Team:UC Davis/Database

From 2013.igem.org

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<a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="http://2013.igem.org/wiki/images/9/95/UCD_2013_BCDDv2_Banner.jpg" class="banner" width=967px height=226/></a>
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<a href="http://2013.igem.org/Team:UC_Davis/Database"><img src="http://2013.igem.org/wiki/images/3/30/Depotbanner_UCDavis_mod.jpg" class="banner" width=967px height=226/></a>
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Sharing is what makes us human, but as synthetic biologists, how can we improve the ways we share with each other? Originally proposed as a way for our team to share the multivariate characterization data for our RiboTALs, The Depot was expanded to promote sharing in iGEM for any BioBrick type.  
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The BioBrick Characterization Data Depot (the Depot) is a way for teams to share their characterization data with the world. It uses a <a href="http://2013.igem.org/Team:UC_Davis/Database/Standards">semi-standardized</a> database designed to be both flexible and structured. Originally intended to share the multivariate characterization data of riboTALs, the Depot was repurposed for sharing characterization data of all part types.
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         <a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="http://2013.igem.org/wiki/images/4/4e/Depotbutton_UCDavis.jpg" class="blur"></a>
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        <a href="http://dilbert.cs.ucdavis.edu/Depot/"><h1 id="randcss5">Visit <br> the <br>    Depot</h1></a>
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     <li><a href="#motivation">Motivation</a></li>
     <li><a href="#motivation">Motivation</a></li>
     <li><a href="#approaches">Approaches</a></li>
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     <li><a href="#example_upload">Example Upload</a></li>
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     <li><a href="#upload">Uploading</a></li>
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     <li><a href="#search">Searching</a></li>
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<h1 class="title">Motivation: Empowerment and Openness</h1>
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<h1 class="title">Motivation: Sharing</h1>
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The from the iGEM DNA distribution kit and registry, to the eagerness of faculty and universities across the globe, the iGEM competition empowers students to make a raw idea into a tangible, presentable project. This fact is made clear depth by the number and depth of projects in past years.<a href="#external_links"><sup>1,2</sup></a>
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Our team wanted to share our work in the clearest and most useful way possible, given the multivariance of RiboTals. We did so in the prescribed way of sharing part characterizations through the iGEM registry's experience pages, but excel charts and text summaries left us feeling like we could do more to communicate our work. An imminent solution was to upload our raw, RiboTal data in an intuitive, easy-to-follow form; we implemented such a solution in what we call The Depot, which we expanded to include characterization data for all part types.
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In addition to being a useful way for iGEM-ers to share their data, The Depot can be a platform for iGEM-ers to think about the human elements of synthetic biology. In participating in The Depot, iGEM-ers would encounter issues of sharing raw data such as, <br>  
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However, as BioBrick circuits become more complex, their design process can be dramatically slowed by the large number of relationships and dependencies between their individual parts. Empowering iGEM-ers with an standardized, accessible database for the characterization of BioBrick parts is the clear solution to address problems in high complexity circuits.<a href="#ref">[1]</a>
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-How would others want to use my work? <br>
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-Who is my work relevant to, and how should I account for that? <br>
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-What can be standardized to make shared data comparable, and therefore more useful for everyone? <br><br>
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In addition to empowering iGEM-ers, a uploading data to a standardized characterization database promotes openness. In other biological applications, such as genomic sequencing<a href="#external_links"><sup>3</sup></a> and protein structuring<a href="#external_links"><sup>4</sup></a>, open data is the norm for strong reasons; open data allows communities to validate successes and understand failures, while supporting future researchers downstream. For these reasons, iGEM is founded upon an open community. Open data through the Depot is another way for iGEM-ers to contribute to an open community.
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We are very excited to present The Depot as an intuitive way to share data, as well as a platform to iGEM-ers to think about the human elements of sharing their work.  
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<h1 class="title">Approaches: Past, and the Depot</h1>
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<h1 class="title">Approaches to Data Standardization: </h1>
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Past approaches to designing a BioBrick characterization database dealt with  difficult questions<a href="#external_links"><sup>5</sup></a> dealing with two main topics: what are reasonable standards that a database can enforce, and how to make characterizations across labs or experiments comparable. To answer these questions, one would have to make many, many decisions. Decisions like choosing between the use of different characterization protocols, lab equipment, machine settings, data format, and on and on for each part type.  Additionally, these decisions are posed in a global scale, where accessibility and timetables are major concerns. More so, because synthetic biology is a relatively young field, many facets of part characterizations are likely to change. The complexity of decisions and synthetic biology's youth make shelving the idea of a completely standardized database very appealing.  
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An online database needs its standards; unfortunately, Biobrick-raw-data (BRD), standardization has been and still is a difficult problem to address because it requires answering many interconnected questions of comparability and enforceability<a href="#external_links"><sup>1</sup></a>. Additionally, BRD standardization is even harder to address because the needs of the community, in both and wet and dry lab, are not strictly defined in an young, changing field like synthetic biology.
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Our approach, The Depot, is not an attempt to answer all BRD standardization questions at once. We instead focused two matters, data <b>format</b> standards and openness of raw data, while keeping the aforementioned issues of comparability and enforceability in mind.
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We agreed, at least in some senses. An enforced, strictly standardized database for all part types is unlike our approach we took for the Depot. In our approach, we instead created data and protocol standards for the promoters, a simple part that also have a history<a href="#external_links"><sup>6</sup></a> of data standardization; for the other part types, we created a flexible data format to accommodate different methods of characterization and data types that teams could possibly use.
 
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totally unpolished: For our new part part RiboTal, we wanted to see how it functions before making data standards for it. Go see how we went about answering some data standards issues here: link.
 
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<h1 class="title">Example Upload</h1>
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<h1 class="title">Uploading to the Depot<a href="#top" class="to_top">^back to top</a></h1>
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   The process is straightforward. Users register, then upload their four files that adhere to Depot <a href="http://2013.igem.org/Team:UC_Davis/Database/Standards">standards</a>, as well as other relevant information to their experiment. A prototype page that shows the basic functional elements is shown here. <p><img src="http://2013.igem.org/wiki/images/4/46/UCD_depot_upload.png"></p>
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   The process is straightforward. Users register, then upload their four files that adhere to Depot <a href="http://2013.igem.org/Team:UC_Davis/Database/Standards">standards</a>, as well as other information relevant to their experiment. A prototype page that shows the basic functional elements is shown here.  
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<p><img src="http://2013.igem.org/wiki/images/4/46/UCD_depot_upload.png" class="genpic" width=650></p>
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<h1 class="title">Example Search</h1>
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<h1 class="title">Searching The Depot</h1>
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Search functionality current offers searching for part types across all experiments, or for all data for a particular experiment. The results of your searches are immediately downloadable. Search functionality is to be expanded upon.
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Which results in the downloadable table partially shown here:</p>
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  <img src="http://2013.igem.org/wiki/images/9/99/UCD_search_output.png" class="genpic" height=250 width=650>
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       <a href="http://dilbert.cs.ucdavis.edu/Depot/"><h3>Visit the Depot</h3></a>
       <a href="http://dilbert.cs.ucdavis.edu/Depot/"><h3>Visit the Depot</h3></a>
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       <a href="http://2013.igem.org/Team:UC_Davis/Database/Initial_Population">
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       <a href="http://2013.igem.org/Team:UC_Davis/Database/Initial_Population"><h3>Initial Population</h3></a>
       <a href="http://2013.igem.org/Team:UC_Davis/Database/Initial_Population"><h3>Initial Population</h3></a>
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      <a href="http://2013.igem.org/Team:UC_Davis/Database">
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      <a href="http://2013.igem.org/Team:UC_Davis/Database"><h3>About the Depot</h3></a>
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      <p>Check out the motivations behind the Depot.
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<a id="ref"><h3>References</h3></a>
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[1] M Galdzicki, D Chandran, JH Gennari, HM Sauro, "Design and Analysis of Bio-molecular Circuits", pp. 281, 2011
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<a href="http://link.springer.com/chapter/10.1007/978-1-4419-6766-4_13#page-1">[1] Galdzicki, Michal and Chandran, Deepak and Gennari, John H and Sauro, Herbert M, "Data Model Standardization for Synthetic Biomolecular Circuits and Systems", Design and Analysis of Bio-molecular Circuits, pp. 281, 2011 </a>
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<a id="external_links"><h3>External Links</h3></a>
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<sup>1 </sup><a href="http://2011.igem.org/Jamborees">http://2011.igem.org/Jamborees</a><br>
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<sup>1 </sup><a href="http://openwetware.org/wiki/Parts_characterization#Discussion_Topics">http://openwetware.org/wiki/Parts_characterization#Discussion_Topics</a><br>
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<sup>2 </sup><a href="http://2012.igem.org/Jamborees">http://2012.igem.org/Jamborees</a><br>
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<sup>3 </sup><a href="http://www.ncbi.nlm.nih.gov/genbank">http://www.ncbi.nlm.nih.gov/genbank</a><br>
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<sup>4 </sup><a href="http://www.pdb.org/pdb/home/home.do">http://www.pdb.org/pdb/home/home.do</a><br>
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<sup>5 </sup><a href="http://openwetware.org/wiki/Parts_characterization#Discussion_Topics">http://openwetware.org/wiki/Parts_characterization#Discussion_Topics</a><br>
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<sup>6 </sup><a href="http://www.jbioleng.org/content/3/1/4">http://www.jbioleng.org/content/3/1/4</a>
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Latest revision as of 03:46, 29 October 2013

Sharing is what makes us human, but as synthetic biologists, how can we improve the ways we share with each other? Originally proposed as a way for our team to share the multivariate characterization data for our RiboTALs, The Depot was expanded to promote sharing in iGEM for any BioBrick type.

Motivation: Sharing

Our team wanted to share our work in the clearest and most useful way possible, given the multivariance of RiboTals. We did so in the prescribed way of sharing part characterizations through the iGEM registry's experience pages, but excel charts and text summaries left us feeling like we could do more to communicate our work. An imminent solution was to upload our raw, RiboTal data in an intuitive, easy-to-follow form; we implemented such a solution in what we call The Depot, which we expanded to include characterization data for all part types.

In addition to being a useful way for iGEM-ers to share their data, The Depot can be a platform for iGEM-ers to think about the human elements of synthetic biology. In participating in The Depot, iGEM-ers would encounter issues of sharing raw data such as,
-How would others want to use my work?
-Who is my work relevant to, and how should I account for that?
-What can be standardized to make shared data comparable, and therefore more useful for everyone?

We are very excited to present The Depot as an intuitive way to share data, as well as a platform to iGEM-ers to think about the human elements of sharing their work.

Approaches to Data Standardization:

An online database needs its standards; unfortunately, Biobrick-raw-data (BRD), standardization has been and still is a difficult problem to address because it requires answering many interconnected questions of comparability and enforceability1. Additionally, BRD standardization is even harder to address because the needs of the community, in both and wet and dry lab, are not strictly defined in an young, changing field like synthetic biology.

Our approach, The Depot, is not an attempt to answer all BRD standardization questions at once. We instead focused two matters, data format standards and openness of raw data, while keeping the aforementioned issues of comparability and enforceability in mind.

Uploading to the Depot^back to top

The process is straightforward. Users register, then upload their four files that adhere to Depot standards, as well as other information relevant to their experiment. A prototype page that shows the basic functional elements is shown here.

Searching The Depot

Search functionality current offers searching for part types across all experiments, or for all data for a particular experiment. The results of your searches are immediately downloadable. Search functionality is to be expanded upon.

Which results in the downloadable table partially shown here:

Visit the Depot

Data Standards

See the Depot's standards and data requirements so you can share your data as well.

Initial Population

See how we initially populated the Depot.

About the Depot

Check out the motivations behind the Depot.