Team:Paris Bettencourt/SensiGEM

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<div id="grouptitle">SensiGEM: A biosensor database</div>
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<p><i>Please shut off your ad-blocker utility should <a href="http://www.sensigem.org/">SensiGEM</a> not appear. You may also wish to see a graphical explanation of the <a href="#Explanation">database below</a>.</i></p>
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      <p><br>SensiGEM is the iGEM Biosensor database generated by the teams Paris Bettencourt 2013 and Calgary 2013. In this database you can find fast and easy what biosensor projects were already done by past iGEM Teams. Up to now, SensiGEM is a searchable database for all biosensors in iGEM, but we hope that many other project categories will follow soon.  To be able to select the projects that fit into the database, we composed a joint definition of what is a biosensor according to the Calgary-Paris collaboration, after reading and discussing.</p>
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      <p>Together with our collaborate the iGEM Team Calgary 2013 we identified all the different biosensors in the registry, added them</p>
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      <p><br>into our database and categorized them by years. To adapt the database to needs of the user, we integrated an interface that allows an easy search through the database after different criteria that can be selected. It is possible to search after teams, years, tracks, inputs/outputs, awards and much more. But also a keyword search is integrated.</p>
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       <p>With this work we hope to help future teams as well as others interested in biosensors to get an overview of what has been done in iGEM so far. It might also be a helo for future iGEM teams to select a new biosensor project. Have a look how to use SensiGEM!
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  <h2>Step 1</h2>
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  <p>One reaching sensigem.org, you will see a list of all biosensor projects which have been entered in the iGEM competition since 2007. You may scroll through this list, or filter the projects by clicking the "filter projects" button at the to of the page.</p>
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<h2>Step 2</h2>
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<p>The "filter projects" dialogue will open a window, allowing you to search and sort the database by multiple parameters. These include team name, year, and project category, as well as the ability to search by the input the sensor responds to and the output that it gives as a response.<>
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<h2>Step 3</h2>
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<p>Sorting will return a list of projects which match the category you are interested in. Each project provides the information pertaining to the team which developed it, the project abstract, as well as information about the track, uses, applications, and inputs/outputs of the sensor. A link to the project wiki also is provided if further details are desired.</p>
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      <p><b>The Paris-Bettencourt-Calgary iGEM collaboration started last June when a few members from each team met at the SB6.0 synbio conference in London. After a few beers and lab stories, we learned that despite coming from the opposite sides of the globe, we were using synthetic biology to build biosensors to sense DNA. While our systems were targeted solve different problems, we were struck by a number of commonalities between these projects. Please see the Figure 1 for a breakdown of these differences.
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       <p>As we shared our projects, we recalled how there was a lack of DNA biosensor parts in the Parts Registry. Moreover, we complained about the lack of organization of biosensors in the registry. The veteran iGEMers on each team mentioned that biosensors had consistently finished as grand prize winners in previous years of iGEM. We were curious how biosensors have evolved since the beginning of iGEM and how our projects fit into the context of the iGEM Parts Registry.
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    <p><i>Please shut off your ad-blocker utility should <a href="http://www.sensigem.org/">SensiGEM</a> not appear. You may also wish to see a graphical explanation of the <a href="#Explanation">database below</a>.</i></p>
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<b>Figure 1.</b> The Calgary and Paris Bettencourt biosensors both sense DNA, albeit with some differences in how they function mechanistically.
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  <h2>SensiGEM - A biosensor database</h2>
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    We decided to collaborate to answer these questions. Since our initial meeting in London, members of each team have conferenced weekly on Skype. After accustoming ourselves to the eight hour time difference, we developed SensiGEM, a collaborative database in which we catalogued all the biosensors in the history of iGEM.
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    Before sinking our teeth into past Wikis, we realized that we had different definitions of biosensors. We asked each other a fundamental question: What is a biosensor? We developed the following definition: A biosensor is an engineered system that relies on biological systems or components to detect and report a condition. The condition(s) detected and reported could encompass an environmental, biological, chemical or synthetic aspect or compound in the sensor’s environment or surroundings.
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Once agreeing on the nature of biosensors, we split up the Wikis from 2007 onward between Calgary and Paris-Bettencourt. We analyzed 936 project Wikis from 2007 to 2013 by hand, incorporating the projects which matched our biosensor definition into the collaborative SensiGEM database. We included 229 projects on </p>
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    <p> the database, some of which were biosensors as per the definition, as well as other projects containing biosensor elements that aligned with our definition.</p>
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     <p>We designed this database with future iGEM teams in mind, with tools for efficient navigation biosensors according to inputs, outputs, and their intended application. We made both SensiGEM’s source code and underlying data available under the permissive MIT license. This means that other teams can either collaborate with us on our version of the database or host their own independent copies. We foresee SensiGEM as a resource where future iGEM teams can showcase their biosensors.<br>
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  <h2>Lessons from SensiGEM</h2>
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     <p>We conducted some preliminary analysis of the database in SensiGEM to see how our projects stand in the current iGEM biosensor landscape.</p>
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     <p>We conducted some preliminary analysis of the database in SensiGEM to see how our projects stand in the current iGEM biosensor landscape as well as to get an overview of what types of biosensors have been developed for iGEM.<br>
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In Figure 2, we can see the portion of biosensors of all iGEM projects since 2007. There is a clear linear increase in number of iGEM projects, but the number of biosensors per year varies and doesn’t follow a trend.<br>
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How successful Biosensor were in the previous years (Advance to Championship, Awards, Finalists) can be seen in Figure 3. Something that also interested us was to see how many biosensors are in the Track Health and Medicine as we developed a biosensor for that Category (Figure 4). Other facts we wanted get from the database are, how many biosensors already targeted DNA (Figure 5) and what is the distribution of other inputs, sensed by previous biosensors (Figure 6).</p>
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<b>Figure 5.</b> Number of iGEM biosensor projects in comparison to how many of these targeted DNA like the Calgary team and we did.<br>
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<h2>Step 1</h2>
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<p>One reaching sensigem.org, you will see a list of all biosensor projects which have been entered in the iGEM competition since 2007. You may scroll through this list, or filter the projects by clicking the "filter projects" button at the to of the page.</p>
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<b>Figure 6.</b> Overview of the different types of inputs for the biosensors in iGEM and how many teams used those inputs since 2007.<br>
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<b>Figure 2.</b> Number of iGEM projects since 2007 in comparison to number of Biosensor iGEM projects since 2007.<br>
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<p>The "filter projects" dialogue will open a window, allowing you to search and sort the database by multiple parameters. These include team name, year, and project category, as well as the ability to search by the input the sensor responds to and the output that it gives as a response.
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<b>Figure 3.</b> Success of Biosensor iGEM projects since 2007. Listed are the numbers of teams that advanced to the Championship (since 2009), that won awards or were finalists (since 2007).<br>
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<b>Figure 4.</b> Number of iGEM projects since 2007 in the Track Helath and Medicine and how many of these are/were biosensors<br>
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<p>Sorting will return a list of projects which match the category you are interested in. Each project provides the information pertaining to the team which developed it, the project abstract, as well as information about the track, uses, applications, and inputs/outputs of the sensor. A link to the project wiki also is provided if further details are desired.</p>
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    <p>Given the similarities between each of our systems in overall function, we have begun development of BioBricks to apply each system to the other team's problem. By testing each system on a different problem, we intend to show how each system can be deployed as a modular, platform technology.</p>
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<p>We also intend to further improve our database to more easily get information of the actual sensing system (sensitive/inducible promoter, other targeting methods like CRISPRs, TALEs,…).</p>
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    <p>Important for the success of our cooperation was to regularly see each other on Skype. It is way easier to talk in person than to communicate by mail as misunderstandings and questions could be solved directly. We used Asana.com to set up tasks for each team that completed until the next week. Setting up those weekly tasks was a good idea as we were not overwhelmed by a lot of work but having those small tasks we could process them in time. Also the splitting up of work, as we did for example for the Wikis, was very helpful and part of the success to reach our goal in time.<br>
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    <p>For future collaborations, setting up weekly tasks and skyeing every week worked well for us! Also important is that both teams have the same idea of the aim of the collaboration as well as how to achieve it. With the Calgary Team 2013 we found a great partner that fit to what we imagined!</p>
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Latest revision as of 14:39, 26 October 2013


SensiGEM is the iGEM Biosensor database generated by the teams Paris Bettencourt 2013 and Calgary 2013. In this database you can find fast and easy what biosensor projects were already done by past iGEM Teams. Up to now, SensiGEM is a searchable database for all biosensors in iGEM, but we hope that many other project categories will follow soon. To be able to select the projects that fit into the database, we composed a joint definition of what is a biosensor according to the Calgary-Paris collaboration, after reading and discussing.

Together with our collaborate the iGEM Team Calgary 2013 we identified all the different biosensors in the registry, added them


into our database and categorized them by years. To adapt the database to needs of the user, we integrated an interface that allows an easy search through the database after different criteria that can be selected. It is possible to search after teams, years, tracks, inputs/outputs, awards and much more. But also a keyword search is integrated.

With this work we hope to help future teams as well as others interested in biosensors to get an overview of what has been done in iGEM so far. It might also be a helo for future iGEM teams to select a new biosensor project. Have a look how to use SensiGEM!

Please shut off your ad-blocker utility should SensiGEM not appear. You may also wish to see a graphical explanation of the database below.

Step 1

One reaching sensigem.org, you will see a list of all biosensor projects which have been entered in the iGEM competition since 2007. You may scroll through this list, or filter the projects by clicking the "filter projects" button at the to of the page.

Step 2

The "filter projects" dialogue will open a window, allowing you to search and sort the database by multiple parameters. These include team name, year, and project category, as well as the ability to search by the input the sensor responds to and the output that it gives as a response.

Step 3

Sorting will return a list of projects which match the category you are interested in. Each project provides the information pertaining to the team which developed it, the project abstract, as well as information about the track, uses, applications, and inputs/outputs of the sensor. A link to the project wiki also is provided if further details are desired.

Centre for Research and Interdisciplinarity (CRI)
Faculty of Medicine Cochin Port-Royal, South wing, 2nd floor
Paris Descartes University
24, rue du Faubourg Saint Jacques
75014 Paris, France
+33 1 44 41 25 22/25
team2013@igem-paris.org
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