Team:METU-BIN Ankara/Notebook

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<div class="m4b margin"><h6>See our software, it's online!</h6>
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<a href="#" target="_blank"><img src="http://www.metu.edu.tr/~e172018/images/metu-bin/m4b.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="#" target="_blank">Click on here or the logo!</a>
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<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank"><img src="http://2011.igem.org/wiki/images/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!
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Revision as of 19:10, 20 September 2011

METU-BIN iGEM Software TeamProject: Mining for BioBricks

Notebook

March 2011

Kick-Off of METU-BIN iGEM Software Team: 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.

Reaching out to our Potential Sponsors: 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. 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.

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.

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.

April 2011

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.

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 human practice page.

During the month of April our effort to find sponsorships continued and we have visited few companies in Ankara, Turkey.

May 2011

Our first potential sponsor was the METU-Technopolis, who have promised to cover the team registration fees for the competition.

METU-BIN registered iGEM 2011 as a software team.

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.

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.

To work more effectively on our Project and to improve our knowledge we started to read articles and discuss them at our weekly meetings.

  • 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
  • Anthony D. Hill, Jonathan R. Tomshine, Emma M. B. Weeding, Vassilios Sotiropoulos, Yiannis N. Kaznessis, Yiannis N. Kaznessis. SynBioSS: the synthetic biology modeling suite. Bioinformatics, 2008
  • Ernesto Andrianantoandro, Subhayu Basu,David K Karig, Ron Weiss. Synthetic biology: new engineering rules for an emerging discipline. Bioinformatics. 2006
  • Priscilla E. M. Purnick, Ron Weiss. The second wave of synthetic biology: from modules to systems. Nature. 2009
  • Raik Grunberg, Luis Serrano. Strategies for protein synthetic biology. Nucleic Acid Research, 2010
  • Sean C. Sleight, Bryan A. Bartley, Jane A. Lieviant, Herbert M. Sauro. In-Fusion BioBrick assembly and re-engineering, 2010
  • Yizhi Cai, Mandy L. Wilson, Jean Peccoud. GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. NAR, 2010
  • Barry Canton, Anna Labno, Drew Endy. Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology, 2008
  • Tom Ellis, Xiao Wang, James J Collins. Diversity-based, model-guided construction of synthetic gene networks with predicted functions, Nature Biotechnology, 2009
  • Kurt W Kohn and Mirit I Aladjem. Circuit diagrams for biological networks, Molecular Systems Biology, 2006
  • Yong-Jun Shin, Mehrdad Nourani.Statecharts for Gene Network Modeling, PLoS ONE, 2009
  • Christopher A Voigt. Genetic parts to program bacteria, Current Opinion in Biotechnology, 2006

We looked into last years software teams and discussed their projects.

June 2011

We all had final exams on the first two weeks.

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:

  • Prof. Charles DELISI: Dean Emeritus, College of Engineering, Boston University
  • Prof. Charles CANTOR: Chairman of Sequenom, Inc’s Scientific Advisory
  • Board and Chief Scientific Officer, Boston University
  • Prof. Aravind JOSHI: University of Pennsylvania
  • Prof. Selim ÜNLÜ: Associate Dean for Research and Graduate Programs, Boston University
  • Prof.Asuman ÖZDAĞLAR ACEMOĞLU: Electrical Engineering and Computer Science Department, MIT

We talked to Prof.Charles CANTOR and took his advices about our project and iGEM.

Kick off Of Summer Meetings (14th June) : We are starting to work on our project again.

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).

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.

Software developers are discussing how they will design the algorithm's first part.

July 2011

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.

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.

12th June: We test the algorithm for the first time.

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.

August 2011

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.

A national news chanel 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.

All this media attention helped to secure a big fund from by Akgun Yazılım in August 2011.

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.

We have full fill 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.

September 2011

Developers continue working on scoring and final the GUI design.

10th September: Our software is moved to web.

We have published and shared code and other material on GitHub.

We began to design our iGEM wiki. We shared the work and we all are working on our wiki content.

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 collobration during this presentation.

We also asked the other iGEM teams for collobration.

We have collaborated with a team at Uppsala and METU-Ankara.

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.