Difference between revisions of "Team:Michigan Software/Description"

 
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<h2> Project Description </h2>
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<h1> Project Description </h1>
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Choosing apt and reliable protocols for new experiments is a problem that productive wet labs routinely face. However, it is difficult to know in detail which protocols will produce the best results. Experimental practices may differ immensely across laboratories, and precise details of these practices may be lost or forgotten as skilled faculty or students leave the lab to pursue other endeavors. These two realities give rise to a vast number of experimental protocols of which many are left with undocumented experiential knowledge. Furthermore, no tool yet exists to allow wet lab investigators to measure and compare the efficacy of protocols before executing them forthright.
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<h2>The Problem</h2>
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;At its core, synthetic biology is the practice of genetically engineering novel organisms to perform a particular function. However, <a href="https://peerj.com/articles/148">recent review studies</a> estimate only 10-25% of published scientific results are reproducible. A <a href="https://2014.igem.org/Team:Michigan_Software/Project#Description">2014 survey</a> conducted by the University of Michigan Biological Software Team confirmed that the repeatability problem exists in synthetic biology, with <em>every scientist surveyed reporting prior struggles with replicating protocols.</em> The majority of these scientists indicate <em>unclear language and missing steps</em> are the greatest contributors to the irreproducibility of synthetic biology protocols. A <a href="https://2015.igem.org/Team:Michigan_Software/Outreach">follow up study</a> was conducted by this year's Software team, resulting in similar conclusions. ProtoCat 2.0 is designed to address both of these issues by making it easier for scientists to share troubleshooting techniques and submit edits to existing protocols.  
  
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<h2>The Solution</h2>
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Such fragmentation in protocol methods and their documentation may to some degree hamper scientific progress. From the immense number of protocols currently in use, there are few well-defined protocols that are generally agreed upon by the scientific community, in part due to the lack of a system that can supply a measure of a protocol’s acceptance compared to its variants. In turn, the lack of commonly accepted protocols and their inadequate documentation has the potential to affect experimental reproducibility through method inconsistencies across laboratories and across succession of investigators.
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Every respondent indicated that they would use a database to browse and download protocols, <em>with over 85% indicating that they would upload and maintain their own protocols if such a site existed</em>. ProtoCat 2.0 is a free database of crowd sourced protocols designed to make existing protocols more repeatable and enable more accurate computational models of biological systems. We believe this can most efficiently be accomplished with a commitment to open source protocols and a broader more active community of digital troubleshooters. ProtoCat 2.0 works to establish such a community by giving anyone with an internet connection or smartphone access to a repository of synthetic biology protocols collected from all over the world. Additionally, ProtoCat 2.0 encourages the development of higher quality, more repeatable protocols by allowing users to document trails, rate, review, and edit existing methods, and easily locate related protocols.
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<img src = "https://static.igem.org/mediawiki/2015/7/7f/Team_Michigan_Software_Collaboration.png" width=24% />
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In order to address these problems, we set out to build a database that integrates a crowdsourced ratings and comments system to clearly document, rate, elaborate, review, and organize variants of experimental protocols. Such a tool serves as a curator for protocol variants and enables wet lab investigators to compare protocol efficacies. Furthermore, the crowdsourced ratings system quantifies a protocol’s acceptance within the scientific community and can serve as a useful criterion to assist with finding and selecting from common protocols. In addition, a protocol comments system provides an avenue through which experiential knowledge can be passed along. As an extension to the protocol database, we will also develop a dynamic calculator that can run user-defined theoretical calculations for any protocol, such as limiting reagent, yield, or even the monetary cost of the materials used. The calculator further assists investigators in comparing and performing protocols. In all, these tools will help wet lab investigators to document, organize, and compare protocols to assist with scientific experimentation.
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<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
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<h5>What should this page contain?</h5>
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<li> A clear and concise description of your project.</li>
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<li>A detailed explanation of why your team chose to work on this particular project.</li>
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<li>References and sources to document your research.</li>
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<h4>Advice on writing your Project Description</h4>
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We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.
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Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
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<h4>References</h4>
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<p>iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you though about your project and what works inspired you.</p>
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<h4>Inspiration</h4>
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<p>See how other teams have described and presented their projects: </p>
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<li><a href="https://2014.igem.org/Team:Imperial/Project"> Imperial</a></li>
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<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> UC Davis</a></li>
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<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">SYSU Software</a></li>
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Latest revision as of 14:01, 18 September 2015


Michigan Software 2015

Project Description

The Problem

     At its core, synthetic biology is the practice of genetically engineering novel organisms to perform a particular function. However, recent review studies estimate only 10-25% of published scientific results are reproducible. A 2014 survey conducted by the University of Michigan Biological Software Team confirmed that the repeatability problem exists in synthetic biology, with every scientist surveyed reporting prior struggles with replicating protocols. The majority of these scientists indicate unclear language and missing steps are the greatest contributors to the irreproducibility of synthetic biology protocols. A follow up study was conducted by this year's Software team, resulting in similar conclusions. ProtoCat 2.0 is designed to address both of these issues by making it easier for scientists to share troubleshooting techniques and submit edits to existing protocols.

The Solution

     Every respondent indicated that they would use a database to browse and download protocols, with over 85% indicating that they would upload and maintain their own protocols if such a site existed. ProtoCat 2.0 is a free database of crowd sourced protocols designed to make existing protocols more repeatable and enable more accurate computational models of biological systems. We believe this can most efficiently be accomplished with a commitment to open source protocols and a broader more active community of digital troubleshooters. ProtoCat 2.0 works to establish such a community by giving anyone with an internet connection or smartphone access to a repository of synthetic biology protocols collected from all over the world. Additionally, ProtoCat 2.0 encourages the development of higher quality, more repeatable protocols by allowing users to document trails, rate, review, and edit existing methods, and easily locate related protocols.
                Share it                                                              Try it                                                   Like it