Team:METU-BIN Ankara/Team

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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>
<div class="act_header"><h1><span>METU-BIN iGEM Software Team<span>Project: <span>Mining for BioBricks</span></span></span></h1></div>
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<li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Project" class="projectLink">Project</a>
<li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Project" class="projectLink">Project</a>
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     <li><a href="#">Introduction</a></li>
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     <li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Project#Introduction">Introduction</a></li>
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        <li><a href="#">Design</a></li>
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<li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Project#Algorithm">Algorithm</a></li>
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<li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Project#Construction_of_Relational_Database">Construction of Relational Database</a></li>
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         <li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Project#Scoring">EDGE-SUM Scoring</a></li>
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         <li><a href="#">Scoring</a></li>
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         <li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Project#Results">Results</a></li>
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         <li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Project#System_Specifications">System Specifications</a></li>
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<li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Collaborations" class="collaborationsLink">Collaborations</a></li>
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<li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/FuturePlans" class="plansLink">Future Plans</a></li>
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<li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/NextVersion" class="versionLink">Next Version</a></li>
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<li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Sponsors" class="sponsorsLink">Sponsors</a></li>
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<li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/FromPress" class="pressLink">From Press</a></li>
<li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Contact" class="contactLink">Contact</a></li>
<li><a href="http://2011.igem.org/Team:METU-BIN_Ankara/Contact" class="contactLink">Contact</a></li>
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<h2>Team</h2>
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<h2>Team: <span class="cont">Attribution and Contributions</span></h2>
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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 3 advisors from different disciplines such as Biology, Molecular Biology, Electronics, Computer Science, Mathematics, Statistics and Bioinformatics.</p>
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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>
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<h3>Students</h3>
<h3>Students</h3>
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<h4>Gökçe OĞUZ</h4>
<h4>Gökçe OĞUZ</h4>
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<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 :) 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.</p>
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<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>
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<h4>Burcu YALDIZ</h4>
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<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>
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<h4>Gökhan ERSOY</h4>
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<h4>İsmail ASLANER</h4>
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<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 an MSc. 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. In our team, I am responsible of software development. Good luck for all teams! :)</p>
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<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>
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<h4>Ogün ADEBALİ</h4>
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<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>
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<h4>Saygın KARAASLAN</h4>
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<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>
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<h4>Ebru ŞAHİN</h4>
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<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>
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<h4>Gökhan ERSOY</h4>
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<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>
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<p>Contact: goksoy66 [at] gmail [dot] com</p></span>
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<h4>Güngör BUDAK</h4>
<h4>Güngör BUDAK</h4>
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<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 a 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. In the team, my contributions were to get the relational data of bioparts in PartsRegistry and save it in a standard way for computer engineers to use it. Then, I coded and designed the wiki page, and also I designed the team logo.</p>
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<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>
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<p>Contact: gngrbdk [at] gmail [dot] com</p>
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<h3>Advisors</h3>
<h3>Advisors</h3>
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<h4>Seyedsasan HASHEMIKHABIR</h4>
<h4>Seyedsasan HASHEMIKHABIR</h4>
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<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. 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.</p>
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<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>
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<h4>Yener TUNCEL</h4>
<h4>Yener TUNCEL</h4>
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<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. My master thesis is about microRNA module networks in complex human diseases. I am very deeply interested in systems biology and its applications in personalized medicine, pharmacogenomics and synthetic 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 behaivour, its overall mechanism and its dynamics.</p>
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<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>
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<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>
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<h4>Yeşim AYDIN SON</h4>
<h4>Yeşim AYDIN SON</h4>
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<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>
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<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>
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<h4>Tolga CAN</h4>
<h4>Tolga CAN</h4>
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<div class="m4b margin"><h6>See our software, it's online!</h6>
<div class="m4b margin"><h6>See our software, it's online!</h6>
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<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" 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="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">Click on here</a> or the logo!
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<a href="http://dayhoff.ii.metu.edu.tr:8080/m4b" target="_blank"><img style="width: 276px;margin:0;" src="http://2011.igem.org/wiki/images/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>
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<div class="social margin"><h6>Find us on</h6>
<div class="social margin"><h6>Find us on</h6>
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Latest revision as of 22:53, 21 November 2011

METU-BIN iGEM Software TeamProject: Mining for BioBricks

Team: Attribution and Contributions

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.

Students

Gökçe OĞUZ

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 :) 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.

Burcu YALDIZ

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. In the team I am responsible for editorial issues and organizing the sponsorship application.

İsmail ASLANER

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.

Ogün ADEBALİ

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. 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. 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.

Saygın KARAASLAN

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. 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.

Ebru ŞAHİN

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 I’m on the editorial board.

Gökhan ERSOY

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. 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. :) I would like to thank my teachers, advisors and friends for their hardwork. Good luck for all teams! :)

Contact: goksoy66 [at] gmail [dot] com

Güngör BUDAK

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. 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.

Contact: gngrbdk [at] gmail [dot] com

Advisors

Seyedsasan HASHEMIKHABIR

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. 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.

Yener TUNCEL

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. 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.

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.

Instructors

Yeşim AYDIN SON

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.

Tolga CAN

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.