenance of drug therapies in complex diseases.</p><br />
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<h4>Tolga CAN</h4><br />
<p class="p">Tolga Can received his PhD in Computer Science at the University of California at Santa Barbara in 2004. He is currently an Assistant Professor of the Department of Computer Engineering, Middle East Technical University, Ankara, Turkey. His main research interests are in bioinformatics, especially prediction and analysis of protein-protein interaction networks, and statistical methods such as graphical models and kernel methods.</p><br />
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<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank">Click to see</a>!<br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>Project</h2><br />
<br />
<h3><a name="Introduction"></a>Introduction</h3><br />
<p class="p">While the interest to the field of synthetic biology is uprising, iGEM and Parts Registry is getting more important for researchers interested working in the field of synthetic biology. As the number of attendees and teams to iGEM competition increases each year, number of BioBricks submitted to the Parts Registry are increasing too. As we all know, Parts Registry is an inimitable library for synthetic biologists. Although it is an important source of information and tool for biologists, the parts are not organized very well. Therefore, while constructing devices, synthetic biologists usually faces following difficulties at the pre-experimental stage:</p><br />
<ul><br />
<li>Searching through the Parts</li><br />
<li>Deciding if the parts needed are already in the database or not</li><br />
<li>Deciding which BioBrick will work effectively with which</li><br />
<li>Finding the most accurate combination between the parts</li><br />
<li>Constructing the most effectively working devices</li><br />
</ul><br />
<p class="p">Figuring out all these answers is time consuming and takes too much effort. Our main goal as 2011 METU-BIN iGEM Software team was to provide a web based tool that helps synthetic biologists at the pre-experimental step to search the Part Registry with input and output keywords and to design their genetic constructs using the biobricks provided in the 2011 distribution of DNA constructs.</p><br />
<br />
<p class="p"><strong>M4B: Mining for Biobricks</strong> is developed to aid synthetic biologist. Our software proposes a method which can be utilized in pre-experimental step as a supporter data mining tool. Following the user defined input and output parameters, M4B lists all possible composite devices and ranks them according to the novel scoring measurement developed by METU-BIN.</p><br />
<br />
<h4>Aim</h4><br />
<p class="p">Main goal of our 2011 project is to provide a web based tool that helps synthetic biologists at the pre-experimental step to design their genetic constructs according to their input and output parameters.</p><br />
<ul><br />
<li>A network of all bioparts in 2011 distribution will be generated, which describes the functional relations between the subatomic bioparts.</li><br />
<li>A search algorithm will be developed to reveal all possible device combinations for the user defined input and output within bioparts of 2011 distribution.</li><br />
<li>Visualization tools will be applied for graphical representation of the results.</li><br />
<li>A web-based user interface will be provided for the developed software.</li><br />
</ul><br />
<h3><a name="Algorithm"></a>Algorithm</h3><br />
<p class="p">M4B is developed using Java Web Technologies. Web programming enables user- and PC-friendly products. Users do not need to install any program on their PC, and so they do not need to waste PC resources for programs. A web application can easily be reached using a simple web-browser from any PC and from anywhere in the world . It is the most important property of M4B.</p><br />
<h4>Flowcharts for the Algorithms</h4><br />
<div><br />
<a href="https://static.igem.org/mediawiki/2011/b/bb/Search_algorithm3.png" target="_blank"><img style="width:290px;margin-right:10px;" src="https://static.igem.org/mediawiki/2011/b/bb/Search_algorithm3.png" /></a><a href="https://static.igem.org/mediawiki/2011/a/a4/Scoring_algorithm.png" target="_blank"><img style="width:290px;margin-right:10px;" src="https://static.igem.org/mediawiki/2011/a/a4/Scoring_algorithm.png" /></a><br />
</div><br />
<p class="p">In detail, we have used Java Applet to serve M4B on the net. And to store data of M4B, we have used an instance of MySQL database. We've created tables for all XML files of PartsRegistry. For example, they contain part info, deep subparts and specific subparts info, scars info, etc. In addition we've added a few more tables to implement algorithm. They are for interaction relations between parts, scores of main parts, scores of edges, etc.</p> <br />
<p class="p">For the implementation of M4B, a huge biobrick network is constructed using information in the PartsRegistry database. With information of interactions between edges, we are creating a part network. It is a hashtable of hashtables. By the use of hashtables, we can easily find the input part on network to start searching. All useful information about a part is stored in a type of Part. It has following fields.</p><br />
<br />
<ul><br />
<li>partID</li><li>partType</li><li>promoterType</li><li>output</li><li>terminator</li><li>nextParts</li></ul><br />
<br />
<p class="p">After constructing the network, we are making a search for the list of all possible composite devices beginning with given input and output parameters. To traverse whole graph, we are using a customized version of the famous graph traversal algorithm, <strong>DFS (Depth First Search)</strong>. In DFS, it is making a search on one way until the leaf node, then if it cannot find it goes back to last disjoint point and goes on searching until next leaf node.</p><br />
<br />
<img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/2/26/Algorithm_img.gif" /><br />
<br />
<p class="p">Using the quick access property of hashtable we are finding the input part on network. If the given input is found on the graph once, we go over all the descendant nodes until finding the expected output. While searching an output node, all nodes traversed are being recorded. When the output is found, the recorded path is added to the “results list”. Else, it is discarded until the last disjoint point, and a new path is searched continuing from that point. After all possible paths are found, the list of paths is shown on the GUI.</p><br />
<br />
<p class="p">One can also search for the devices starting with a constitutive promoter. To do this, user shouldn't enter the input parameter. By this empty input information, algorithm looks for constitutive promoters to start as an input point. "$" sign is used as symbolic input for constitutive promoters.</p><br />
<br />
<p class="p">When we are searching for the expected output, we may find different outputs. If that output continues with a Promoter as an Input, it means that we are starting to add the parts of next device. A composite part can have more than one device. So we've added an input field to specify the maximum device count of results. User can change the number of device count using this field.</p><br />
<br />
<p class="p">Let's talk about visualization of the graph. If user selects an input from the list, it parses all parts from selected device and looks for it is type from network. Then, it creates a node of that type. We are using icons of Parts Registry for the types of parts. And we are using yFiles for visualization.</p><br />
<br />
<p class="p">If user selects a node in the graph, it queries the information about that part from tables created using XML files of Parts Registry.</p><br />
<br />
<p class="p">Quick search when typing the input name is the user friendly property of M4B. No need for a “Find” button.</p><br />
<br />
<p class="p">The other feature of the program is printing the results. Most of users wants to save their results. It enables saving.</p><br />
<br />
<h3><a name="Construction_of_Relational_Database"></a>Extraction of Relations of Bioparts and Construction of Relational Database</h3><br />
<br />
<p class="p">Parts Registry contains various types of biobricks and connections in between parts. In our software, we aimed to develop an algorithm which goes over the devices and finds connections between biobricks to present users all possible constructed devices. However, it was very difficult to go over biobricks and find the relations in not very well organized Parts Registry. For that reason, we have decided to form a ”Part Connections Database” by examining all the bilateral relations between biobricks which will be used by our program, M4B. By this way, the complex information in Parts Registry will be simplified and our algorithm will work faster and more effectively.</p><br />
<br />
<p class="p">The biology group focused on all of the four 384 well plates of 2011 distribution and extracted information between connections and devices in a standard way. This information is stored into a relational database and enables queries from remote computer programs.</p><br />
<br />
<p class="p">Our software group developed a toolbox to help biology group in storing the part relations into the new database of connections between biobricks. Using this tool, we were able to minimize the possibility of mistakes while entering bilateral relations manually. More importantly, this organized the database entries in a standardized way, according to the requirements of Mining for BioBricks to run the searching algorithm easily.</p><br />
<br />
<img style="margin-bottom:5px;display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/a/ab/Input-output-gadget.png" /><br />
<small>Figure 1: The toolbox which was used while building the “Part Connections Database” by our biology group.</small><br />
<img style="margin-bottom:5px;display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/7/7e/Input-output-relations.png" /><br />
<small>Figure 2: A screen shot from our temporary file of “relational database”</small><br />
<p class="p">As there are various types of biobricks in the Parts Registry, we set up rules to organize the “relational database” in an appropriate way.</p><br />
<br />
<br />
<h4>Rules</h4><br />
<p class="p">The most important rule is “A constructed device formed by combination of promoter-ribosome binding site-gene-terminator, respectively, is the minimal functional device.”</p><br />
<br />
<p class="p">This is the major rule, because without these 4 major biobrick types, a device cannot work. In addition to this, without knowing the description of “basic device” it is impossible for us to present accurate results to users.<br />
Although Parts Registry contains various types of biobricks, in our database there are 4 basic biobricks which are promoters, ribosome binding sites, genes, and terminators. This helped us to simplify the complex information in the Parts Registry in our initial attempt of mining.</p><br />
<br />
<p class="p">In addition to 4 basic biobrick types, there are inputs and outputs which are our software’s parameters. Inputs are chosen according to promoters. Both activators and inhibitors of promoters were listed in our database. Main source of activators and inhibitors was the information from the Parts Registry. The reason of listing inhibitors was to filter out constructed devices which do not produce the required outputs. When a constructed device is formed by multiple devices, although the input activates first device’s promoter, it may inhibit other promoters of following devices. Outputs were chosen according to the genes, the product they synthesize. Although, most of the time, input and output information was extracted from Parts Registry, sometimes external sources were used as well because of the uninformative part descriptions at Parts Registry. External sources such as NCBI, PubMed and wiki of the team who submitted the biobrick to iGEM were used.</p><br />
<br />
<p class="p">Constitutive promoters are entered without any input, but especially their “constitutiveness” is recorded as a property in our relations database.</p><br />
<br />
<p class="p">In our software, after constructing a device by combining biobricks to construct multiple devices, combination between devices is formed according to this rule: “Output of the first gene will be the input of the following promoter(s)”</p><br />
<br />
<p class="p">According to this rule, first promoter will be activated by given Input and the product of first gene will be used as activator of the following promoters. By activation of the promoters, genes will synthesize the output. By this way, the constructed complex is expected to work effectively.</p><br />
<br />
<p class="p">In Parts Registry, there are composite parts, translation units, generators, reporters, inverters, intermediate devices, and signaling devices. As Parts Registry 2011 distribution was being examined in detail, to simplify these parts, their connection information was simplified to promoter-ribosome binding site-gene-terminator relation by our biological knowledge. This rule is explained with details as seen below:</p><br />
<br />
<ul><br />
<li>Reporters<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/2/27/Reporter-img.png" /><br />
<p class="p">The biobricks which synthesize fluorescent proteins are classified as “reporters” as they give out light to report something. We accepted these parts as “genes” because they are synthesizing proteins.</p></li><br />
<br />
<br />
<li>Translational Units<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/4/48/Translational-units-img.png" /><br />
<p class="p">Combination of ribosome binding site and gene is classified as “translational units”. We accepted this as two biobricks rather than one. Therefore the bilateral relation between ribosome binding site and gene was entered in our database.</p></li><br />
<br />
<br />
<li>Inverters<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/c/c0/Inverters-img.png" /><br />
<p class="p">Inverters were challenging parts; they are formed from more than 2 biobricks. Rather than accepting this as one biobrick, we accepted this part as a combination of four biobricks. Therefore, we entered bilateral relations between each biobricks as ribosome binding site-gene, gene-terminator, and terminator- promoter. We also entered gene-output and input-promoter connections.</p></li><br />
<br />
<li>Composites<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/b/bc/Composites_img.png" /></li><br />
<br />
<li>Generators<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/b/b1/Generators-img.png" /></li><br />
<br />
<li>Signalling Devices<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/7/7d/Signalling_img.png" /></li><br />
<br />
<li>Intermediate Devices<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/8/84/Intermediate-parts-img.png" /><br />
<br />
<p class="p">Composite parts, generators, signaling devices, and intermediate devices were also challenging parts like inverters. They don’t have a specific rule about how many and which types of biobricks they consist of. However, we accepted them as complex subdevices and entered bilateral relation between each connected biobricks.</p><br />
</li><br />
</ul><br />
<p class="p">In METU-BIN 2011 project, our main priority was to focus on (minimal) Functional devices. Therefore we named DNAs, RNAs, and Tags as “accessories” because they are not vital for a device to work. However, we know that using these accessories during construction helps devices work more effectively by adding some extra features. For that reason, it’s in on future plan to form a database for these accessories and present them to our users in their query results.</p><br />
<br />
<br />
<br />
<h3><a name="Scoring"></a>EDGE-SUM Scoring</h3><br />
<p class="p">In order to provide the biologists a reliability measure about the<br />
M4B suggested composite devices, we devised a scoring mechanism.<br />
Composite devices found by M4B could be ranked by simple measures such<br />
as device count, path length, or whether a specific part is included<br />
in the device or not. Instead of these simple scoring mechanisms, we<br />
decided to propose a more eloborate scoring algorithm that takes into<br />
account status, rating, quality, and results of a device available in<br />
the Parts Registry. Such a scoring mechanim makes use of information<br />
provided by the community and it will be useful to decide which<br />
devices are more “valuable” than others if a set of alternative<br />
devices are available for a given input-output pair.</p><br />
<br />
<p class="p">To compute a score for a novel composite device, we first calculate a<br />
score for each edge in the composite device. To compute an edge score,<br />
we find all the existing devices in the Parts Registry that contain<br />
that specific edge and compute an accumulated score for that edge by<br />
summing up the scores of these existing Parts Registry devices that<br />
contain the edge. All the edge scores are normalized to the interval<br />
[0,1] by a sigmoid function. After finding the scores of all edges in<br />
a novel composite device found by M4B, we sum the logarithms of these<br />
edge scores which is equal to logarithm of the multiplication of<br />
scores. If we cannot compute a score for an edge (when the edge is completely<br />
new for example) we use a small number for that edge, similar to the idea of<br />
pseudocounts in profile HMMs. Since, this logarithm is a negative number we raise it to the<br />
power of e again to report the final score between 0.0 and 1.0. Values<br />
close to 1.0 indicate more reliable devices. EDGE-SUM SCORES are categorized into three classes according to their numeric range only. Gold-silver and bronze categories are assigned just for easy visualization of the results.</p><br />
<br />
<p class="p">To calculate the score of an existing Parts Registry device, we use<br />
the following features of devices. In addition, we give a relative<br />
importance to each of these features as suggested by our biologist<br />
team members. These relative importance weights is just a heuristic<br />
and can be optimized in future versions of M4B.</p><br />
<br />
<p class="p"><br />
<table width="625" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_status</th><br />
<th>Available</th><br />
<th>Planning</th><br />
<th>Missing</th><br />
<th>Deleted</th><br />
<th>Unavailable</th><br />
<th>Informational</th><br />
</tr><br />
<tr><br />
<td>1.0</td><br />
<td>0.1</td><br />
<td>0.0</td><br />
<td>0.0</td><br />
<td>0.0</td><br />
<td>0.2</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="650" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">best_quality</th><br />
<th>Partially Confirmed</th><br />
<th>None</th><br />
<th>Confirmed</th><br />
<th>Long Part</th><br />
<th>Questionable</th><br />
<th>Bad Sequencing</th><br />
</tr><br />
<tr><br />
<td>0.5</td><br />
<td>0.0</td><br />
<td>1.0</td><br />
<td>0.2</td><br />
<td>0.1</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="200" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_rating </th><br />
<th>1</th><br />
<th>NULL</th><br />
</tr><br />
<tr><br />
<td>1.0</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="500" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_results</th><br />
<th>None</th><br />
<th>Works</th><br />
<th>Fails</th><br />
<th>Issues</th><br />
<th>NULL</th><br />
</tr><br />
<tr><br />
<td>0.0</td><br />
<td>1.0</td><br />
<td>0.0</td><br />
<td>0.2</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p">For example, if a device is Available, Partially Confirmed and Works,<br />
its score will be "1.0+0.5+1.0 = 2.5". And, if an edge is included in<br />
this device, that edge is going to inherit the score of 2.5 and all<br />
these inherited scores from other devices that contain the edge is<br />
accumulated to compute the raw (unnormalized) score of that edge.</p><br />
<br />
<h3><a name="Results"></a>Results</h3><br />
<p class="p">Our software, M4B: Mining for BioBricks, provides many features saving of time, money and effort for scientists. With this software, scientists don't need to do long-term research and have expensive lab tools.</p><br />
<p class="p">Since it's online and can be used via any updated browser, users don't need to install it and carry it with themselves in order to use it on another computer. With this feature, they can use our software on all the computers having updated system. Also, they don't have to provide any place in their storage device.</p><br />
<br />
<br />
<h3><a name="System_Specifications"></a>Recommended Minimum System Specifications</h3><br />
<ul><br />
<li>Intel Pentium 2Ghz</li><br />
<li>512 MB Ram</li><br />
<li>Java Runtime Environment 1.6</li><br />
<li>128K Internet Speed</li><br />
<li>Supported web browsers: Firefox, Chrome, Safari, Internet Explorer</li><br />
</ul><br />
<br />
</div><br />
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<br />
<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank"><img src="https://static.igem.org/mediawiki/2011/3/31/M4b_logo.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">Click on here</a> or the logo!<br />
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</html></div>Gngrhttp://2011.igem.org/File:Search_algorithm3.pngFile:Search algorithm3.png2011-10-27T17:34:59Z<p>Gngr: </p>
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<div></div>Gngrhttp://2011.igem.org/File:Scoring_algorithm.pngFile:Scoring algorithm.png2011-10-27T17:33:52Z<p>Gngr: </p>
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<div></div>Gngrhttp://2011.igem.org/Team:METU-BIN_AnkaraTeam:METU-BIN Ankara2011-10-26T20:06:40Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h3 class="boxheader m4btab">M4B: Mining for BioBricks</h3><br />
<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img class="boximage imgm4b" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a><br />
<span class="boxtext">It's a miner that goes over all the parts and finds the possible devices for you! <a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank">See our software, it's online!</a></span><br />
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<img class="boximage" src="https://static.igem.org/mediawiki/2011/0/06/Metu-bin-project.png" /><br />
<span class="boxtext">Our project aims to provide a software tool to facilitate selection process of the right parts for their experiments in minimum amount of time and effort. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project">Read more</a>.</span><br />
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<h3 class="boxheader collaborationtab">Collaborations</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/1/1c/Metu-bin-collaboration.png" /><br />
<span class="boxtext">It's very important that on projects or even a little work people should collaborate always to reach the best! Thus, we consider it as a key factor to succeed. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Collaborations">See it</a>.</span><br />
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<img class="boximage" src="https://static.igem.org/mediawiki/2011/5/51/Metu-bin-hpractice.png" /><br />
<span class="boxtext">Science and technology are not only for students, academicians but they are also for children and people with other interests. Thus, we've been with them together. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice">See</a>.</span><br />
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<br />
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<h3 class="boxheader safetytab">Safety</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/ec/Metu-bin-safety.png" /><br />
<span class="boxtext">Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Safety">Read more</a>.</span><br />
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<h3 class="boxheader teamtab">Team</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/e5/Metu-bin-team.png" /><br />
<span class="boxtext">METU-BIN team with Prof. Dr. Charles Cantor at Informatics Science Festival 2011 at METU. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Team">Meet the team</a>.</span><br />
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<h3 class="boxheader notebooktab">Notebook</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/c/cd/Metu-bin-notebook.png" /><br />
<span class="boxtext">We want to inform you about our adventures when getting ready for the iGEM competition. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Notebook">Take a look</a>.</span><br />
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<div class="margin"><h6>Why do you need M4B?</h6><br />
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<div class="margin"><h6>Do you care safety?</h6><br />
Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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<h3 style="color:#ccc;"><em>Our Sponsors</em></h3><br />
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</html></div>Gngrhttp://2011.igem.org/File:TUBITAK-Logo.pngFile:TUBITAK-Logo.png2011-10-26T19:56:32Z<p>Gngr: </p>
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<div></div>Gngrhttp://2011.igem.org/Team:METU-BIN_AnkaraTeam:METU-BIN Ankara2011-10-24T17:30:13Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h3 class="boxheader m4btab">M4B: Mining for BioBricks</h3><br />
<a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank"><img class="boximage imgm4b" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a><br />
<span class="boxtext">It's a miner that goes over all the parts and finds the possible devices for you! <a href="https://2011.igem.org/Team:METU-BIN_Ankara/M4B" target="_blank">See our software, it's online!</a></span><br />
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<h3 class="boxheader projecttab">Project</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/0/06/Metu-bin-project.png" /><br />
<span class="boxtext">Our project aims to provide a software tool to facilitate selection process of the right parts for their experiments in minimum amount of time and effort. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project">Read more</a>.</span><br />
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<h3 class="boxheader collaborationtab">Collaborations</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/1/1c/Metu-bin-collaboration.png" /><br />
<span class="boxtext">It's very important that on projects or even a little work people should collaborate always to reach the best! Thus, we consider it as a key factor to succeed. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Collaborations">See it</a>.</span><br />
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<h3 class="boxheader hpracticetab">Human Practice</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/5/51/Metu-bin-hpractice.png" /><br />
<span class="boxtext">Science and technology are not only for students, academicians but they are also for children and people with other interests. Thus, we've been with them together. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice">See</a>.</span><br />
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<h3 class="boxheader safetytab">Safety</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/ec/Metu-bin-safety.png" /><br />
<span class="boxtext">Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Safety">Read more</a>.</span><br />
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<h3 class="boxheader teamtab">Team</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/e5/Metu-bin-team.png" /><br />
<span class="boxtext">METU-BIN team with Prof. Dr. Charles Cantor at Informatics Science Festival 2011 at METU. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Team">Meet the team</a>.</span><br />
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<h3 class="boxheader notebooktab">Notebook</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/c/cd/Metu-bin-notebook.png" /><br />
<span class="boxtext">We want to inform you about our adventures when getting ready for the iGEM competition. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Notebook">Take a look</a>.</span><br />
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<div class="margin"><h6>Why do you need M4B?</h6><br />
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<div class="margin"><h6>Do you care safety?</h6><br />
Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_Ankara/M4BTeam:METU-BIN Ankara/M4B2011-10-24T17:29:45Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h2>Project</h2><br />
<br />
<h3><a name="Introduction"></a>Introduction</h3><br />
<p class="p">While the interest to the field of synthetic biology is uprising, iGEM and Parts Registry is getting more important for researchers interested working in the field of synthetic biology. As the number of attendees and teams to iGEM competition increases each year, number of BioBricks submitted to the Parts Registry are increasing too. As we all know, Parts Registry is an inimitable library for synthetic biologists. Although it is an important source of information and tool for biologists, the parts are not organized very well. Therefore, while constructing devices, synthetic biologists usually faces following difficulties at the pre-experimental stage:</p><br />
<ul><br />
<li>Searching through the Parts</li><br />
<li>Deciding if the parts needed are already in the database or not</li><br />
<li>Deciding which BioBrick will work effectively with which</li><br />
<li>Finding the most accurate combination between the parts</li><br />
<li>Constructing the most effectively working devices</li><br />
</ul><br />
<p class="p">Figuring out all these answers is time consuming and takes too much effort. Our main goal as 2011 METU-BIN iGEM Software team was to provide a web based tool that helps synthetic biologists at the pre-experimental step to search the Part Registry with input and output keywords and to design their genetic constructs using the biobricks provided in the 2011 distribution of DNA constructs.</p><br />
<br />
<p class="p"><strong>M4B: Mining for Biobricks</strong> is developed to aid synthetic biologist. Our software proposes a method which can be utilized in pre-experimental step as a supporter data mining tool. Following the user defined input and output parameters, M4B lists all possible composite devices and ranks them according to the novel scoring matrix developed by METU-BIN.</p><br />
<br />
<h4>Aim</h4><br />
<p class="p">Main goal of our 2011 project is to provide a web based tool that helps synthetic biologists at the pre-experimental step to design their genetic constructs according to their input and output parameters.</p><br />
<ul><br />
<li>A network of all bioparts in 2011 distribution will be generated, which describes the functional relations between the subatomic bioparts.</li><br />
<li>A search algorithm will be developed to reveal all possible device combinations for the user defined input and output within bioparts of 2011 distribution.</li><br />
<li>Visualization tools will be applied for graphical representation of the results.</li><br />
<li>A web-based user interface will be provided for the developed software.</li><br />
</ul><br />
<h3><a name="Algorithm"></a>Algorithm</h3><br />
<p class="p">M4B is developed using Java Web Technologies. Web programming enables user- and PC-friendly products. Users do not need to install any program on their PC, and so they do not need to waste PC resources for programs. A web application can easily be reached using a simple web-browser from any PC and from anywhere in the world . It is the most important property of M4B.</p><br />
<p class="p">In detail, we have used Java Applet to serve M4B on the net. And to store data of M4B, we have used an instance of MySQL database. We've created tables for all XML files of PartsRegistry. For example, they contain part info, deep subparts and specific subparts info, scars info, etc. In addition we've added a few more tables to implement algorithm. They are for interaction relations between parts, scores of main parts, scores of edges, etc.</p> <br />
<p class="p">For the implementation of M4B, a huge biobrick network is constructed using information in the PartsRegistry database. With information of interactions between edges, we are creating a part network. It is a hashtable of hashtables. By the use of hashtables, we can easily find the input part on network to start searching. All useful information about a part is stored in a type of Part. It has following fields.</p><br />
<br />
<ul><br />
<li>partID</li><li>partType</li><li>promoterType</li><li>output</li><li>terminator</li><li>nextParts</li></ul><br />
<br />
<p class="p">After constructing the network, we are making a search for the list of all possible composite devices beginning with given input and output parameters. To traverse whole graph, we are using a customized version of the famous graph traversal algorithm, <strong>DFS (Depth First Search)</strong>. In DFS, it is making a search on one way until the leaf node, then if it cannot find it goes back to last disjoint point and goes on searching until next leaf node.</p><br />
<br />
<img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/2/26/Algorithm_img.gif" /><br />
<br />
<p class="p">Using the quick access property of hashtable we are finding the input part on network. If the given input is found on the graph once, we go over all the descendant nodes until finding the expected output. While searching an output node, all nodes traversed are being recorded. When the output is found, the recorded path is added to the “results list”. Else, it is discarded until the last disjoint point, and a new path is searched continuing from that point. After all possible paths are found, the list of paths is shown on the GUI.</p><br />
<br />
<p class="p">One can also search for the devices starting with a constitutive promoter. To do this, user shouldn't enter the input parameter. By this empty input information, algorithm looks for constitutive promoters to start as an input point. "$" sign is used as symbolic input for constitutive promoters.</p><br />
<br />
<p class="p">When we are searching for the expected output, we may find different outputs. If that output continues with a Promoter as an Input, it means that we are starting to add the parts of next device. A composite part can have more than one device. So we've added an input field to specify the maximum device count of results. User can change the number of device count using this field.</p><br />
<br />
<p class="p">Let's talk about visualization of the graph. If user selects an input from the list, it parses all parts from selected device and looks for it is type from network. Then, it creates a node of that type. We are using icons of Parts Registry for the types of parts. And we are using yFiles for visualization.</p><br />
<br />
<p class="p">If user selects a node in the graph, it queries the information about that part from tables created using XML files of Parts Registry.</p><br />
<br />
<p class="p">Quick search when typing the input name is the user friendly property of M4B. No need for a “Find” button.</p><br />
<br />
<p class="p">The other feature of the program is printing the results. Most of users wants to save their results. It enables saving.</p><br />
<br />
<h3><a name="Construction_of_Relational_Database"></a>Extraction of Relations of Bioparts and Construction of Relational Database</h3><br />
<br />
<p class="p">Parts Registry contains various types of biobricks and connections in between parts. In our software, we aimed to develop an algorithm which goes over the devices and finds connections between biobricks to present users all possible constructed devices. However, it was very difficult to go over biobricks and find the relations in not very well organized Parts Registry. For that reason, we have decided to form a ”Part Connections Database” by examining all the bilateral relations between biobricks which will be used by our program, M4B. By this way, the complex information in Parts Registry will be simplified and our algorithm will work faster and more effectively.</p><br />
<br />
<p class="p">The biology group focused on all of the four 384 well plates of 2011 distribution and extracted information between connections and devices in a standard way. This information is stored into a relational database and enables queries from remote computer programs.</p><br />
<br />
<p class="p">Our software group developed a toolbox to help biology group in storing the part relations into the new database of connections between biobricks. Using this tool, we were able to minimize the possibility of mistakes while entering bilateral relations manually. More importantly, this organized the database entries in a standardized way, according to the requirements of Mining for BioBricks to run the searching algorithm easily.</p><br />
<br />
<img style="margin-bottom:5px;display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/a/ab/Input-output-gadget.png" /><br />
<small>Figure 1: The toolbox which was used while building the “Part Connections Database” by our biology group.</small><br />
<img style="margin-bottom:5px;display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/7/7e/Input-output-relations.png" /><br />
<small>Figure 2: A screen shot from our “relational database”</small><br />
<p class="p">As there are various types of biobricks in the Parts Registry, we set up rules to organize the “relational database” in an appropriate way.</p><br />
<br />
<br />
<h4>Rules</h4><br />
<p class="p">The most important rule is “A constructed device formed by combination of promoter-ribosome binding site-gene-terminator, respectively, is the minimal functional device.”</p><br />
<br />
<p class="p">This is the major rule, because without these 4 major biobrick types, a device cannot work. In addition to this, without knowing the description of “basic device” it is impossible for us to present accurate results to users.<br />
Although Parts Registry contains various types of biobricks, in our database there are 4 basic biobricks which are promoters, ribosome binding sites, genes, and terminators. This helped us to simplify the complex information in the Parts Registry in our initial attempt of mining.</p><br />
<br />
<p class="p">In addition to 4 basic biobrick types, there are inputs and outputs which are our software’s parameters. Inputs are chosen according to promoters. Both activators and inhibitors of promoters were listed in our database. Main source of activators and inhibitors was the information from the Parts Registry. The reason of listing inhibitors was to filter out constructed devices which do not produce the required outputs. When a constructed device is formed by multiple devices, although the input activates first device’s promoter, it may inhibit other promoters of following devices. Outputs were chosen according to the genes, the product they synthesize. Although, most of the time, input and output information was extracted from Parts Registry, sometimes external sources were used as well because of the uninformative part descriptions at Parts Registry. External sources such as NCBI, PubMed and wiki of the team who submitted the biobrick to iGEM were used.</p><br />
<br />
<p class="p">Constitutive promoters are entered without any input, but especially their “constitutiveness” is recorded as a property in our relations database.</p><br />
<br />
<p class="p">In our software, after constructing a device by combining biobricks to construct multiple devices, combination between devices is formed according to this rule: “Output of the first gene will be the input of the following promoter(s)”</p><br />
<br />
<p class="p">According to this rule, first promoter will be activated by given Input and the product of first gene will be used as activator of the following promoters. By activation of the promoters, genes will synthesize the output. By this way, the constructed complex is expected to work effectively.</p><br />
<br />
<p class="p">In Parts Registry, there are composite parts, translation units, generators, reporters, inverters, intermediate devices, and signaling devices. As Parts Registry 2011 distribution was being examined in detail, to simplify these parts, their connection information was simplified to promoter-ribosome binding site-gene-terminator relation by our biological knowledge. This rule is explained with details as seen below:</p><br />
<br />
<ul><br />
<li>Reporters<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/2/27/Reporter-img.png" /><br />
<p class="p">The biobricks which synthesize fluorescent proteins are classified as “reporters” as they give out light to report something. We accepted these parts as “genes” because they are synthesizing proteins.</p></li><br />
<br />
<br />
<li>Translational Units<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/4/48/Translational-units-img.png" /><br />
<p class="p">Combination of ribosome binding site and gene is classified as “translational units”. We accepted this as two biobricks rather than one. Therefore the bilateral relation between ribosome binding site and gene was entered in our database.</p></li><br />
<br />
<br />
<li>Inverters<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/c/c0/Inverters-img.png" /><br />
<p class="p">Inverters were challenging parts; they are formed from more than 2 biobricks. Rather than accepting this as one biobrick, we accepted this part as a combination of four biobricks. Therefore, we entered bilateral relations between each biobricks as ribosome binding site-gene, gene-terminator, and terminator- promoter. We also entered gene-output and input-promoter connections.</p></li><br />
<br />
<li>Composites<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/b/bc/Composites_img.png" /></li><br />
<br />
<li>Generators<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/b/b1/Generators-img.png" /></li><br />
<br />
<li>Signalling Devices<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/7/7d/Signalling_img.png" /></li><br />
<br />
<li>Intermediate Devices<br><img style="display:block;border:1px solid #ccc;" src="https://static.igem.org/mediawiki/2011/8/84/Intermediate-parts-img.png" /><br />
<br />
<p class="p">Composite parts, generators, signaling devices, and intermediate devices were also challenging parts like inverters. They don’t have a specific rule about how many and which types of biobricks they consist of. However, we accepted them as complex subdevices and entered bilateral relation between each connected biobricks.</p><br />
</li><br />
</ul><br />
<p class="p">In METU-BIN 2011 project, our main priority was to focus on (minimal) Functional devices. Therefore we named DNAs, RNAs, and Tags as “accessories” because they are not vital for a device to work. However, we know that using these accessories during construction helps devices work more effectively by adding some extra features. For that reason, it’s in on future plan to form a database for these accessories and present them to our users in their query results.</p><br />
<br />
<br />
<br />
<h3><a name="Scoring"></a>EDGE-SUM Scoring</h3><br />
<p class="p">In order to provide the biologists a reliability measure about the<br />
M4B suggested composite devices, we devised a scoring mechanism.<br />
Composite devices found by M4B could be ranked by simple measures such<br />
as device count, path length, or whether a specific part is included<br />
in the device or not. Instead of these simple scoring mechanisms, we<br />
decided to propose a more eloborate scoring algorithm that takes into<br />
account status, rating, quality, and results of a device available in<br />
the Parts Registry. Such a scoring mechanim makes use of information<br />
provided by the community and it will be useful to decide which<br />
devices are more “valuable” than others if a set of alternative<br />
devices are available for a given input-output pair.</p><br />
<br />
<p class="p">To compute a score for a novel composite device, we first calculate a<br />
score for each edge in the composite device. To compute an edge score,<br />
we find all the existing devices in the Parts Registry that contain<br />
that specific edge and compute an accumulated score for that edge by<br />
summing up the scores of these existing Parts Registry devices that<br />
contain the edge. All the edge scores are normalized to the interval<br />
[0,1] by a sigmoid function. After finding the scores of all edges in<br />
a novel composite device found by M4B, we sum the logarithms of these<br />
edge scores which is equal to logarithm of the multiplication of<br />
scores. If we cannot compute a score for an edge (when the edge is completely<br />
new for example) we use a small number for that edge, similar to the idea of<br />
pseudocounts in profile HMMs. Since, this logarithm is a negative number we raise it to the<br />
power of e again to report the final score between 0.0 and 1.0. Values<br />
close to 1.0 indicate more reliable devices. EDGE-SUM SCORES are categorized into three classes according to their numeric range only. Gold-silver and bronze categories are assigned just for easy visualization of the results.</p><br />
<br />
<p class="p">To calculate the score of an existing Parts Registry device, we use<br />
the following features of devices. In addition, we give a relative<br />
importance to each of these features as suggested by our biologist<br />
team members. These relative importance weights is just a heuristic<br />
and can be optimized in future versions of M4B.</p><br />
<br />
<p class="p"><br />
<table width="625" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_status</th><br />
<th>Available</th><br />
<th>Planning</th><br />
<th>Missing</th><br />
<th>Deleted</th><br />
<th>Unavailable</th><br />
<th>Informational</th><br />
</tr><br />
<tr><br />
<td>1.0</td><br />
<td>0.1</td><br />
<td>0.0</td><br />
<td>0.0</td><br />
<td>0.0</td><br />
<td>0.2</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="650" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">best_quality</th><br />
<th>Partially Confirmed</th><br />
<th>None</th><br />
<th>Confirmed</th><br />
<th>Long Part</th><br />
<th>Questionable</th><br />
<th>Bad Sequencing</th><br />
</tr><br />
<tr><br />
<td>0.5</td><br />
<td>0.0</td><br />
<td>1.0</td><br />
<td>0.2</td><br />
<td>0.1</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="200" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_rating </th><br />
<th>1</th><br />
<th>NULL</th><br />
</tr><br />
<tr><br />
<td>1.0</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p"><br />
<table width="500" border="1" cellspacing="0" cellpadding="0"><br />
<tr><br />
<th rowspan="2">part_results</th><br />
<th>None</th><br />
<th>Works</th><br />
<th>Fails</th><br />
<th>Issues</th><br />
<th>NULL</th><br />
</tr><br />
<tr><br />
<td>0.0</td><br />
<td>1.0</td><br />
<td>0.0</td><br />
<td>0.2</td><br />
<td>0.0</td><br />
</tr><br />
</table><br />
</p><br />
<br />
<p class="p">For example, if a device is Available, Partially Confirmed and Works,<br />
its score will be "1.0+0.5+1.0 = 2.5". And, if an edge is included in<br />
this device, that edge is going to inherit the score of 2.5 and all<br />
these inherited scores from other devices that contain the edge is<br />
accumulated to compute the raw (unnormalized) score of that edge.</p><br />
<br />
<h3><a name="Results"></a>Results</h3><br />
<p class="p">Our software, M4B: Mining for BioBricks, provides many features saving of time, money and effort for scientists. With this software, scientists don't need to do long-term research and have expensive lab tools.</p><br />
<p class="p">Since it's online and can be used via any updated browser, users don't need to install it and carry it with themselves in order to use it on another computer. With this feature, they can use our software on all the computers having updated system. Also, they don't have to provide any place in their storage device.</p><br />
<br />
<br />
<h3><a name="System_Specifications"></a>Recommended Minimum System Specifications</h3><br />
<ul><br />
<li>Intel Pentium 2Ghz</li><br />
<li>512 MB Ram</li><br />
<li>Java Runtime Environment 1.6</li><br />
<li>128K Internet Speed</li><br />
<li>Supported web browsers: Firefox, Chrome, Safari, Internet Explorer</li><br />
</ul><br />
<br />
</div><br />
<div id="sidebar"><br />
<!-- SAME AREA STARTS --><br />
<br />
<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank"><img src="https://static.igem.org/mediawiki/2011/3/31/M4b_logo.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">Click on here</a> or the logo!<br />
<div class="clearfixed"></div><br />
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<h3 class="boxheader m4btab">M4B: Mining for BioBricks</h3><br />
<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank"><img class="boximage imgm4b" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /></a><br />
<span class="boxtext">It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">See our software, it's online!</a></span><br />
</div><br />
<br />
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<h3 class="boxheader projecttab">Project</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/0/06/Metu-bin-project.png" /><br />
<span class="boxtext">Our project aims to provide a software tool to facilitate selection process of the right parts for their experiments in minimum amount of time and effort. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project">Read more</a>.</span><br />
</div><br />
<br />
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<img class="boximage" src="https://static.igem.org/mediawiki/2011/1/1c/Metu-bin-collaboration.png" /><br />
<span class="boxtext">It's very important that on projects or even a little work people should collaborate always to reach the best! Thus, we consider it as a key factor to succeed. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Collaborations">See it</a>.</span><br />
</div><br />
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<h3 class="boxheader hpracticetab">Human Practice</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/5/51/Metu-bin-hpractice.png" /><br />
<span class="boxtext">Science and technology are not only for students, academicians but they are also for children and people with other interests. Thus, we've been with them together. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice">See</a>.</span><br />
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<h3 class="boxheader safetytab">Safety</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/ec/Metu-bin-safety.png" /><br />
<span class="boxtext">Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Safety">Read more</a>.</span><br />
</div><br />
<br />
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<h3 class="boxheader teamtab">Team</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/e5/Metu-bin-team.png" /><br />
<span class="boxtext">METU-BIN team with Prof. Dr. Charles Cantor at Informatics Science Festival 2011 at METU. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Team">Meet the team</a>.</span><br />
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<h3 class="boxheader notebooktab">Notebook</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/c/cd/Metu-bin-notebook.png" /><br />
<span class="boxtext">We want to inform you about our adventures when getting ready for the iGEM competition. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Notebook">Take a look</a>.</span><br />
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</div><br />
<br />
<div class="margin"><h6>Do you care safety?</h6><br />
Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_AnkaraTeam:METU-BIN Ankara2011-10-24T17:10:13Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h3 class="boxheader m4btab">M4B: Mining for BioBricks</h3><br />
<img class="boximage imgm4b" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /><br />
<span class="boxtext">It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">See our software, it's online!</a></span><br />
</div><br />
<br />
<div class="box"><br />
<h3 class="boxheader projecttab">Project</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/0/06/Metu-bin-project.png" /><br />
<span class="boxtext">Our project aims to provide a software tool to facilitate selection process of the right parts for their experiments in minimum amount of time and effort. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project">Read more</a>.</span><br />
</div><br />
<br />
<br />
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<h3 class="boxheader collaborationtab">Collaborations</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/1/1c/Metu-bin-collaboration.png" /><br />
<span class="boxtext">It's very important that on projects or even a little work people should collaborate always to reach the best! Thus, we consider it as a key factor to succeed. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Collaborations">See it</a>.</span><br />
</div><br />
<br />
<br />
<div class="box"><br />
<h3 class="boxheader hpracticetab">Human Practice</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/5/51/Metu-bin-hpractice.png" /><br />
<span class="boxtext">Science and technology are not only for students, academicians but they are also for children and people with other interests. Thus, we've been with them together. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice">See</a>.</span><br />
</div><br />
<br />
<div class="box last"><br />
<h3 class="boxheader safetytab">Safety</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/ec/Metu-bin-safety.png" /><br />
<span class="boxtext">Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Safety">Read more</a>.</span><br />
</div><br />
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<h3 class="boxheader teamtab">Team</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/e5/Metu-bin-team.png" /><br />
<span class="boxtext">METU-BIN team with Prof. Dr. Charles Cantor at Informatics Science Festival 2011 at METU. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Team">Meet the team</a>.</span><br />
</div><br />
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<h3 class="boxheader notebooktab">Notebook</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/c/cd/Metu-bin-notebook.png" /><br />
<span class="boxtext">We want to inform you about our adventures when getting ready for the iGEM competition. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Notebook">Take a look</a>.</span><br />
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<div class="margin"><h6>Why do you need M4B?</h6><br />
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</div><br />
<br />
<div class="margin"><h6>Do you care safety?</h6><br />
Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_AnkaraTeam:METU-BIN Ankara2011-10-24T17:09:36Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<img class="boximage imgm4b" src="https://static.igem.org/mediawiki/2011/8/89/M4bGUI.png" /><br />
<span class="boxtext">It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">See our software, it's online!</a></span><br />
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<img class="boximage" src="https://static.igem.org/mediawiki/2011/0/06/Metu-bin-project.png" /><br />
<span class="boxtext">Our project aims to provide a software tool to facilitate selection process of the right parts for their experiments in minimum amount of time and effort. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project">Read more</a>.</span><br />
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<img class="boximage" src="https://static.igem.org/mediawiki/2011/1/1c/Metu-bin-collaboration.png" /><br />
<span class="boxtext">It's very important that on projects or even a little work people should collaborate always to reach the best! Thus, we consider it as a key factor to succeed. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Collaborations">See it</a>.</span><br />
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<img class="boximage" src="https://static.igem.org/mediawiki/2011/5/51/Metu-bin-hpractice.png" /><br />
<span class="boxtext">Science and technology are not only for students, academicians but they are also for children and people with other interests. Thus, we've been with them together. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice">See</a>.</span><br />
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<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/ec/Metu-bin-safety.png" /><br />
<span class="boxtext">Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Safety">Read more</a>.</span><br />
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<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/e5/Metu-bin-team.png" /><br />
<span class="boxtext">METU-BIN team with Prof. Dr. Charles Cantor at Informatics Science Festival 2011 at METU. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Team">Meet the team</a>.</span><br />
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<img class="boximage" src="https://static.igem.org/mediawiki/2011/c/cd/Metu-bin-notebook.png" /><br />
<span class="boxtext">We want to inform you about our adventures when getting ready for the iGEM competition. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Notebook">Take a look</a>.</span><br />
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Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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</html></div>Gngrhttp://2011.igem.org/File:M4bGUI.pngFile:M4bGUI.png2011-10-24T17:09:14Z<p>Gngr: </p>
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<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div><br />
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<h3 class="boxheader m4btab">M4B: Mining for BioBricks</h3><br />
<img class="boximage imgm4b" src="https://static.igem.org/mediawiki/2011/0/06/Metu-bin-project.png" /><br />
<span class="boxtext">It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">See our software, it's online!</a></span><br />
</div><br />
<br />
<div class="box"><br />
<h3 class="boxheader projecttab">Project</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/0/06/Metu-bin-project.png" /><br />
<span class="boxtext">Our project aims to provide a software tool to facilitate selection process of the right parts for their experiments in minimum amount of time and effort. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project">Read more</a>.</span><br />
</div><br />
<br />
<br />
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<h3 class="boxheader collaborationtab">Collaborations</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/1/1c/Metu-bin-collaboration.png" /><br />
<span class="boxtext">It's very important that on projects or even a little work people should collaborate always to reach the best! Thus, we consider it as a key factor to succeed. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Collaborations">See it</a>.</span><br />
</div><br />
<br />
<br />
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<h3 class="boxheader hpracticetab">Human Practice</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/5/51/Metu-bin-hpractice.png" /><br />
<span class="boxtext">Science and technology are not only for students, academicians but they are also for children and people with other interests. Thus, we've been with them together. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice">See</a>.</span><br />
</div><br />
<br />
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<h3 class="boxheader safetytab">Safety</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/ec/Metu-bin-safety.png" /><br />
<span class="boxtext">Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Safety">Read more</a>.</span><br />
</div><br />
<br />
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<h3 class="boxheader teamtab">Team</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/e5/Metu-bin-team.png" /><br />
<span class="boxtext">METU-BIN team with Prof. Dr. Charles Cantor at Informatics Science Festival 2011 at METU. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Team">Meet the team</a>.</span><br />
</div><br />
<br />
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<h3 class="boxheader notebooktab">Notebook</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/c/cd/Metu-bin-notebook.png" /><br />
<span class="boxtext">We want to inform you about our adventures when getting ready for the iGEM competition. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Notebook">Take a look</a>.</span><br />
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<div class="margin"><h6>Do you care safety?</h6><br />
Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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</html></div>Gngrhttp://2011.igem.org/Team:METU-BIN_AnkaraTeam:METU-BIN Ankara2011-10-20T22:03:35Z<p>Gngr: </p>
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<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara" class="homeLink">Home</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Team" class="teamLink">Team</a></li><br />
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<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project#Introduction">Introduction</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project#Algorithm">Algorithm</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project#Construction_of_Relational_Database">Construction of Relational Database</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project#Scoring">EDGE-SUM Scoring</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project#Results">Results</a></li><br />
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<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#HIBIT11_Roundtable">HIBIT'11 Roundtable</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#Teknovasyon_2011">Teknovasyon 2011</a></li><br />
<li><a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice#DNA_School">DNA School</a></li><br />
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<h2>Home</h2><br />
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<h3 class="boxheader m4btab">M4B: Mining for BioBricks</h3><br />
<img class="boximage imgm4b" src="https://static.igem.org/mediawiki/2011/0/06/Metu-bin-project.png" /><br />
<span class="boxtext">It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">See our software, it's online!</a></span><br />
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<h3 class="boxheader projecttab">Project</h3><br />
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<span class="boxtext">Our project aims to provide a software tool to facilitate selection process of the right parts for their experiments in minimum amount of time and effort. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Project">Read more</a>.</span><br />
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<h3 class="boxheader collaborationtab">Collaborations</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/1/1c/Metu-bin-collaboration.png" /><br />
<span class="boxtext">It's very important that on projects or even a little work people should collaborate always to reach the best! Thus, we consider it as a key factor to succeed. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Collaborations">See it</a>.</span><br />
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<h3 class="boxheader hpracticetab">Human Practice</h3><br />
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<span class="boxtext">Science and technology are not only for students, academicians but they are also for children and people with other interests. Thus, we've been with them together. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/HumanPractice">See</a>.</span><br />
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<h3 class="boxheader safetytab">Safety</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/ec/Metu-bin-safety.png" /><br />
<span class="boxtext">Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Safety">Read more</a>.</span><br />
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<h3 class="boxheader teamtab">Team</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/e/e5/Metu-bin-team.png" /><br />
<span class="boxtext">METU-BIN team with Prof. Dr. Charles Cantor at Informatics Science Festival 2011 at METU. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Team">Meet the team</a>.</span><br />
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<h3 class="boxheader notebooktab">Notebook</h3><br />
<img class="boximage" src="https://static.igem.org/mediawiki/2011/c/cd/Metu-bin-notebook.png" /><br />
<span class="boxtext">We want to inform you about our adventures when getting ready for the iGEM competition. <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Notebook">Take a look</a>.</span><br />
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<div class="m4b margin"><h6>See our software, it's online!</h6><br />
<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank"><img src="https://static.igem.org/mediawiki/2011/3/31/M4b_logo.png" /></a>M4B: Mining for BioBricks. It's a miner that goes over all the parts and finds the possible devices for you! <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">Click on here</a> or the logo!<br />
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<div class="margin"><h6>Why do you need M4B?</h6><br />
<iframe src="http://player.vimeo.com/video/29400632?title=0&amp;byline=0&amp;portrait=0" width="276" height="175" frameborder="0" webkitAllowFullScreen allowFullScreen></iframe><div class="clearfixed"></div><br />
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<div class="margin"><h6>Do you care safety?</h6><br />
Let's test! METU-Ankara team prepared a test for this, and one of the members of our team coded. We are happy to share this. :) <a href="https://2011.igem.org/Team:METU-BIN_Ankara/Self-EvaluationTest">Go to test!</a><br />
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<h6>Read our tweets!</h6><br />
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<h3 style="color:#ccc;"><em>Our Sponsors</em></h3><br />
<span style="margin-left:40px;float:left;"><a class="opac" href="http://www.akgunyazilim.com.tr/" target="_blank"><img style="width:300px;height:auto;" src="https://static.igem.org/mediawiki/2011/0/09/Akgun.png" /></a></span><span style="float:left;width:150px;margin:0 60px;"><a class="opac" href="http://www.ii.metu.edu.tr/" target="_blank"><img style="width:150px;height:auto;" src="https://static.igem.org/mediawiki/2011/5/5e/Ii.png" /></a><br />
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