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| padding-bottom: 10px; | | padding-bottom: 10px; |
| background-color: black; | | background-color: black; |
- | background-image: url('https://static.igem.org/mediawiki/2010/4/44/Metu-background.png'); | + | background-image: url('https://static.igem.org/mediawiki/2010/d/de/Metu-bg3.jpg'); |
| background-attachment: fixed; | | background-attachment: fixed; |
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| font: 13px Tahoma, Arial, Helvetica, sans-serif; | | font: 13px Tahoma, Arial, Helvetica, sans-serif; |
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- | padding: 30px 0px 30px 0; | + | padding: 0; |
| } | | } |
| .content2 .text { | | .content2 .text { |
- | width: 800px; | + | width: 900px; |
| bottom: 0px; | | bottom: 0px; |
- | height: 420px; | + | height: 500px; |
| margin: 0 auto; | | margin: 0 auto; |
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| line-height: 1em; | | line-height: 1em; |
| color: navy; | | color: navy; |
| + | } |
| + | .content2 .text a{ |
| + | color:#A4C4EB; |
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| .content2 .text strong { | | .content2 .text strong { |
| font-size: 12px; | | font-size: 12px; |
- | color: purple; | + | color: aqua; |
| } | | } |
| .homepage { | | .homepage { |
| width: 900px; | | width: 900px; |
- | height: 500px; | + | height: 365px; |
- | top: 50px;
| + | |
| margin: 0 auto; | | margin: 0 auto; |
- | background: url('https://static.igem.org/mediawiki/2010/1/13/Metu-home.png') no-repeat; | + | background: url('1https://static.igem.org/mediawiki/2010/1/13/Metu-home.png') no-repeat; |
| position: relative; | | position: relative; |
- | padding: 50px 0px 50px 0; | + | } |
| + | #homecontainer{ |
| + | padding: 10px 30px 10px 20px; |
| + | width:800px; |
| + | height:300px; |
| + | position: absolute; |
| + | bottom: 40px; |
| + | left:40px; |
| + | text-align:justify; |
| + | opacity:0.85; |
| + | background-color:#000; |
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| #smallwrap { | | #smallwrap { |
- | width: 750px; | + | width: 880px; |
| margin: 0 auto; | | margin: 0 auto; |
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| .smallbox { | | .smallbox { |
- | width: 350px; | + | width: 410px; |
| float: left; | | float: left; |
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| -webkit-box-shadow: 0px 0px 10px #333; | | -webkit-box-shadow: 0px 0px 10px #333; |
| box-shadow: 0px 0px 10px #333; | | box-shadow: 0px 0px 10px #333; |
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| .smalltext { | | .smalltext { |
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| font-size: 11px; | | font-size: 11px; |
| overflow: auto; | | overflow: auto; |
| + | color: black; |
| } | | } |
- | .alternative { | + | .month { |
- | background-color: silver; | + | width: 120px; |
| + | float: left; |
| + | font-size: 15px; |
| + | font-weight: bold; |
| + | padding: 10px; |
| + | background-color: #fc3c3c; |
| + | clear: both; |
| + | } |
| + | .general { |
| + | width: 800px; |
| + | float: left; |
| + | font-size: 12px; |
| + | text-transform: none; |
| + | font-weight: normal; |
| + | padding: 10px; |
| + | background-color: orange; |
| + | clear: both; |
| + | } |
| + | .week1, .week3 { |
| + | width: 180px; |
| + | float: left; |
| + | font-size: 12px; |
| + | padding-right: 5px; |
| + | font-weight: normal; |
| + | background-color: #1e6dd4; |
| + | padding: 10px; |
| + | } |
| + | .week2, .week4 { |
| + | width: 180px; |
| + | float: left; |
| + | font-size: 12px; |
| + | padding-right: 5px; |
| + | font-weight: normal; |
| + | background-color: #3fff72; |
| + | padding: 10px; |
| + | } |
| + | .lower { |
| + | width: 800px; |
| + | clear: both; |
| + | } |
| + | #notebook2 { |
| + | width: 900px; |
| + | color: black; |
| + | margin: 0 auto 20 auto; |
| + | } |
| + | #week { |
| + | font-size: 14px; |
| + | font-weight: bold; |
| + | } |
| + | #sponsorlist li{float:left; text-decoration:none; margin:20px;} |
| + | .black { |
| + | color: black; |
| } | | } |
| .selected { | | .selected { |
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| z-index: 20; | | z-index: 20; |
| } | | } |
| + | #introvideo {width:480px; length:360px; margin:20px auto; margin-bottom:0;} |
| + | #home {overflow:auto;} |
| img[src*="/wiki/skins/common/images/wiki.png"] { | | img[src*="/wiki/skins/common/images/wiki.png"] { |
| width: 0; | | width: 0; |
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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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| <div class="text"> | | <div class="text"> |
| <h2>Team</h2> | | <h2>Team</h2> |
- | <div id="slider" style="opacity: 1;"> | + | <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 |
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| </div> | | </div> |
| <div class="smallbox"> | | <div class="smallbox"> |
- | <h2>Tolga Can</h2> | + | <h2 class="black">Tolga Can</h2> |
| <img src="https://static.igem.org/mediawiki/2010/c/c3/Metu-tolgahoca.jpg"> | | <img src="https://static.igem.org/mediawiki/2010/c/c3/Metu-tolgahoca.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
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| </div> | | </div> |
| </div> | | </div> |
- | <div class="smallbox alternative"> | + | <div class="smallbox"> |
- | <h2>Yeşim Aydın-Son</h2> | + | <h2 class="black">Yeşim Aydın-Son</h2> |
| <img src="https://static.igem.org/mediawiki/2010/d/d5/Metu-yesimhoca.jpg"> | | <img src="https://static.igem.org/mediawiki/2010/d/d5/Metu-yesimhoca.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
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| </div> | | </div> |
| </div> | | </div> |
- | <div class="smallbox alternative"> | + | <div class="smallbox"> |
- | <h2>Ömer Nebil Yaveroğlu</h2> | + | <h2 class="black">Ömer Nebil Yaveroğlu</h2> |
- | <img src=""> | + | <img src="https://static.igem.org/mediawiki/2010/5/53/Metu-omerhoca.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
- | <p>Content here</p> | + | <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> | | </div> |
| <div class="smallbox"> | | <div class="smallbox"> |
- | <h2>Burak Yılmaz</h2> | + | <h2 class="black">Burak Yılmaz</h2> |
| <img src="https://static.igem.org/mediawiki/2010/a/a2/Metu-burak.jpg"> | | <img src="https://static.igem.org/mediawiki/2010/a/a2/Metu-burak.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
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| </div> | | </div> |
| <div class="smallbox" style="margin: 0 auto; float: none"> | | <div class="smallbox" style="margin: 0 auto; float: none"> |
- | <h2>Muhammad Akif Ağca</h2> | + | <h2 class="black">Muhammed Akif Ağca</h2> |
- | <img src=""> | + | <img src="https://static.igem.org/mediawiki/2010/1/10/Metu-akif2.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
- | <p>Content here</p> | + | <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> | | </div> |
| <div class="clear"> | | <div class="clear"> |
| </div> | | </div> |
- | <div class="smallbox alternative"> | + | <div class="smallbox"> |
- | <h2>Cihan Taştan</h2> | + | <h2 class="black">Cihan Taştan</h2> |
| <img src="https://static.igem.org/mediawiki/2010/d/d8/Metu-cihan.jpg"> | | <img src="https://static.igem.org/mediawiki/2010/d/d8/Metu-cihan.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
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| </div> | | </div> |
| <div class="smallbox"> | | <div class="smallbox"> |
- | <h2>Hassan Salehe Matar</h2> | + | <h2 class="black">Hassan Salehe Matar</h2> |
| <img src="https://static.igem.org/mediawiki/2010/3/3c/Metu-hassan.jpg"> | | <img src="https://static.igem.org/mediawiki/2010/3/3c/Metu-hassan.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
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| </div> | | </div> |
| <div class="smallbox"> | | <div class="smallbox"> |
- | <h2>Ayub Rokhman Wakhid</h2> | + | <h2 class="black">Ayub Rokhman Wakhid</h2> |
| <img src="https://static.igem.org/mediawiki/2010/9/92/Metu-ayub.jpg"> | | <img src="https://static.igem.org/mediawiki/2010/9/92/Metu-ayub.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
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| </div> | | </div> |
| </div> | | </div> |
- | <div class="smallbox alternative"> | + | <div class="smallbox"> |
- | <h2>Muhammad Fakhry Syauqy</h2> | + | <h2 class="black">Muhammad Fakhry Syauqy</h2> |
| <img src="https://static.igem.org/mediawiki/2010/f/fd/Metu-fakhry.jpg"> | | <img src="https://static.igem.org/mediawiki/2010/f/fd/Metu-fakhry.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
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| </div> | | </div> |
| </div> | | </div> |
- | <div class="smallbox alternative"> | + | <div class="smallbox"> |
- | <h2>Saygın Karaaslan</h2> | + | <h2 class="black">Saygın Karaaslan</h2> |
| <img src="https://static.igem.org/mediawiki/2010/6/6f/Metu-saygin.jpg"> | | <img src="https://static.igem.org/mediawiki/2010/6/6f/Metu-saygin.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
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| </div> | | </div> |
| <div class="smallbox"> | | <div class="smallbox"> |
- | <h2>Yener Tuncel</h2> | + | <h2 class="black">Yener Tuncel</h2> |
| <img src="https://static.igem.org/mediawiki/2010/d/dd/Metu-yener.jpg"> | | <img src="https://static.igem.org/mediawiki/2010/d/dd/Metu-yener.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
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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 542: |
Line 1,018: |
| <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> |
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| BioGuide in iGEM 2011. </i></p> | | BioGuide in iGEM 2011. </i></p> |
| <br> | | <br> |
- | <h2>NEW PARTS REGISTRY FORM SUGGESTED FOR THE NEW STANDARDS</h2> | + | <h2>New Parts Registry Form Suggested for The New Standards</h2> |
| <img src="https://static.igem.org/mediawiki/2010/1/17/Metu-form1.png"> | | <img src="https://static.igem.org/mediawiki/2010/1/17/Metu-form1.png"> |
| <h3>Description</h3> | | <h3>Description</h3> |
Line 862: |
Line 1,340: |
| <p>according to the clicks of above options, search is modified</p> | | <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/2010/5/54/Metu-form3.png"> |
- | <img src="https://static.igem.org/mediawiki/2010/1/1d/Metu-form4.png"> | + | <img src="https://static.igem.org/mediawiki/2010/1/1d/Metu-form4.png"> |
| + | <h3>Description</h3> |
| <p>Assume on the part image; </p> | | <p>Assume on the part image; </p> |
| <ul> | | <ul> |
Line 916: |
Line 1,395: |
| <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> |
Line 922: |
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| </div> | | </div> |
| <div id="download2" class="item"> | | <div id="download2" class="item"> |
- | <div class="content2">
| |
- | <div class="text">
| |
- | <h2>Code</h2>
| |
- | </div>
| |
- | </div>
| |
- | </div>
| |
- | <div id="miscellaneous2" class="item">
| |
- | <div class="content2">
| |
- | <div class="text">
| |
- | <h2>Human Practices</h2>
| |
- | </div>
| |
- | </div>
| |
- | </div>
| |
- | <div class="clear">
| |
- | </div>
| |
- | <!-- 3rd row -->
| |
- | <div class="item">
| |
- | </div>
| |
- | <div class="item">
| |
- | </div>
| |
- | <div class="item">
| |
- | </div>
| |
- | <div class="item">
| |
- | </div>
| |
- | <div id="project3" class="item">
| |
- | <div class="content2">
| |
- | <div class="text">
| |
- | <h2>Material</h2>
| |
- | </div>
| |
- | </div>
| |
- | </div>
| |
- | <div class="item">
| |
- | </div>
| |
- | <div id="download3" class="item">
| |
| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
| <h2>User Guide</h2> | | <h2>User Guide</h2> |
- | </div>
| + | <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> |
- | </div>
| + | <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> |
- | </div>
| + | <img src="https://static.igem.org/mediawiki/2010/6/60/Metu-guide1.jpg"> |
- | <div id="miscellaneous3" class="item"> | + | <p>Wanted features of outputs can be selected by either from list or entering individually into text boxes.</p> |
- | <div class="conty of Standard Parts </h4>
| + | <img src="https://static.igem.org/mediawiki/2010/c/c0/Metu-guide2.jpg"> |
- | <ul>
| + | <p>Then click on the “Show Parts ” button.</p> |
- | <li><strong>56% of participants think that it is not easy to search
| + | <img src="https://static.igem.org/mediawiki/2010/9/95/Metu-guide3.jpg"> |
- | for the parts in Registry of Standard Parts.</strong> Many comments
| + | <p>Then the program will show you the parts have specified I/O properties</p> |
- | indicate a need for a better search engine and more flexible keyword
| + | <img src="https://static.igem.org/mediawiki/2010/7/7f/Metu-guide4.jpg"> |
- | search options, especially excepting aliases. Also many are longing
| + | <p>To see the properties of a part just click on it.</p> |
- | for recognizable parts names, which will ease searching with keyword.
| + | <img src="https://static.igem.org/mediawiki/2010/3/33/Metu-guide5.jpg"> |
- | </li>
| + | <img src="https://static.igem.org/mediawiki/2010/2/27/Metu-guide6.jpg"> |
- | </ul>
| + | <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> |
- | <p><i>Partnership with Google and enforcing standardized parts names
| + | |
- | are suggested </i></p>
| + | |
- | <p><i>As a global organization iGEM can offer the Parts Registry in
| + | |
- | different languages and more illustrations describing how the system
| + | |
- | works.</i></p>
| + | |
- | <h4>Content of Registry of Standard Parts </h4>
| + | |
- | <ul>
| + | |
- | <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>
| + | |
- | </li>
| + | |
- | <li><strong>55% of participants think that there are enough and
| + | |
- | useful parts distributed in iGEM Plates that we can use in our projects.
| + | |
- | </strong></li>
| + | |
- | </ul>
| + | |
- | <p>Even though most agree the number of parts in the registry is impressive,
| + | |
- | still they find it limited when it comes to design different devices
| + | |
- | for diverse applications especially in different species other than
| + | |
- | E. Coli. Participants believe that if there are more functional standardized
| + | |
- | parts, especially protein coding sequences and promoter-RBS , they can
| + | |
- | design devices according to the needs of the community instead of designing
| + | |
- | what can simply be assembled into a device. </p>
| + | |
- | <p><i>Encouraging development of vectors and standards for new species
| + | |
- | and new standardized parts in different research areas is suggested.
| + | |
- | </i></p>
| + | |
- | <p><i>Enforcing submission of right DNA sequences and working conditions
| + | |
- | for each part is suggested.</i> </p>
| + | |
- | <p><i>Few recommend expanding iGEM into a collaborative effort rather
| + | |
- | than an undergraduate tournament, which will increase the number and
| + | |
- | the diversity of the parts designed and submitted all throughout the
| + | |
- | year. </i></p>
| + | |
- | <h4>Submission to the Parts Registry </h4>
| + | |
- | <ul>
| + | |
- | <li><strong>52% of participants said that they have not encountered
| + | |
- | difficulties during submitting parts.</strong> Even though participants
| + | |
- | are satisfied with the web interface of the registry, most complains
| + | |
- | 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, which is that The nomenclature of part IDs such as construct,
| + | |
- | device, composite parts, protein generator, is confusing as there
| + | |
- | is no consensus on how to use them correctly.</strong> </li>
| + | |
- | </ul>
| + | |
- | <p><i>Terminology and categorization used on iGEM’s Parts Registry should
| + | |
- | be re-described and correct use of terminology should be enforced during
| + | |
- | the submission process.</i> </p>
| + | |
- | <ul>
| + | |
- | <li><strong>75% of participants agree that different, specified
| + | |
- | submission interfaces should be designed for contructs, promoter,
| + | |
- | RBS, CDS and terminals is needed during Registry of Standard Parts.</strong>
| + | |
- | But, there are very strong and valid arguments against it such as,
| + | |
- | losing the flexibility of the registry will not allow future submission
| + | |
- | of unclassified parts. </li>
| + | |
- | </ul>
| + | |
- | <p><i>We suggest keeping the parts submission interface as is, until
| + | |
- | these concerns are addressed.</i> </p>
| + | |
- | <ul>
| + | |
- | <li><strong>75% of participants agree that Out-dated, un-available
| + | |
- | and not-characterized parts in the Registry of Standard Parts should
| + | |
- | be removed to an archive after the consent of the designer.</strong>
| + | |
- | </li>
| + | |
- | </ul>
| + | |
- | <p>“It would be great to see some sort of organization like this! I
| + | |
- | agree that unavailable parts should be followed up on and removed if
| + | |
- | necessary. I also think that parts which are not sufficiently documented
| + | |
- | should be highlighted in some way. Once these parts are identified,
| + | |
- | teams can actively characterize them as part of their projects or as
| + | |
- | side projects.” </p>
| + | |
- | <p>“Think about these things: (i) who decides when a part is out-dated,
| + | |
- | and how can that person know that an old part cannot have a novel use
| + | |
- | in the future? (ii) likewise, an uncharacterized part may be both characterized
| + | |
- | and used in the future” </p>
| + | |
- | <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
| + | |
- | are in line with the enforced standards.</i> </p>
| + | |
- | <ul>
| + | |
- | <li><strong>91% of participants have same opinion with us, which
| + | |
- | is that standardization of the nomenclatures used for each different
| + | |
- | composition of parts is necessary.</strong></li>
| + | |
- | </ul>
| + | |
- | <h4>Standards that should be enforced and Additional New Standards
| + | |
- | </h4>
| + | |
- | <p>According to our survey, from high rated to low, these standards
| + | |
- | have been rated which has been used while assigning a name to parts
| + | |
- | </p>
| + | |
- | <ul>
| + | |
- | <li><strong>33% Type of part</strong> </li>
| + | |
- | <li><strong>17% Input</strong> </li>
| + | |
- | <li><strong>17% Output</strong> </li>
| + | |
- | <li><strong>14% Version</strong> </li>
| + | |
- | <li><strong>10% Year</strong> </li>
| + | |
- | <li><strong>9% Group</strong> </li>
| + | |
- | </ul>
| + | |
- | <p>Along with above, having short recognizable part names along with
| + | |
- | function and performance , Genbank/EMBL link and organism information
| + | |
- | is important. </p>
| + | |
- | <ul>
| + | |
- | <li><strong>93% of participants have said that for the parts that
| + | |
- | are marked as “WORKS” distinguishing the parts with quantitative
| + | |
- | experimental validation vs parts without this information is important.</strong>
| + | |
- | Most participants have encountered with similar problems about parts
| + | |
- | that don’t work under their lab conditions or works but not they
| + | |
- | were claimed for. </li>
| + | |
- | <li><strong>89% of participants have same opinion with us, which
| + | |
- | 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 not characterized will be an appropriate measure
| + | |
- | for standardization of Biobrick database.</strong> </li>
| + | |
- | </ul>
| + | |
- | <p><i>In order to overcome these problems we suggest enforcing the working
| + | |
- | conditions title for the registry entrance, in order to collect quantitative
| + | |
- | experimental details on submitted parts, which might slow down the registration
| + | |
- | process but will definitely increase the quality of the database.</i>
| + | |
- | </p>
| + | |
- | <ul>
| + | |
- | <li><strong>61% of participants agree that POPS (Polymerase Per
| + | |
- | Second) should be assigned to every part or biobricks with a promoter,
| + | |
- | where appropriate. - 57% of participants have been agree that RIPS
| + | |
- | (Ribosome per Second) should be assigned to every part or biobricks
| + | |
- | with a RBS brick.</strong> </li>
| + | |
- | </ul>
| + | |
- | <p>Though most participants agree the need for POPS and RBS information
| + | |
- | , they are concerned about the workload it would bring to individual
| + | |
- | labs. </p>
| + | |
- | <p>“To do this, the Registry need to define a reliable and easy method
| + | |
- | of determining the PoPS for teams to use. However, I would say that
| + | |
- | there are better systems for quantifying promoter output than PoPS,
| + | |
- | and they should be used instead, if possible”. </p>
| + | |
- | <ul>
| + | |
- | <li><strong>67% of participants have thought that entering POPS
| + | |
- | information should not be mandatory while submitting new parts.
| + | |
- | Similarly, 65% of participants disagree that entering RIBS information
| + | |
- | should be mandatory while submitting new parts </strong></li>
| + | |
- | </ul>
| + | |
- | <p>Even though the researchers feeling the need for this information
| + | |
- | they are shying away from requesting it as a mandatory title for parts
| + | |
- | registry as it would be difficult for underfunded and inexperienced
| + | |
- | groups to perform these measurements. </p>
| + | |
- | <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
| + | |
- | efficiency of the parts. Additionally iGEM should the responsibility
| + | |
- | and provide the measurements for the each promoter and gene included
| + | |
- | in the distributions. The second choice would be even 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. </i></p>
| + | |
- | <ul>
| + | |
- | <li><strong>82% of participants have thought that information on
| + | |
- | working conditions of the parts should be mandatory while submitting
| + | |
- | new parts.</strong> Most find submiting the detailed experimental
| + | |
- | information and working conditions is crucial and even easier than
| + | |
- | submitting measurements of POPS or RBS. </li>
| + | |
- | </ul>
| + | |
- | <h4>Definitions you would like to see at the Registry of Standard Parts
| + | |
- | </h4>
| + | |
- | <ul>
| + | |
- | <li><strong>Transcriptional efficiency 13%</strong> </li>
| + | |
- | <li><strong>Protein lifetime 10%</strong> </li>
| + | |
- | <li><strong>Ribosome binding efficiency 10%</strong> </li>
| + | |
- | <li><strong>mRNA lifetime 9%</strong> </li>
| + | |
- | <li><strong>Translation initiation and efficiency 9%</strong>
| + | |
- | </li>
| + | |
- | <li><strong>Protein concentration 9%</strong> </li>
| + | |
- | <li><strong>Cooperative effects with other molecules 9%</strong>
| + | |
- | </li>
| + | |
- | <li><strong>Protein-DNA binding rates and efficiencies 8%</strong>
| + | |
- | </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>
| + | |
- | <p>Additional titles includes: Catalytic rates and affinities for substrates,
| + | |
- | leakiness of promoter in lack of stimulus, POPS at various inducer/repressor
| + | |
- | concentrations. </p>
| + | |
- | <h4>Efficiency of the Database Entries </h4>
| + | |
- | <ul>
| + | |
- | <li><strong>86% of participants would like to see a ranking/rating
| + | |
- | 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>
| + | |
- | Few had concerns about how well the rating system will work for
| + | |
- | rarely used parts while the widely used parts would even more popular
| + | |
- | due the the rating system. Still many believes this would be one
| + | |
- | futher towards a peer-reviewed quality control system for the parts.
| + | |
- | </li>
| + | |
- | <li><strong>61% of participants agreed that parts should be updated
| + | |
- | regularly by the designers, where most agreed at least when there
| + | |
- | is new information on the parts.</strong> It has also been suggested
| + | |
- | to give permission to all the users of that part for updating information.
| + | |
- | </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>
| + | |
- | <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
| + | |
- | more efficient” </p>
| + | |
- | <p>“Some parts may be rare or new and have low efficiency, but can be
| + | |
- | very important! Getting rid of them would eliminate any chance of improvement
| + | |
- | to these parts, which not only a qualifier for an iGEM gold medal, but
| + | |
- | also one of the focuses of biobricks.” </p>
| + | |
- | <p><i>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.</i> </p>
| + | |
- | <h4>New Options for the Parts Registry Database </h4>
| + | |
- | <ul>
| + | |
- | <li><strong>96% of participants are like minded with us that it
| + | |
- | will be useful to have a link out to the gene/protein information
| + | |
- | of the parts and - %97 of participants have been agree that they
| + | |
- | 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>
| + | |
- | <h4>NEW PARTS REGISTRY FORM SUGGESTED FOR THE NEW STANDARDS</h4>
| + | |
- | <p><a href=">
| + | |
- | Link out to the form</a><p></p>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | <div class="clear">
| + | |
- | </div>
| + | |
- | <!-- 2nd row -->
| + | |
- | <div class="item">
| + | |
- | </div> | + | |
- | <div class="item">
| + | |
- | </div> | + | |
- | <div class="item"> | + | |
- | </div>
| + | |
- | <div class="item">
| + | |
- | </div>
| + | |
- | <div id="project2" class="item">
| + | |
- | <div class="content2">
| + | |
- | <div class="text">
| + | |
- | <h2>Design</h2>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | <div class="item">
| + | |
- | </div>
| + | |
- | <div id="download2" class="item">
| + | |
- | <div class="content2">
| + | |
- | <div class="text">
| + | |
- | <h2>Code</h2>
| + | |
| </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> |
Line 1,340: |
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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 class="item"> | | <div class="item"> |
| </div> | | </div> |
- | <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">
| |
| </div> | | </div> |
| <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> | | </div> |
| <div class="clear"> | | <div class="clear"> |
| + | </div> |
| + | <!-- 9th row --> |
| + | <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> |
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| + | </div> |
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| + | <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> |
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| </div> | | </div> |
| <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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| </div> | | </div> |
| <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> |
| </li> | | </li> |
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| <li><a class="panel" href="#miscellaneous3">Safety</a></li> | | <li><a class="panel" href="#miscellaneous3">Safety</a></li> |
| <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> |