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| </div> | | </div> |
| <div id="home" class="item"> | | <div id="home" class="item"> |
- | <div class="homepage"> | + | <div id="introvideo"> |
| + | <embed width="480" height="360" quality="high" bgcolor="#000000" name="main" id="main" allowfullscreen="true" allowscriptaccess="always" src="http://www.dnatube.com/nvlab/player/player.swf?config=http://www.dnatube.com/nvlab/econfig.php?key=ddbdf3eff0f505975b6a" type="application/x-shockwave-flash" /></div><div class="homepage"> |
| + | <div id="homecontainer"><h3>Abstract</h3> |
| + | <p>As Synthetic Biology field is on the rise, iGEM also grows up and number of parts in parts registry increase with submission of more complex constructs each year. Our first milestone was to perform more efficient standardization on parts entry due to facing some difficulty while running our algorithms on the parts registry. We also used Software Requirements Specification, Software Design Description and Quality Plan approaches to define requirements for each part and building blocks, risks and design art elements of the designed software program.</p> |
| + | <p>Next, we have used graph theoretic modeling to visualize relations between parts and to standardize representation of the parts as much as possible. It will help us when we try to find input-output relations between either biobrick parts or constructs. By this way, our program BIOGUIDE will act as a guide for searhing biobricks and will provide alternative pathway choices to users for construction of the most reliable devices with respect to given inputs and expected outputs.</p> |
| + | </div> |
| </div> | | </div> |
| </div> | | </div> |
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| <h2>Team</h2> | | <h2>Team</h2> |
| <div id="slider"> | | <div id="slider"> |
- | <img alt="" src="https://static.igem.org/mediawiki/2010/e/e7/Metu-slide1.jpg"> | + | <img alt="" src="https://static.igem.org/mediawiki/2010/f/f3/Metu-team1.jpg"> |
- | <img alt="" src="https://static.igem.org/mediawiki/2010/e/e1/Metu-slide2.jpg"> | + | <img alt="" src="https://static.igem.org/mediawiki/2010/d/d4/Metu-team2.jpg"> |
- | <img alt="" src="https://static.igem.org/mediawiki/2010/b/b8/Metu-slide3.jpg"> | + | <img alt="" src="https://static.igem.org/mediawiki/2010/3/34/Metu-team3.jpg"> |
| + | <img alt="" src="https://static.igem.org/mediawiki/2010/d/d8/Metu-team4.jpg"> |
| + | <img alt="" src="https://static.igem.org/mediawiki/2010/0/03/Metu-team5.jpg"> |
| + | <img alt="" src="https://static.igem.org/mediawiki/2010/b/be/Metu-team6.jpg"> |
| </div> | | </div> |
- | <p>METU Turkey Software is an interdisciplinary team of 8 students and | + | <p>METU Turkey Software is an interdisciplinary team of 7 students and |
- | 3 advisors from various backgrounds such as Molecular Biology, Bioinformatics, | + | 4 advisors from various backgrounds such as Molecular Biology, Bioinformatics, |
| Computer Engineering and Computer Education and Instructional Technology. | | Computer Engineering and Computer Education and Instructional Technology. |
| We have put our knowledge and experience in our fields together to bring | | We have put our knowledge and experience in our fields together to bring |
| a much needed solution to a daily problem in field of synthetic biology | | a much needed solution to a daily problem in field of synthetic biology |
| for iGEM 2010</p> | | for iGEM 2010</p> |
| + | <div id="smallwrap"> |
| + | </div> |
| + | <div class="smallbox"> |
| + | <h2 class="black">Tolga Can</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/c/c3/Metu-tolgahoca.jpg"> |
| + | <div class="smalltext"> |
| + | <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> |
| + | </div> |
| + | </div> |
| + | <div class="smallbox"> |
| + | <h2 class="black">Yeşim Aydın-Son</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/d/d5/Metu-yesimhoca.jpg"> |
| + | <div class="smalltext"> |
| + | <p>Yeşim, has received her M.D in 1999 from HÜTF, Ankara and |
| + | completed her Ph.D at University of TN, Knoxville on Genome |
| + | Science and Technology in 2006. After working as a research |
| + | fellow at City of Hope National Medical Center, Duarte,CA , |
| + | she has recently accepted her current position at METU Informatics |
| + | Institute as an Assistant Professor of Medical Informatics. |
| + | She is 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 is working on building a new integrated |
| + | application for genome wide association of SNP biomarkers and |
| + | discovery of genes and pathways related to diseases, where SNP |
| + | genotyping data from both microarray and next generation sequencing |
| + | experiments can be analyzed in all-in-one step. </p> |
| + | </div> |
| + | </div> |
| + | <div class="smallbox"> |
| + | <h2 class="black">Ömer Nebil Yaveroğlu</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/5/53/Metu-omerhoca.jpg"> |
| + | <div class="smalltext"> |
| + | <p>Ömer Nebil Yaveroğlu is currently a PhD Student in Imperial |
| + | College, London. He has worked as a teaching assistant between |
| + | 2008 – 2010 in the Computer Engineering Department of Middle |
| + | East Turkey. Throughout his MSc studies, he tried to understand |
| + | the orthological similarities between the protein interaction |
| + | networks of different species using graph theory. He helped |
| + | the group as an advisor in the computing related discussions</p> |
| + | </div> |
| + | </div> |
| + | <div class="smallbox"> |
| + | <h2 class="black">Burak Yılmaz</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/a/a2/Metu-burak.jpg"> |
| + | <div class="smalltext"> |
| + | <p>I am a recent graduate of METU Molecular Biology and Genetics |
| + | department and now studying towards my masters degree on Molecular |
| + | Bioengineering at METU. My interest in synthetic biology did |
| + | start during my undergraduate years and after graduation I started |
| + | up the Sentegen company which is the first biotechnology based |
| + | company focused on synthetic biology in Turkey. I continue my |
| + | research and training in synthetic biology while also contributing |
| + | to the development of the field in my country. We need new scientific |
| + | revolutions to solve huge problems of life and emerging field |
| + | of synthetic biology is best candidate for biotechnological |
| + | revolution. I am interested in synthetic biology applications, |
| + | along with Lab-on-a-Chip devices for molecular biology techniques, |
| + | and we are designing gene synthesis chips to produce biobricks |
| + | - raw materials of synthetic garage biology- faster and cheaper. |
| + | I enjoy snowboarding, cycling and write poems.</p> |
| + | </div> |
| + | </div> |
| + | <div class="clear"> |
| + | </div> |
| + | <div class="smallbox" style="margin: 0 auto; float: none"> |
| + | <h2 class="black">Muhammed Akif Ağca</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/1/10/Metu-akif2.jpg"> |
| + | <div class="smalltext"> |
| + | <p>In bachelor he has worked on Software Development, Database Management, Instructional Technologies, and Bioinformatics. He was developing the software and leading the team. |
| + | A new page to his life is starting at 2011 after becoming a graduate of Computer Education and Instructional Technologies. He says that " If we can use technology and science efficiently we can solve too many problems in the world, but if can use. That is if we can manage those we can solve the problems and organize the world with minimum problems " which is a study field Science Technology and Management ( STM ) which is the field he will start to work in 2011 ".</p> |
| + | </div> |
| + | </div> |
| + | <div class="clear"> |
| + | </div> |
| + | <div class="smallbox"> |
| + | <h2 class="black">Cihan Taştan</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/d/d8/Metu-cihan.jpg"> |
| + | <div class="smalltext"> |
| + | <p>2010 is the last year for me as B.S degree at Molecular Biology |
| + | and Genetics department. Moreover, I am studying at Computer |
| + | Engineering as my minor department. My research will be on Scientist |
| + | position at Cancer and Virology Relationship (Let's say Viral |
| + | Oncology) by integrating novel technices of Bioinformatics and |
| + | Synthetic Biology approaches. This is my second year at iGEM.</p> |
| + | </div> |
| + | </div> |
| + | <div class="smallbox"> |
| + | <h2 class="black">Hassan Salehe Matar</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/3/3c/Metu-hassan.jpg"> |
| + | <div class="smalltext"> |
| + | <p>Ascended up the hills of Kilimanjaro, crossed over the savannah |
| + | of Serengeti and finally landed on the country of Istanbul my |
| + | name is Hassan Salehe. I'm a final year undergraduate student |
| + | at the Department of Computer Engineering, Middle East Technical |
| + | University. In Metu Turkey Software I'm a database administrator |
| + | and a core Software developer. I'm interested in software development, |
| + | database management, Computer networks and Bioiformatics I do |
| + | marathon, I like swimming and I'm fond of action movies.Oh, |
| + | I was about to forget to tell you that I also like traveling. |
| + | Thanks!</p> |
| + | </div> |
| + | </div> |
| + | <div class="smallbox"> |
| + | <h2 class="black">Ayub Rokhman Wakhid</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/9/92/Metu-ayub.jpg"> |
| + | <div class="smalltext"> |
| + | <p>From the country of thousand islands, across the ocean he |
| + | came to Ankara. Now he is finishing his undergraduate study |
| + | at the Department of Computer Education and Instructional Technology, |
| + | Middle East Technical University. This is the first time he |
| + | joined IGEM. He is in design team in Metu Turkey Software. He |
| + | has interest in animation, web development, and instructional |
| + | technologies.</p> |
| + | </div> |
| + | </div> |
| + | <div class="smallbox"> |
| + | <h2 class="black">Muhammad Fakhry Syauqy</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/f/fd/Metu-fakhry.jpg"> |
| + | <div class="smalltext"> |
| + | <p>A senior undergraduate student of Computer Education and |
| + | Instructional Technology at Middle East Technical University. |
| + | He came far away from Indonesia to Ankara, Turkey, to make a |
| + | great leap on his life. His role in this team is designer. Together |
| + | with Ayub, they designs the team's wiki, poster. He is interested |
| + | in 2D and 3D designing, web developing and animation. He loves |
| + | playing football and working with computer. His motto is "Possibilities |
| + | are limitless" </p> |
| + | </div> |
| + | </div> |
| + | <div class="smallbox"> |
| + | <h2 class="black">Saygın Karaaslan</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/6/6f/Metu-saygin.jpg"> |
| + | <div class="smalltext"> |
| + | <p>Our multimedia support and the core of our design and animation |
| + | team. Saygın, is a senior in Biology department at METU and |
| + | about to launch his own scientific animation company. After |
| + | graduation he will be continuing his academic studies on medical |
| + | informatics, scientific data visualization and 3D molecular |
| + | animations. He has recently completed the production of OCW |
| + | for molecular biology laboratory lectures as video-notes. Never |
| + | says no to a good soccer game or mafia II. We look forward for |
| + | the day for the premier of his documentary on "History of Science"</p> |
| + | </div> |
| + | </div> |
| + | <div class="smallbox"> |
| + | <h2 class="black">Yener Tuncel</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/d/dd/Metu-yener.jpg"> |
| + | <div class="smalltext"> |
| + | <p>I have graduated from METU Molecular Biology and Genetics |
| + | department and just started the Bioinformatics Graduate Program |
| + | this fall. My main research interests is in systems biology, |
| + | and its applications. Currently I am focused on genome wide |
| + | association of SNP biomarkers, where we will utilize systems |
| + | biology approaches for discovering disease gene and pathway |
| + | associations after highthrough-put genotyping studies. During |
| + | the course of our research on the iGEM project this summer as |
| + | a Molecular Biologist I worked on the standardization of the |
| + | parts information for our applicaiton database. Also, as a Bioinformatician |
| + | in training, contributed to the development of the algorithms |
| + | for the BioGuide software. Besides research, I develop educational |
| + | tools for biology and bioinformatics education and getting used |
| + | to do couples dancing. </p> |
| + | </div> |
| + | </div> |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="text"> | | <div class="text"> |
| <h2>Notebook</h2> | | <h2>Notebook</h2> |
- | </div> | + | <div id="notebook2"> |
| + | <div class="month"> |
| + | January</div> |
| + | <div class="general"> |
| + | <p>Brain Storming about the iGEM. </p> |
| + | <ul> |
| + | <li>What is iGEM.</li> |
| + | <li>Previous Wet-Lab Projects developed at METU.</li> |
| + | <li>What kind of projects can be developed as a software |
| + | team.</li> |
| + | </ul> |
| + | <p>NOTE: The first software team in Turkey...</p> |
| + | </div> |
| + | <div class="month"> |
| + | February</div> |
| + | <div class="general"> |
| + | <ul> |
| + | <li>Reading articles about iGEM WetLab and Software team |
| + | projects.</li> |
| + | <li>Looking for the members of the team.</li> |
| + | <li>Looking for the instructors who can consult the team. |
| + | </li> |
| + | </ul> |
| + | </div> |
| + | <div class="month"> |
| + | March</div> |
| + | <div class="general"> |
| + | <ul> |
| + | <li>Employing a member to team interested in Synthetic Biology.</li> |
| + | <li>Reading articles about Synthetic Biology, Bioinformatics |
| + | and Bio Engineering.</li> |
| + | <li>Founding the team [ An instructor, and student members |
| + | ]</li> |
| + | </ul> |
| + | </div> |
| + | <div class="month"> |
| + | April</div> |
| + | <div class="general"> |
| + | At this month we have started regular workshop about Synthetic |
| + | Biology, Bioengineering, and Bioinformatics. |
| + | <ul> |
| + | <li>This month biologists in the team telling the needed |
| + | basics to software group.</li> |
| + | </ul> |
| + | </div> |
| + | <div class="lower"> |
| + | <div class="week1" style="height: 150px;"> |
| + | <div id="week"> |
| + | Week 1</div> |
| + | <p>Workshop -1</p> |
| + | <p>[Biology basics, What is Synthetic Biology?, and the |
| + | works in this field ]</p> |
| + | </div> |
| + | <div class="week2" style="height: 150px;"> |
| + | <div id="week"> |
| + | Week 2</div> |
| + | <p>Workshop -2</p> |
| + | <p>[What is Synthetic Biology?, and the works in this field |
| + | ]</p> |
| + | </div> |
| + | <div class="week3" style="height: 150px;"> |
| + | <div id="week"> |
| + | Week 3</div> |
| + | <p>Workshop -3</p> |
| + | <p>[iGEM, Parts, Biobricks, and Devices ]</p> |
| + | </div> |
| + | <div class="week4" style="height: 150px;"> |
| + | <div id="week"> |
| + | Week 4</div> |
| + | <p>Workshop – 4</p> |
| + | <p>[iGEM, Parts, Biobricks, and Devices ]</p> |
| + | </div> |
| + | </div> |
| + | <div class="month"> |
| + | May</div> |
| + | <div class="general"> |
| + | At this month we have completed our workshops, and as the masters |
| + | in this field started meeting with instructors. / |
| + | <ul> |
| + | <li>Meanwhile, looking for sponsors [We have designed a |
| + | document telling the iGEM, previous project and our project |
| + | generally and started to send it private companies who can |
| + | found us.] </li> |
| + | <li>This month it is turn to software group; they are transferring |
| + | the basics of software concepts to biologists in the team. |
| + | </li> |
| + | <li>Furthermore, we are discussing about how we can apply |
| + | the basics of computer engineering to synthetic biology |
| + | and iGEM parts. </li> |
| + | </ul> |
| + | </div> |
| + | <div class="lower"> |
| + | <div class="week1" style="height: 180px;"> |
| + | <div id="week"> |
| + | Week 1</div> |
| + | <p>Meeting -1</p> |
| + | <p>[First, discussion on articles that have been selected |
| + | by consulters. Then, brain storming about the selected iGEM |
| + | projects from previous years and our project ]</p> |
| + | </div> |
| + | <div class="week2" style="height: 180px;"> |
| + | <div id="week"> |
| + | Week 2</div> |
| + | <p>Meeting -2[with consulters ]</p> |
| + | <p>[Tellingtheprevious projects to consulters and telling |
| + | our initial idea about project. Then, brainstorming about |
| + | our project. ]</p> |
| + | </div> |
| + | <div class="week3" style="height: 180px;"> |
| + | <div id="week"> |
| + | Week 3</div> |
| + | <p>Meeting -3</p> |
| + | <p>[Basic databaseconcepts and iGEM parts. ]</p> |
| + | </div> |
| + | <div class="week4" style="height: 180px;"> |
| + | <div id="week"> |
| + | Week 4</div> |
| + | <p>Meeting -4</p> |
| + | <p>[What is ER Diagram and How we can develop a database |
| + | model for iGEM parts with ER Model. ]</p> |
| + | </div> |
| + | </div> |
| + | <div class="month"> |
| + | June</div> |
| + | <div class="general"> |
| + | <p>At this month software group is going on to tell the basics |
| + | of software development and programming and computer engineering, |
| + | discussions about the computer engineering approaches are continuing.</p> |
| + | <ul> |
| + | <li>Furthermore, we have constructed the design group for |
| + | web page, poster, presentation, and an attractive animation |
| + | telling us.</li> |
| + | </ul> |
| + | </div> |
| + | <div class="lower"> |
| + | <div class="week1" style="height: 250px;"> |
| + | <div id="week"> |
| + | Week 1</div> |
| + | <p>Meeting – 5</p> |
| + | <p>[Graph theory, Graph theoretic modeling, and graphical |
| + | modeling of iGEM parts. Using Input Output loops on iGEM |
| + | parts. ]</p> |
| + | </div> |
| + | <div class="week2" style="height: 250px;"> |
| + | <div id="week"> |
| + | Week 2</div> |
| + | <p>Meeting – 6 [ With Consulters ]</p> |
| + | <ul> |
| + | <li>Project Description. </li> |
| + | <li>Our tasks on holiday.</li> |
| + | <li>Telling our project and basic concepts to design |
| + | team.</li> |
| + | <li>Discussion on storyboard for animation.</li> |
| + | </ul> |
| + | </div> |
| + | <div style="height: 250px; background-color: #1e6dd4; padding: 10px;"> |
| + | <div id="week"> |
| + | Week 3 and Week 4</div> |
| + | <p align="center">HAVE a NICE HOLIDAY</p> |
| + | <p align="center">SEE YOU ON JULY 1 as a POWERFUL TEAM; |
| + | <em>“METU TURKEY SOFTWARE”</em>.</p> |
| + | </div> |
| + | </div> |
| + | <div class="month"> |
| + | July</div> |
| + | <div class="general"> |
| + | <p>At this month we have started to develop application. And |
| + | divided the team to 3 groups [ Software - Gene – Design ].</p> |
| + | <ul> |
| + | <li>Gene group is providing row data to software group by |
| + | extracting it from the part registery and other resources.</li> |
| + | <li>Software group is developing application.</li> |
| + | <li>Designers are learning new design tools, and applying |
| + | those to our project [Not all Members of the group working |
| + | actively for the team].</li> |
| + | </ul> |
| + | <p><u>NOTE: Members are not strictly assigned to a group; this |
| + | is just for organization of tasks.</u></p> |
| + | </div> |
| + | <div class="lower"> |
| + | <div class="week1" style="height: 600px;"> |
| + | <div id="week"> |
| + | Week 1</div> |
| + | <p>Meeting-7</p> |
| + | <ul> |
| + | <li>Take stock for current situation.</li> |
| + | <li>Discussion on web, poster, animation design.</li> |
| + | <li>Discussion on storyboard for animation.</li> |
| + | <li>Task analyses for each group [ Software, Gene, Design |
| + | ].</li> |
| + | </ul> |
| + | </div> |
| + | <div class="week2" style="height: 600px;"> |
| + | <div id="week"> |
| + | Week 2</div> |
| + | <p>Meeting – 8</p> |
| + | <p>Checking the tasks of each group. </p> |
| + | <p>· Software Group</p> |
| + | <ul> |
| + | <li>Database Design</li> |
| + | <li>Interface for DB.</li> |
| + | <li>Designing a basic SRS and SDD to be able to state |
| + | the requirements of application exactly .</li> |
| + | </ul> |
| + | <p>· Gene Group</p> |
| + | <ul> |
| + | <li>Extracting I/O information for each part in part |
| + | registry according to specified standards by Gene group.</li> |
| + | <li>Discussion about expectation from the software. |
| + | </li> |
| + | </ul> |
| + | <p>· Design Group</p> |
| + | <ul> |
| + | <li>Team Logo</li> |
| + | <li>Web site</li> |
| + | <li>Poster</li> |
| + | <li>Animation</li> |
| + | <li>Presentation</li> |
| + | </ul> |
| + | </div> |
| + | <div style="height: 600px; background-color: #1e6dd4; padding: 10px"> |
| + | <div id="week"> |
| + | Week 3 and Week 4 |
| + | <p>DOING THE TASKS.</p> |
| + | </div> |
| + | </div> |
| + | </div> |
| + | <div class="month"> |
| + | August</div> |
| + | <div class="general"> |
| + | <p>At this month we have started to apply graph theory on iGEM |
| + | parts. We have specified nodes, edges, graph types. Furthermore, |
| + | we have started to develop a new “ Part Registery Form ” to |
| + | be able to more standardize the part entry to be able to apply |
| + | some algorithms on the parts more efficiently.</p> |
| + | </div> |
| + | <div class="lower"> |
| + | <div class="week1" style="height: 350px;"> |
| + | <div id="week"> |
| + | Week 1</div> |
| + | <p>Meeting -8</p> |
| + | <p>/ </p> |
| + | <ul> |
| + | <li>Node data extraction algorithm.</li> |
| + | <li>Node description. </li> |
| + | <li>Visualization of nodes.</li> |
| + | <li>Pathway finding according to specified I/O properties.</li> |
| + | <li>Representing the nodes with original images.</li> |
| + | </ul> |
| + | </div> |
| + | <div class="week2" style="height: 350px;"> |
| + | <div id="week"> |
| + | Week 2</div> |
| + | <p>Meeting -9</p> |
| + | <ul> |
| + | <li>Whichone is node part or subparts or both are nodes |
| + | in different graphs?</li> |
| + | <li>Part Combination rules.</li> |
| + | <li>Web site, Poster Content</li> |
| + | <li>Animation storyboard. </li> |
| + | <li>Survey for new “Part Registery Standarts”.</li> |
| + | <li>NewPart Registery Form.</li> |
| + | </ul> |
| + | </div> |
| + | <div class="week3" style="height: 350px;"> |
| + | <div id="week"> |
| + | Week 3</div> |
| + | <p>Meeting -10</p> |
| + | <p>/ </p> |
| + | <ul> |
| + | <li>Extraction of Part Combination Rules </li> |
| + | <li>Web, poster, presentation contents generally. |
| + | </li> |
| + | <li></li> |
| + | </ul> |
| + | </div> |
| + | <div class="week4" style="height: 350px;"> |
| + | <div id="week"> |
| + | Week 4</div> |
| + | <p>Meeting -11</p> |
| + | <ul> |
| + | <li>USTC and Berkeley projects.[ https://2009.igem.org/Team:USTC_Software |
| + | and https://2009.igem.org/Team:Berkeley_Software </li> |
| + | <li>Graphical representation of node relations. </li> |
| + | <li>Part Combination Rules </li> |
| + | <li>Subpart Combinations Rules </li> |
| + | <li>Expectations from the software (SRS: Functional; |
| + | Requirements) </li> |
| + | </ul> |
| + | </div> |
| + | </div> |
| + | <div class="month"> |
| + | September</div> |
| + | <div class="general"> |
| + | At this time all bases for application were nearly to finish, |
| + | the software group was waiting row data from the gene group. |
| + | Meanwhile, they were working on code bases.</div> |
| + | <div class="lower"> |
| + | <div class="week1" style="height: 350px;"> |
| + | <div id="week"> |
| + | Week 1 </div> |
| + | <p>DOING THE TASKS. </p> |
| + | </div> |
| + | <div class="week2" style="height: 350px;"> |
| + | <div id="week"> |
| + | Week 2</div> |
| + | <p>Meeting -12</p> |
| + | <ul> |
| + | <li>Final Database </li> |
| + | <li>Final Graphs </li> |
| + | <li>GUI </li> |
| + | <li>Expectations from the software (SRS: Functional |
| + | Requirements) (Suggestions)</li> |
| + | <li>Survey details</li> |
| + | </ul> |
| + | </div> |
| + | <div class="week3" style="height: 350px;"> |
| + | <div id="week"> |
| + | Week 3</div> |
| + | <p>Meeting -13</p> |
| + | <ul> |
| + | <li>Animation (Storyboard, timeline) </li> |
| + | <li>Web site (Suggestions to web site) </li> |
| + | <li>Poster (How we can use 3D stereoscopic image, How |
| + | we can tell the development progress and our concepts |
| + | by 3D effect etc...) </li> |
| + | <li>Presentation ( Suggestions about presentation )</li> |
| + | </ul> |
| + | </div> |
| + | <div class="week4" style="height: 350px;"> |
| + | <div id="week"> |
| + | Week 4</div> |
| + | <p>Meeting -14</p> |
| + | <ul> |
| + | <li>Final Graphs </li> |
| + | <li>GUI ( about 70 % is over ) </li> |
| + | <li>How to send the software to other teams for collaboration |
| + | ( just general ideas, details will be talked later ). |
| + | </li> |
| + | <li>With survey or not , can it shade the software? |
| + | </li> |
| + | <li>What to ask to teams while sending?</li> |
| + | </ul> |
| + | </div> |
| + | </div> |
| + | <div class="month"> |
| + | October</div> |
| + | <div class="general"> |
| + | <p>Now everything is nearly over, it is time to put everything |
| + | together.</p> |
| + | <ul> |
| + | <li>Gene group explaining the methods that we have used |
| + | during project.</li> |
| + | <li>Software group finalizing, software, testing it importing |
| + | new function according to collaboration results with METU |
| + | TURKEY wet lab team., trying to solve infinite bugs…</li> |
| + | <li>Design group putting all together…</li> |
| + | <li>Meanwhile, all team is writing the content for web, |
| + | poster, and presentation.</li> |
| + | </ul> |
| + | </div> |
| + | <div class="lower"> |
| + | <div class="week1" style="height: 170px;"> |
| + | <div id="week"> |
| + | Week 1</div> |
| + | <p>Meeting -15</p> |
| + | <ul> |
| + | <li>BioGuide Application, missing points.</li> |
| + | <li>Content writing</li> |
| + | <li>Web, poster, animation</li> |
| + | </ul> |
| + | </div> |
| + | <div style="float: left; width: 540px; height: 170px; font-weight: normal; background-color: #3fff72; padding: 10px;"> |
| + | <div id="week"> |
| + | Week 2, Week 3, & Week 4 |
| + | <p>GOOD NEWS Infinite meetings started :) </p> |
| + | <ul> |
| + | <li>Writing content [shared it, tasks assigned to |
| + | members according to their fields.]</li> |
| + | <li>Software; debugging, testing, adding functions…</li> |
| + | <li>Designers web, poster, presentation, animation, |
| + | importing content…</li> |
| + | </ul> |
| + | </div> |
| + | </div> |
| + | </div> |
| + | <div class="month"> |
| + | November</div> |
| + | <div class="general"> |
| + | <p align="center">November 1 – 12 is our ticket dates,</p> |
| + | <p align="center">See you in BOSTON …</p> |
| + | <p align="center">METU TURKEY SOFTWARE</p> |
| + | </div> |
| + | </div> |
| + | </div><h3>Follow our discussion topic at <a href="http://groups.google.com.tr/group/software_MetuTurkey/topics">our googlegroups</a></h3> |
| + | |
| </div> | | </div> |
| </div> | | </div> |
Line 338: |
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| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
- | <h2>Download</h2> | + | <h2>Download Executable and Code</h2> |
| + | <p>You can download BioGUIDE at <a href="http://sourceforge.net/projects/bioguide">http://sourceforge.net/projects/bioguide</a></p> |
| + | <p>Download & install it and feel it's power!!</p> |
| </div> | | </div> |
| </div> | | </div> |
Line 347: |
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| <h2>Collaboration</h2> | | <h2>Collaboration</h2> |
| <h3>Part Registry Survey</h3> | | <h3>Part Registry Survey</h3> |
- | <p><a href="">Click here to go to survey page..</a></p> | + | <p> |
| + | <a href="http://www.kwiksurveys.com/online-survey.php?surveyID=HIMIGG_469f28c4&ooo=HKDDJHO_95dcbe36"> |
| + | Click here to go to survey page..</a></p> |
| <br> | | <br> |
| <h3>Results</h3> | | <h3>Results</h3> |
Line 359: |
Line 1,043: |
| <li>Lethbridge</li> | | <li>Lethbridge</li> |
| <li>WashU</li> | | <li>WashU</li> |
- | <li>...</li>
| |
- | <li>...</li>
| |
- | <li>...</li>
| |
| </ul> | | </ul> |
| <li>Out of 244 participants between 10 to 22.10.2010, 57% of the | | <li>Out of 244 participants between 10 to 22.10.2010, 57% of the |
Line 375: |
Line 1,056: |
| <h4>Browsing the Registry of Standard Parts </h4> | | <h4>Browsing the Registry of Standard Parts </h4> |
| <ul> | | <ul> |
- | <li><strong>56% of participants think that it is not easy to search for | + | <li><strong>56% of participants think that it is not easy to search |
- | the parts in Registry of Standard Parts.</strong> Many comments indicate | + | for the parts in Registry of Standard Parts.</strong> Many comments |
- | a need for a better search engine and more flexible keyword search | + | indicate a need for a better search engine and more flexible keyword |
- | options, especially excepting aliases. Also many are longing for | + | search options, especially excepting aliases. Also many are longing |
- | recognizable parts names, which will ease searching with keyword. | + | for recognizable parts names, which will ease searching with keyword. |
| </li> | | </li> |
| </ul> | | </ul> |
- | <p>Partnership with Google and enforcing standardized parts names | + | <p><i>Partnership with Google and enforcing standardized parts names |
- | are suggested </p> | + | are suggested </i></p> |
- | <p>As a global organization iGEM can offer the Parts Registry in | + | <p><i>As a global organization iGEM can offer the Parts Registry in |
| different languages and more illustrations describing how the system | | different languages and more illustrations describing how the system |
- | works.</p> | + | works.</i></p> |
- | <h4>Content of Registry of Standard Parts </h4>
| + | <h4>Content of Registry of Standard Parts </h4> |
| <ul> | | <ul> |
| <li><strong>57% of participants agree that the number of parts registered | | <li><strong>57% of participants agree that the number of parts registered |
| in the Registry of Standard Parts is not enough for their projects.</strong> | | in the Registry of Standard Parts is not enough for their projects.</strong> |
| </li> | | </li> |
- | <li><strong>55% of participants think that there are enough and useful parts | + | <li><strong>55% of participants think that there are enough and |
- | distributed in iGEM Plates that we can use in our projects. </strong></li> | + | useful parts distributed in iGEM Plates that we can use in our projects. |
| + | </strong></li> |
| </ul> | | </ul> |
| <p>Even though most agree the number of parts in the registry is impressive, | | <p>Even though most agree the number of parts in the registry is impressive, |
Line 402: |
Line 1,084: |
| design devices according to the needs of the community instead of designing | | design devices according to the needs of the community instead of designing |
| what can simply be assembled into a device. </p> | | what can simply be assembled into a device. </p> |
- | <p>Encouraging development of vectors and standards for new species | + | <p><i>Encouraging development of vectors and standards for new species |
| and new standardized parts in different research areas is suggested. | | and new standardized parts in different research areas is suggested. |
- | </p> | + | </i></p> |
- | <p>Enforcing submission of right DNA sequences and working conditions | + | <p><i>Enforcing submission of right DNA sequences and working conditions |
- | for each part is suggested. </p> | + | for each part is suggested.</i> </p> |
- | <p>Few recommend expanding iGEM into a collaborative effort rather than | + | <p><i>Few recommend expanding iGEM into a collaborative effort rather |
- | an undergraduate tournament, which will increase the number and the | + | than an undergraduate tournament, which will increase the number and |
- | diversity of the parts designed and submitted all throughout the year. | + | the diversity of the parts designed and submitted all throughout the |
- | </p> | + | year. </i></p> |
| <h4>Submission to the Parts Registry </h4> | | <h4>Submission to the Parts Registry </h4> |
| <ul> | | <ul> |
- | <li><strong>52% of participants said that they have not encountered difficulties | + | <li><strong>52% of participants said that they have not encountered |
- | during submitting parts.</strong> Even though participants are satisfied | + | difficulties during submitting parts.</strong> Even though participants |
- | with the web interface of the registry, most complains about the | + | are satisfied with the web interface of the registry, most complains |
- | pSB1C3 as the new standard plasmid to submit DNA. </li> | + | about the pSB1C3 as the new standard plasmid to submit DNA. </li> |
- | <li><strong>71% of participants are like minded with our team's opinion, | + | <li><strong>71% of participants are like minded with our team's |
- | which is that The nomenclature of part IDs such as construct, device, | + | opinion, which is that The nomenclature of part IDs such as construct, |
- | composite parts, protein generator, is confusing as there is no | + | device, composite parts, protein generator, is confusing as there |
- | consensus on how to use them correctly.</strong> </li> | + | is no consensus on how to use them correctly.</strong> </li> |
| </ul> | | </ul> |
- | <p>Terminology and categorization used on iGEM’s Parts Registry should | + | <p><i>Terminology and categorization used on iGEM’s Parts Registry should |
| be re-described and correct use of terminology should be enforced during | | be re-described and correct use of terminology should be enforced during |
- | the submission process. </p> | + | the submission process.</i> </p> |
| <ul> | | <ul> |
- | <li><strong>75% of participants agree that different, specified submission | + | <li><strong>75% of participants agree that different, specified |
- | interfaces should be designed for contructs, promoter, RBS, CDS | + | submission interfaces should be designed for contructs, promoter, |
- | and terminals is needed during Registry of Standard Parts.</strong> But,
| + | RBS, CDS and terminals is needed during Registry of Standard Parts.</strong> |
- | there are very strong and valid arguments against it such as, losing | + | But, there are very strong and valid arguments against it such as, |
- | the flexibility of the registry will not allow future submission | + | losing the flexibility of the registry will not allow future submission |
| of unclassified parts. </li> | | of unclassified parts. </li> |
| </ul> | | </ul> |
- | <p>We suggest keeping the parts submission interface as is, until these | + | <p><i>We suggest keeping the parts submission interface as is, until |
- | concerns are addressed. </p> | + | these concerns are addressed.</i> </p> |
| <ul> | | <ul> |
- | <li><strong>75% of participants agree that Out-dated, un-available and not-characterized | + | <li><strong>75% of participants agree that Out-dated, un-available |
- | parts in the Registry of Standard Parts should be removed to an
| + | and not-characterized parts in the Registry of Standard Parts should |
- | archive after the consent of the designer.</strong> </li>
| + | be removed to an archive after the consent of the designer.</strong> |
| + | </li> |
| </ul> | | </ul> |
| <p>“It would be great to see some sort of organization like this! I | | <p>“It would be great to see some sort of organization like this! I |
Line 450: |
Line 1,133: |
| in the future? (ii) likewise, an uncharacterized part may be both characterized | | in the future? (ii) likewise, an uncharacterized part may be both characterized |
| and used in the future” </p> | | and used in the future” </p> |
- | <p>We suggest building a backup system, such as an archive, to sort | + | <p><i>We suggest building a backup system, such as an archive, to sort |
| out the rarely used, un-available and un-categorized parts until they | | out the rarely used, un-available and un-categorized parts until they |
- | are in line with the enforced standards. </p> | + | are in line with the enforced standards.</i> </p> |
| <ul> | | <ul> |
- | <li><strong>91% of participants have same opinion with us, which is that | + | <li><strong>91% of participants have same opinion with us, which |
- | standardization of the nomenclatures used for each different composition | + | is that standardization of the nomenclatures used for each different |
- | of parts is necessary.</strong></li> | + | composition of parts is necessary.</strong></li> |
| </ul> | | </ul> |
| <h4>Standards that should be enforced and Additional New Standards | | <h4>Standards that should be enforced and Additional New Standards |
| </h4> | | </h4> |
- | <p><strong>According to our survey, from high rated to low, these standards | + | <p>According to our survey, from high rated to low, these standards |
- | have been rated which s be used while assigning a name to parts<strong> </p> | + | have been rated which has been used while assigning a name to parts |
| + | </p> |
| <ul> | | <ul> |
| <li><strong>33% Type of part</strong> </li> | | <li><strong>33% Type of part</strong> </li> |
| <li><strong>17% Input</strong> </li> | | <li><strong>17% Input</strong> </li> |
| <li><strong>17% Output</strong> </li> | | <li><strong>17% Output</strong> </li> |
- | <li><strong>14% Version/<strong> </li> | + | <li><strong>14% Version</strong> </li> |
| <li><strong>10% Year</strong> </li> | | <li><strong>10% Year</strong> </li> |
| <li><strong>9% Group</strong> </li> | | <li><strong>9% Group</strong> </li> |
Line 474: |
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| is important. </p> | | is important. </p> |
| <ul> | | <ul> |
- | <li><strong>93% of participants have said that for the parts that are marked | + | <li><strong>93% of participants have said that for the parts that |
- | as “WORKS” distinguishing the parts with quantitative experimental | + | are marked as “WORKS” distinguishing the parts with quantitative |
- | validation vs parts without this information is important.</strong> Most | + | experimental validation vs parts without this information is important.</strong> |
- | participants have encountered with similar problems about parts | + | Most participants have encountered with similar problems about parts |
| that don’t work under their lab conditions or works but not they | | that don’t work under their lab conditions or works but not they |
| were claimed for. </li> | | were claimed for. </li> |
- | <li><strong>89% of participants have same opinion with us, which is that | + | <li><strong>89% of participants have same opinion with us, which |
- | iGEM should sub-categorize the “WORKS” comment into 1) “Quantitative” | + | is that iGEM should sub-categorize the “WORKS” comment into 1) “Quantitative” |
| for parts which are characterized with experiments and 2) “Qualitative” | | for parts which are characterized with experiments and 2) “Qualitative” |
| for parts which are not characterized will be an appropriate measure | | for parts which are not characterized will be an appropriate measure |
| for standardization of Biobrick database.</strong> </li> | | for standardization of Biobrick database.</strong> </li> |
| </ul> | | </ul> |
- | <p>In order to overcome these problems we suggest enforcing the working | + | <p><i>In order to overcome these problems we suggest enforcing the working |
| conditions title for the registry entrance, in order to collect quantitative | | conditions title for the registry entrance, in order to collect quantitative |
| experimental details on submitted parts, which might slow down the registration | | experimental details on submitted parts, which might slow down the registration |
- | process but will definitely increase the quality of the database. | + | process but will definitely increase the quality of the database.</i> |
| </p> | | </p> |
| <ul> | | <ul> |
- | <li><strong>61% of participants agree that POPS (Polymerase Per Second) | + | <li><strong>61% of participants agree that POPS (Polymerase Per |
- | should be assigned to every part or biobricks with a promoter, where | + | Second) should be assigned to every part or biobricks with a promoter, |
- | appropriate. - 57% of participants have been agree that RIPS (Ribosome | + | where appropriate. - 57% of participants have been agree that RIPS |
- | per Second) should be assigned to every part or biobricks with a | + | (Ribosome per Second) should be assigned to every part or biobricks |
- | RBS brick.</strong> </li> | + | with a RBS brick.</strong> </li> |
| </ul> | | </ul> |
| <p>Though most participants agree the need for POPS and RBS information | | <p>Though most participants agree the need for POPS and RBS information |
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| and they should be used instead, if possible”. </p> | | and they should be used instead, if possible”. </p> |
| <ul> | | <ul> |
- | <li><strong>67% of participants have thought that entering POPS information | + | <li><strong>67% of participants have thought that entering POPS |
- | should not be mandatory while submitting new parts. Similarly, 65% | + | information should not be mandatory while submitting new parts. |
- | of participants disagree that entering RIBS information should be
| + | Similarly, 65% of participants disagree that entering RIBS information |
- | mandatory while submitting new parts </strong></li> | + | should be mandatory while submitting new parts </strong></li> |
| </ul> | | </ul> |
| <p>Even though the researchers feeling the need for this information | | <p>Even though the researchers feeling the need for this information |
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| registry as it would be difficult for underfunded and inexperienced | | registry as it would be difficult for underfunded and inexperienced |
| groups to perform these measurements. </p> | | groups to perform these measurements. </p> |
- | <p>We strongly suggest starting a forum on how to quantify the performance | + | <p><i>We strongly suggest starting a forum on how to quantify the performance |
| of promoters and genes to bring an easy to measure standard for the | | of promoters and genes to bring an easy to measure standard for the |
| efficiency of the parts. Additionally iGEM should the responsibility | | efficiency of the parts. Additionally iGEM should the responsibility |
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| under similar conditions and with experienced researchers, which will | | under similar conditions and with experienced researchers, which will |
| allow user to compare and contrast the efficiencies of the parts more | | allow user to compare and contrast the efficiencies of the parts more |
- | accurately. </p> | + | accurately. </i></p> |
| <ul> | | <ul> |
- | <li><strong>82% of participants have thought that information on working | + | <li><strong>82% of participants have thought that information on |
- | conditions of the parts should be mandatory while submitting new | + | working conditions of the parts should be mandatory while submitting |
- | parts.</strong> Most find submiting the detailed experimental information | + | new parts.</strong> Most find submiting the detailed experimental |
- | and working conditions is crucial and even easier than submitting | + | information and working conditions is crucial and even easier than |
- | measurements of POPS or RBS. </li> | + | submitting measurements of POPS or RBS. </li> |
| </ul> | | </ul> |
| <h4>Definitions you would like to see at the Registry of Standard Parts | | <h4>Definitions you would like to see at the Registry of Standard Parts |
| </h4> | | </h4> |
| <ul> | | <ul> |
- | <li><strong>Transcriptional efficiency 13% </li> | + | <li><strong>Transcriptional efficiency 13%</strong> </li> |
- | <li><strong>Protein lifetime 10% </li> | + | <li><strong>Protein lifetime 10%</strong> </li> |
- | <li><strong>Ribosome binding efficiency 10% </li> | + | <li><strong>Ribosome binding efficiency 10%</strong> </li> |
- | <li><strong>mRNA lifetime 9% </li> | + | <li><strong>mRNA lifetime 9%</strong> </li> |
- | <li><strong>Translation initiation and efficiency 9% </li> | + | <li><strong>Translation initiation and efficiency 9%</strong> |
- | <li><strong>Protein concentration 9% </li> | + | </li> |
- | <li><strong>Cooperative effects with other molecules 9% </li> | + | <li><strong>Protein concentration 9%</strong> </li> |
- | <li><strong>Protein-DNA binding rates and efficiencies 8% </li> | + | <li><strong>Cooperative effects with other molecules 9%</strong> |
- | <li><strong>RNA polymerase affects 8% </li> | + | </li> |
- | <li><strong>System copy count 8% </li> | + | <li><strong>Protein-DNA binding rates and efficiencies 8%</strong> |
- | <li><strong>Protein multimerization 6% </li> | + | </li> |
| + | <li><strong>RNA polymerase affects 8% </strong></li> |
| + | <li><strong>System copy count 8%</strong> </li> |
| + | <li><strong>Protein multimerization 6%</strong> </li> |
| </ul> | | </ul> |
| <p>Additional titles includes: Catalytic rates and affinities for substrates, | | <p>Additional titles includes: Catalytic rates and affinities for substrates, |
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| <h4>Efficiency of the Database Entries </h4> | | <h4>Efficiency of the Database Entries </h4> |
| <ul> | | <ul> |
- | <li><strong>86% of participants would like to see a ranking/rating system | + | <li><strong>86% of participants would like to see a ranking/rating |
- | for the parts by the other iGEM users which will be one indication | + | system for the parts by the other iGEM users which will be one indication |
| of if a part is working and how well in different laboratories.</strong> | | of if a part is working and how well in different laboratories.</strong> |
| Few had concerns about how well the rating system will work for | | Few had concerns about how well the rating system will work for |
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| futher towards a peer-reviewed quality control system for the parts. | | futher towards a peer-reviewed quality control system for the parts. |
| </li> | | </li> |
- | <li><strong>61% of participants agreed that parts should be updated regularly | + | <li><strong>61% of participants agreed that parts should be updated |
- | by the designers, where most agreed at least when there is new information | + | regularly by the designers, where most agreed at least when there |
- | on the parts.</strong> It has also been suggested to give permission to all
| + | is new information on the parts.</strong> It has also been suggested |
- | the users of that part for updating information. </li>
| + | to give permission to all the users of that part for updating information. |
- | <li><strong>73% of participants have been agree with us that excluding the
| + | |
- | low ranking parts or the parts with negative feedback from the future
| + | |
- | plates will increase efficiency of the system.</strong> The major concern
| + | |
- | about excluding any part is losing the variety of parts in the database.
| + | |
- | Few recommends excluding only the parts that are not working.
| + | |
| </li> | | </li> |
| + | <li><strong>73% of participants have been agree with us that excluding |
| + | the low ranking parts or the parts with negative feedback from the |
| + | future plates will increase efficiency of the system.</strong> The |
| + | major concern about excluding any part is losing the variety of |
| + | parts in the database. Few recommends excluding only the parts that |
| + | are not working. </li> |
| </ul> | | </ul> |
- | <p>“Efficiency shouldn't be top priority in a database. First and foremost, | + | <p>“Efficiency shouldn't be top priority in a database. First and foremost, |
| data is the top priority. Excluding those parts would make the system | | data is the top priority. Excluding those parts would make the system |
| more efficient” </p> | | more efficient” </p> |
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| to these parts, which not only a qualifier for an iGEM gold medal, but | | to these parts, which not only a qualifier for an iGEM gold medal, but |
| also one of the focuses of biobricks.” </p> | | also one of the focuses of biobricks.” </p> |
- | <p>We suggest excluding the parts not-working, low rated or with negative | + | <p><i>We suggest excluding the parts not-working, low rated or with |
- | feedbacks from the annual distribution plates but still archive them | + | negative feedbacks from the annual distribution plates but still archive |
- | and make their data available through the parts registry. So the while | + | them and make their data available through the parts registry. So the |
- | the individuals labs are receiving plates with higher rated, fully working | + | while the individuals labs are receiving plates with higher rated, fully |
- | parts for their projects, anyone who wants to work on a more exotic | + | working parts for their projects, anyone who wants to work on a more |
- | part can search through the achieves and re-vitalize the parts stored | + | exotic part can search through the achieves and re-vitalize the parts |
- | there. The challenge of re-vitalization of parts can be encouraged as | + | stored there. The challenge of re-vitalization of parts can be encouraged |
- | an collaborative effort. </p> | + | as an collaborative effort.</i> </p> |
| <h4>New Options for the Parts Registry Database </h4> | | <h4>New Options for the Parts Registry Database </h4> |
| <ul> | | <ul> |
- | <li><strong>96% of participants are like minded with us that it will be | + | <li><strong>96% of participants are like minded with us that it |
- | useful to have a link out to the gene/protein information of the | + | will be useful to have a link out to the gene/protein information |
- | parts and - %97 of participants have been agree that they would | + | of the parts and - %97 of participants have been agree that they |
- | like to know if a part is also involved in known biological pathways.</strong> </li> | + | would like to know if a part is also involved in known biological |
| + | pathways.</strong> </li> |
| + | </ul> |
| + | <p><strong>For receiving pathway information more participants have |
| + | voted for NCBI Cog (59%) than KEGG pathways (38%) when the responses |
| + | for both has been distributed among the choices according to response |
| + | rates.</strong> Adding the blast option to the parts registry has also |
| + | been suggested to locate parts of interest. We are sure all of us would |
| + | like to see gene-protein and pathway information if these information |
| + | was integrated into the database and offered automatically for each |
| + | entry in the database.</p> |
| + | <p><i>We are planning to provide this information about the parts to |
| + | all parts registry users as a build-in option in the next version of |
| + | BioGuide in iGEM 2011. </i></p> |
| + | <br> |
| + | <h2>New Parts Registry Form Suggested for The New Standards</h2> |
| + | <img src="https://static.igem.org/mediawiki/2010/1/17/Metu-form1.png"> |
| + | <h3>Description</h3> |
| + | <p>Warning Boxes: </p> |
| + | <ul> |
| + | <li>If Out-dated, un-available and not-characterized parts exist |
| + | in the Registry of Standard Parts, bring to an archive after the |
| + | consent of the designer. Divide archive into three title: Out-dated, |
| + | un-available and not-characterized parts </li> |
| + | <li>Besides shown as “works”, in the works box there should be explanation |
| + | whether the part is characterized or non-characterized. </li> |
| + | <li>Parts should be updated regularly by the designers </li> |
| + | <li>Excluding the low ranking parts or the parts with negative feedback |
| + | from the future plates </li> |
| + | </ul> |
| + | <p>Characterization Boxes: </p> |
| + | <ul> |
| + | <li>transcriptional efficiency </li> |
| + | <li>mRNA lifetime </li> |
| + | <li>ribosome binding efficiency </li> |
| + | <li>translation initiation and efficiency </li> |
| + | <li>protein lifetime </li> |
| + | <li>protein concentration </li> |
| + | <li>protein multimerization </li> |
| + | <li>protein-DNA binding rates and efficiencies </li> |
| + | <li>cooperative effects with other molecules </li> |
| + | <li>RNA polymerase effects </li> |
| + | <li>system copy count </li> |
| + | </ul> |
| + | <img src="https://static.igem.org/mediawiki/2010/9/91/Metu-form2.png"> |
| + | <h3>Desription</h3> |
| + | <p>Search box </p> |
| + | <ul> |
| + | <li>with click options </li> |
| + | <li>options: searched parts are: |
| + | <ul> |
| + | <li>Available </li> |
| + | <li>Length OK </li> |
| + | <li>Building </li> |
| + | <li>Planning </li> |
| + | <li>Missing </li> |
| + | <li>Unavailable </li> |
| + | </ul> |
| + | </li> |
| + | </ul> |
| + | <p>according to the clicks of above options, search is modified</p> |
| + | <img src="https://static.igem.org/mediawiki/2010/5/54/Metu-form3.png"> |
| + | <img src="https://static.igem.org/mediawiki/2010/1/1d/Metu-form4.png"> |
| + | <h3>Description</h3> |
| + | <p>Assume on the part image; </p> |
| + | <ul> |
| + | <li>part DNA sequence is not confirmed, then tag with "non-confirmed |
| + | DNA sequence" </li> |
| + | <li>non-characterized parts in the Parts Registry are not characterized |
| + | further, then it will be tagged as "deprecated" </li> |
| + | </ul> |
| + | <p>also: </p> |
| + | <ul> |
| + | <li>comment box stated that any team can make comment about experiences |
| + | with the part is opened </li> |
| + | <li>boxes which had been not filled with the data are highlighted; |
| + | <ul> |
| + | <li>transcriptional efficiency </li> |
| + | <li>mRNA lifetime </li> |
| + | <li>ribosome binding efficiency </li> |
| + | <li>translation initiation and efficiency </li> |
| + | <li>protein lifetime </li> |
| + | <li>protein concentration </li> |
| + | <li>protein multimerization </li> |
| + | <li>protein-DNA binding rates and efficiencies </li> |
| + | <li>cooperative effects with other molecules </li> |
| + | <li>RNA polymerase effects </li> |
| + | <li>system copy count </li> |
| + | </ul> |
| + | </li> |
| + | <li>if the part is not characterized but "works" then a "Qualitative |
| + | part" tag is added </li> |
| + | <li>besides "works", "Characterized" or "non-characterized" box |
| + | is added </li> |
| + | <li>ranking/rating stars for the parts voted by the other iGEM users |
| + | which indicate how well the parts perform in different laboratories |
| + | is added. For example 4.5 star voted by 27 teams (number of stars |
| + | and number of votes) </li> |
| </ul> | | </ul> |
- | <p><strong>For receiving pathway information more participants have voted for NCBI
| |
- | Cog (59%) than KEGG pathways (38%) when the responses for both has been
| |
- | distributed among the choices according to response rates.</strong> Adding the
| |
- | blast option to the parts registry has also been suggested to locate
| |
- | parts of interest. We are sure all of us would like to see gene-protein
| |
- | and pathway information if these information was integrated into the
| |
- | database and offered automatically for each entry in the database.</p>
| |
- | <p>We are planning to provide this information about the parts to all
| |
- | parts registry users as a build-in option in the next version of BioGuide
| |
- | in iGEM 2011. </p>
| |
- | <h4>NEW PARTS REGISTRY FORM SUGGESTED FOR THE NEW STANDARDS</h4>
| |
- | <p><a href="">Link out to the form</a></p>
| |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="text"> | | <div class="text"> |
| <h2>Design</h2> | | <h2>Design</h2> |
| + | <a href="https://static.igem.org/mediawiki/2010/6/6a/Metu_Turkey_Software_ER3.jpg"><img src="https://static.igem.org/mediawiki/igem.org/7/71/Metu_Software_ER3.png" /></a> |
| + | |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
- | <h2>Code</h2> | + | <h2>User Guide</h2> |
| + | <object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/Znb1o7cr5dc?hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/Znb1o7cr5dc?hl=en&fs=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/Fk7eJ-Ig_IQ?hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/Fk7eJ-Ig_IQ?hl=en&fs=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object><p>For new users whom want to interest with synthetic biology and for experienced scientists, in our program you have two options for Input Output properties ;</p> |
| + | <p>To find input-output related biobrick parts or larger constructs! If you want to provide specific chemical or physical inputs from external environment, you may choose these inputs from the list. if you want other specific inputs which will be expressed from a coding sequence, the list can provide these specified protein names.</p> |
| + | <img src="https://static.igem.org/mediawiki/2010/6/60/Metu-guide1.jpg"> |
| + | <p>Wanted features of outputs can be selected by either from list or entering individually into text boxes.</p> |
| + | <img src="https://static.igem.org/mediawiki/2010/c/c0/Metu-guide2.jpg"> |
| + | <p>Then click on the “Show Parts ” button.</p> |
| + | <img src="https://static.igem.org/mediawiki/2010/9/95/Metu-guide3.jpg"> |
| + | <p>Then the program will show you the parts have specified I/O properties</p> |
| + | <img src="https://static.igem.org/mediawiki/2010/7/7f/Metu-guide4.jpg"> |
| + | <p>To see the properties of a part just click on it.</p> |
| + | <img src="https://static.igem.org/mediawiki/2010/3/33/Metu-guide5.jpg"> |
| + | <img src="https://static.igem.org/mediawiki/2010/2/27/Metu-guide6.jpg"> |
| + | <p>After clicking, you will see a highlighted pathway on the 2nd graph. Which are the subparts of the clicked part. Showing the sub graph in network.</p> |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="text"> | | <div class="text"> |
| <h2>Human Practices</h2> | | <h2>Human Practices</h2> |
| + | <p>iGEM’s parts registry is the only current database that holds information |
| + | and DNA for over 3000 standard parts for the use of synthetic biology |
| + | community. BioGUIDE is the first designed software that organizes the |
| + | parts in iGEM spring 2010 distribution as possible atomics parts to |
| + | build new biological device and systems for specific input and outputs |
| + | based on graph theory. We are the first group who has applied a novel |
| + | algorithm to search for input/output relations between the parts to |
| + | reveal possible construct assemblies. This new approach will chance |
| + | how the parts registry is used by the scientific community. And the |
| + | availability of software implementing our algorithm with a very user |
| + | friendly graphical user interface will allow all the users of the parts |
| + | registry to explore new and novel constructs according to their parameter |
| + | with ease. Additionally as the BioGUIDE software is an open source ware |
| + | , any user can contribute to the development of the application. So, |
| + | BioGUIDE will be improving with a collaborative effort, which will make |
| + | it even more widely used among the synthetic biologists. </p> |
| + | <p>We also had many collabrations with the teams such as, INSA-Lyon, |
| + | Lethbridge, WashU through our survey and WARSAW as we have participated |
| + | in their survey. Also our sister team METU_TURKEY is our main collaborator. |
| + | They have provided feedback BioGUIDE at different stages of the development. |
| + | And they had the chance to analyze their constructs input/output relations |
| + | throughout this collaboration. </p> |
| + | <p><strong>ALL TEAMS</strong>: The Parts Registry Survey that has been |
| + | developed by METU_TURKEY_SOFTWARE got response from 253 of participant |
| + | from 94 teams. Analysis of the survey results we have received so far |
| + | indicates that we were able outreach to the iGEM community and help |
| + | them verbalize their concerns and suggestions for the parts registry |
| + | standards and the maintenance of the database.</p> |
| + | <p><strong>WARSAW</strong>: Our team members have participated in their |
| + | survey abour iGEM participants profile. </p> |
| + | <p><strong>METU_TURKEY</strong>: Beta testing of the algorithm developed |
| + | and the BioGUIDE software has been performed by METU_TURKEY on few case |
| + | studies. Additionally they have tested their construct for 2010 competition |
| + | with our algorithm. </p> |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="text"> | | <div class="text"> |
| <h2>Material</h2> | | <h2>Material</h2> |
| + | <p>Our main data source for BIO Guide Software Program was the available |
| + | background information of parts distributed in 2010 iGEM plates (Total |
| + | of three384-well plates of dried DNA) to the wetlab teams. This data |
| + | was available through both the parts registry main website (<a href="http://partsregistry.org/Main_Page">http://partsregistry.org/Main_Page</a>) |
| + | in XML format and parts registry libraries (http://partsregistry.org/assembly/libraries.cgi?id=31) |
| + | in Excel format. Data from parts with specific part IDs have been parsed |
| + | with a custom code developed to modify SAX Parser. Then, the rest of |
| + | the data which needs to be standardized according to biological importance |
| + | have been extracted from the Registry of Parts Page manually. The chemical |
| + | (IPTG, galactose etc.) or physical (UV irradiation, temperature etc) |
| + | external inputs and proteins synthesized from a biobrick coding sequence |
| + | can affect promoters on the parts. These effectors are identified under |
| + | the title “Input”. And the “Output” s of these effectors are classified |
| + | as inducers (a molecule that starts gene expression), repressors (blocker |
| + | of attachment of RNA polymerase to promoter), activators (increasing |
| + | the rate of transcription) and inhibitor s(decreasing the rate of transcription). |
| + | These standardizations on the database helped us to build the algorithm |
| + | based on input/output relationships. MySQL Server is used for Database |
| + | development and organization. All of our illustrations for ER and algorithm |
| + | is created in SmartDraw (trial version). Java Programming Language, |
| + | and NetBeans Development environment is used or for software development. |
| + | The graphical visualization of the software is done with Cyctoscape |
| + | and yfiles libraries (trial version) are used for the presentation of |
| + | graphical events. We have utilized css Javascripts for our webdesign. |
| + | Autodesk Maya 2011 with Academic Licence, Adobe Creative Suite 5 Master |
| + | Collection (Trial Version) have been used for animations and illustrations. |
| + | Video tutorial for the BioGUIDE has been created by camstudio and trial |
| + | versions of Flash and After Effects are also used for the videos. |
| + | </p> |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
- | <h2>User Guide</h2> | + | <h2>Supporting Tools</h2> |
| + | <ul> |
| + | <li>SAX Parser ( modified )to parse XML files</li> |
| + | <li>Java ProramingLanguage, NetBeans Developement environment for |
| + | software developement</li> |
| + | <li>MySQL Server for DataBase</li> |
| + | <li>cystoscape for graph visualization</li> |
| + | <li>yfiles library for graph events</li> |
| + | <li>SmartDraw for illutration of ER and Algorithm</li> |
| + | <li>maya & Cinema 4D for 3D animation, Adobe Master Collection and |
| + | Microsoft Expression Studio for design</li> |
| + | <li>CSS, Java Script for web</li> |
| + | </ul> |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="text"> | | <div class="text"> |
| <h2>Safety</h2> | | <h2>Safety</h2> |
| + | <p>Synthetic biology has the potential to impact many areas of society. |
| + | Synthetic biologists may use artificial molecules to reproduce emergent |
| + | behavior from natural biology, with the goal of creating artificial |
| + | life or seeking interchangeable biological parts to assemble them into |
| + | devices and systems that function in a manner not found in nature (Benner |
| + | and Sismour 2005, Endy 2005, Heinemann and Panke 2006, Luisi 2007, Serrano |
| + | 2007).There is possibility of causing intentional or accidental harm |
| + | to humans, agriculture or the environment. While deliberate damage is |
| + | dealt with under the heading biosecurity, the potential unintended consequences |
| + | have to be considered under the term biosafety. As a software developer |
| + | , we have to consider all possible maliciously use of synthetic biology |
| + | tools. However, it is diffucult to understand for which purposesour |
| + | tools will be used, bestway avoiding garage bioterrorism is all parts |
| + | before adding to partsregistry must be checked , looked for toxic affect |
| + | and any environmental or human harmness. After scanning possible candidate |
| + | parts, a committe should decide whether novel part can be added parts |
| + | registry or not.And we can only warn the user about our intention while |
| + | building the application: </p> |
| + | <p>“BioGUIDE v1.0 software is <strong>FOR RESEARCH USE ONLY</strong>, |
| + | no medical or diagnostic use for applications of the novel Biobrick |
| + | constructs generated through our software has been described “</p> |
| + | <p>“No military (defense or combat) applications will be allowed in |
| + | future”</p> |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
- | <h2>Supporting Tools</h2> | + | <h2>Contact</h2> |
| + | <p>For critics, suggestion, or appraisal, you can contact us on |
| + | <a href="mailto:software_metuturkey@googlegroups.com">software_metuturkey@googlegroups.com</a></p> |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="text"> | | <div class="text"> |
| <h2>Future Plan</h2> | | <h2>Future Plan</h2> |
| + | <p>The application we have developed can be used by all iGEM members. |
| + | As the iGEMs database expands and the recognition of the field of Synthetic |
| + | Biology increases, data resources from other biological databases such |
| + | as NCBI might be needed to be integrated to the application. In such |
| + | a situation, extendibility of the application is vital. New data resources |
| + | and new functions should be added easily. </p> |
| + | <p>Before planning ahead, feedback from other teams and iGEM headquarters |
| + | about the BioGuide 1.0 will be collected. That will help us to fill |
| + | in the missing features of the application and check the theories which |
| + | are basis of our algorithms. </p> |
| + | <p>As our application is not geared towards any commercial use and will |
| + | stay as an academic application, keeping track of the weekly developmental |
| + | process on the wiki notebook environment was satisfactory. If the need |
| + | for a commercial application emerges, we should be utilizing professional |
| + | software development approaches to determine the exact requirements |
| + | and to facilitate the use of a common language between interdiciplinary |
| + | members in the team. </p> |
| + | <p>For constructing BioGuide 2.0 we have some plans. </p> |
| + | <h3>Short Term plan:</h3> |
| + | <p>Next year we are planning to generate BioGuide 2.0 by using all parts |
| + | data but inorder to do this we will update our part database but easyway |
| + | is standardization and reorganizing all parts in partsregistrty.org |
| + | according to our suggestion because re-organizing and normalization |
| + | are crucial. We are planning to add new tools to improve graphs.Our |
| + | ultimate aim is finding best pathway based on automated construction |
| + | and input-output relation. BioGuide 2.0 will be more faster because |
| + | we are planning to use OODBMS and all all platform will support BioGuide |
| + | 2.0. </p> |
| + | <h3>Long term plan:</h3> |
| + | <p>We want to improve our algoritm and add more parameter to make graphs |
| + | more effective. Our dream is embeding our software into partsregistry.org |
| + | so no mere iGEMers will choose parts in real time by using our software. |
| + | </p> |
| + | <h3>Suggestions based on PartsRegistry Survey Results</h3> |
| + | <p>First suggesiton is offering fartnership with Google for easy search |
| + | and founding a committe to enforce a standardized nomenclature for terminology |
| + | and parts registry entries. </p> |
| + | <p>We strongly suggest starting a forum on how to quantify the performance |
| + | of promoters and genes to bring an easy to measure standard for the |
| + | efficiency of the parts. Additionally iGEM should assume the responsibility |
| + | and provide the measurements for the each promoter and gene included |
| + | in the distributions. The second choice would beeven better in terms |
| + | of standardization as all the measurement will be performed by one center |
| + | under similar conditions and with experienced researchers, which will |
| + | allow user to compare and contrast the efficiencies of the parts more |
| + | accurately. We suggest excluding the parts not-working, low rated or |
| + | with negative feedbacks from the annual distribution plates but still |
| + | archive them and make their data available through the parts registry. |
| + | So the while the individuals labs are receiving plates with higher rated, |
| + | fully working parts for their projects, anyone who wants to work on |
| + | a more exotic part can search through the achieves and re-vitalize the |
| + | parts stored there. The challenge of re-vitalization of parts can be |
| + | encouraged as an collaborative effort. We are sure, all of us would |
| + | like to see gene-protein and pathway information if these information |
| + | was integrated into the database and offered automatically for each |
| + | entry in the database. We are planning to provide this information about |
| + | the parts to all parts registry users as a build-in option in the next |
| + | version of BioGuide in iGEM 2011. </p> |
| </div> | | </div> |
| </div> | | </div> |
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- | <div id="download5" class="item"> | + | <div class="item"> |
- | <div class="content2">
| + | </div> |
- | <div class="text">
| + | <div id="miscellaneous5" class="item"> |
- | <h2>Contact</h2>
| + | <div class="content2"> |
- | </div>
| + | <div class="text"> |
- | </div>
| + | <h2>Sponsors</h2> |
| + | <ul id="sponsorlist"> |
| + | <li><img src="http://tecrubem.net/wp-content/uploads/2009/09/tubitak.jpg" width="200" height="200"></li> |
| + | <li><img src="https://static.igem.org/mediawiki/igem.org/0/06/METU-Surat.jpg"></li> |
| + | <li><img src="https://static.igem.org/mediawiki/igem.org/6/64/Teknokent.jpg"></li> |
| + | <li><img src="https://static.igem.org/mediawiki/igem.org/d/d8/Sentegen.jpg"></li> |
| + | </ul> |
| + | </div> |
| </div> | | </div> |
- | <div class="item">
| |
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| <div class="clear"> | | <div class="clear"> |
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| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
- | <h2>Modeling</h2> | + | <h2>Graph Modeling</h2> |
| <h3>Graphical Modeling for Bio-Guide</h3> | | <h3>Graphical Modeling for Bio-Guide</h3> |
| <h4>Introduction</h4> | | <h4>Introduction</h4> |
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| <div class="text"> | | <div class="text"> |
| <h2>Results</h2> | | <h2>Results</h2> |
| + | <ul> |
| + | <li>In order to develop BioGuide algorithm, there was a need to |
| + | reorganize and normalize parts information database in partsregistry.org. |
| + | Information of the parts was processed and developed from partsregistry.org |
| + | which includes the PartID, PartName, RFC values, etc , designer |
| + | and contact information and parameters to build a standardized template |
| + | for our algorithm to run smoothly. </li> |
| + | <li>Database standardization is done by analyzing iGEM Spring 2010 |
| + | distribution and collecting information needed for the standardized |
| + | parts. Also new parameters are assigned according to parts input-output |
| + | model like : Inducer, Activator, Repressor, Inhibitor</li> |
| + | <li>For each promoter we have assigned their inducers or repressors |
| + | as input and for protein generator parts we have assigned generated |
| + | proteins as output which maybe activator or repressor of other devices. |
| + | </li> |
| + | <li>iGEM devices are depicted in pictorial forms called flowcharts, |
| + | encapsulation of implementations , decision branching and direction |
| + | are milestones of our algorithm. Following flowcharts are the high |
| + | level representations of our algorithms developed for the BioGuide |
| + | software.</li> |
| + | <li>We run our algorithm on the real combination dataset in order |
| + | to build our input/output relations graphs. We also collected the |
| + | subpart assembly order, such as 1st: promoter, 2nd:rbs, 3rd:coding |
| + | seq, any internal parts and the Last: terminator. Each specific |
| + | Biobrick type has been assigned a number as a unique image ID from |
| + | 1 to 19. </li> |
| + | <li>ImageID assembly orders for each construct have been used to |
| + | extract the type information for each subpart with that construct. |
| + | This innovative approach helped us to reveal 400 possible brick |
| + | combinations present within the 3x384 well plates distributed by |
| + | iGEM in Spring 2010</li> |
| + | <li>Four different graphs were constructed based on graphical modeling |
| + | theory where relations of atomic parts, devices and systems and |
| + | the functional combinations that can build new constructs are presented |
| + | for the iGEMs parts registry database. Three graphs are composed |
| + | of iGEM devices and one graph is based on Biobricks.</li> |
| + | <li>Each graph comprises a set of vertices or nodes and a set of |
| + | edges. In the set of nodes each node represents a device, while |
| + | in the set of edges each edge represents the input-output combination |
| + | of the nodes.</li> |
| + | <li>We arrange a survey to analyze user needs and response, According |
| + | to our survey results, 244 participants are completed our survey |
| + | between 10 to 22.10.2010, 57% of the participant had scientific |
| + | degrees from B.Sc to Professor and 18% had graduate degrees. 18% |
| + | of participants are enrolled in their teams as either Instructors |
| + | or Advisors.INSA-Lyon, Lethbridge, WashU are dedicated as collaborators |
| + | with more than 60% team participation. You can learn more on survey |
| + | results on our collaboration page</li> |
| + | </ul> |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="clear"> | | <div class="clear"> |
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| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div id="project9" class="item"> |
| + | <div class="content2"> |
| + | <div class="text"> |
| + | <h2>Attribution and Contributions</h2> |
| + | <p>The BioGUIDE software is a proud product of METU_TURKEY_SOFTWARE group where the students have presented the problem and come up with the solution with minor advising. This project was not a part of an ongoing project in any of the advisors.</p> |
| + | <p>The biologist of the team have done the preliminary database standardization by analyzing and collected data from the iGEM Spring 2010 distribution. All the algorithms have been developed by the soon-to-be computer scientist in the group. The Parts registry survey and standardization of the database information on parts have been developed through a colloborotative effort within the group. </p> |
| + | <p>Additionally all the logo, illustrations, animations, video and other visual media and web design has been created by the design team in the group.</p> |
| + | </div> |
| + | </div> |
| + | </div> |
| + | <div class="item"> |
| + | </div> |
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| + | </div> |
| + | <div class="item"> |
| + | </div> |
| + | <div id="project10" class="item"> |
| + | <div class="content2"> |
| + | <div class="text"> |
| + | <h2>Development Plans and Project Management</h2> |
| + | <p>The application we are developing can be used by all iGEM members and it’s data is increasing very fast as the iGEM becomes a bigger organization. Moreover, other data resources like NCBI can be imported to this application, hence the user group of application is gets bigger and bigger. In such a situation, extendibility of the application is vital. New data resources and new functions should be added easily. </p> |
| + | <p>Before starting to think about those, first we have to ask to other teams and iGEM headquarters about the BioGuide 1.0 to see the missing points in our idea, and to check our theories. Until developing this idea we were not using professional software approaches. We were planning our weekly tasks and doing those as in the notebook. </p> |
| + | <p>After finding a novel software project we have to change our approach. We have to use professional software development approaches to develop such an application to be able to state the requirements exactly and to use a common language between software oriented and biology oriented members in the team.</p> |
| + | <p>As we mentioned above, our software can be extended, and new data resources can be imported. The requirements are changing and the problem can be understood better in time. Extreme Programming Approach is developed for such software projects. That is the approach we are going to use in BioGuide2.0</p> |
| + | </div> |
| + | </div> |
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| <script type="text/javascript">if (window.runOnloadHook) runOnloadHook();</script> | | <script type="text/javascript">if (window.runOnloadHook) runOnloadHook();</script> |
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| <li><a class="panel" href="#project5">Database Standardization</a></li> | | <li><a class="panel" href="#project5">Database Standardization</a></li> |
| <li><a class="panel" href="#project6">Algorithm</a></li> | | <li><a class="panel" href="#project6">Algorithm</a></li> |
- | <li><a class="panel" href="#project7">Modeling</a></li> | + | <li><a class="panel" href="#project7">Graph Modeling</a></li> |
| <li><a class="panel" href="#project8">Results</a></li> | | <li><a class="panel" href="#project8">Results</a></li> |
| + | <li><a class="panel" href="#project9">Attribution and Contributions</a></li> |
| + | <li><a class="panel" href="#project10">Development Plans</a></li> |
| </ul> | | </ul> |
| </li> | | </li> |
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| <ul class="submenu"> | | <ul class="submenu"> |
- | <li><a class="panel" href="#download">Executable</a></li> | + | <li><a class="panel" href="#download">Executable and Code</a></li> |
- | <li><a class="panel" href="#download2">Code</a></li> | + | <li><a class="panel" href="#download2">User Guide</a></li> |
- | <li><a class="panel" href="#download3">User Guide</a></li>
| + | <li><a class="panel" href="#download3">Supporting Tools</a></li> |
- | <li><a class="panel" href="#download4">Supporting Tools</a></li> | + | <li><a class="panel" href="#download4">Contact</a></li> |
- | <li><a class="panel" href="#download5">Contact</a></li> | + | |
| </ul> | | </ul> |
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| <li> | | <li> |
- | <div class="menutop panel" style="border-bottom-color: rgb(204, 204, 204); border-bottom-width: 1px; border-bottom-style: solid;"> | + | <div class="menutop panel"> |
| <a class="panel" href="#miscellaneous">Miscellaneous</a><div class="toggle toggle-closed"> | | <a class="panel" href="#miscellaneous">Miscellaneous</a><div class="toggle toggle-closed"> |
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| <li><a class="panel" href="#miscellaneous4">Future Plan</a></li> | | <li><a class="panel" href="#miscellaneous4">Future Plan</a></li> |
| + | <li><a class="panel" href="#miscellaneous5">Sponsors</a></li> |
| </ul> | | </ul> |
| </li> | | </li> |