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

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                <h1>Michigan Software Team<br>ProtoCat 3.0 - Project Description</h1>
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<br>
  
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<h3>Background</h3>
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<p>Two years ago the Michigan Biology Software team began development of Protocat 1.0. Like many innovative ideas, Protocat began because of a problem. *Studies* have estimated that only 10-25% of published scientific results are reproducible.  A 2014 survey conducted by the Michigan Biosoft 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 *second study* conducted by last years designed team helped to confirm the sentiments of the first study. These issues are what Protocat has been designed to solve.</p>
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<p><h3 class="grey-text heading-weight">Background</h3><p>
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<p class="p-font grey-text">Two years ago the Michigan Software 2014 team began development of ProtoCat 1.0. Like many innovative ideas, ProtoCat began because of a problem. <a class="a-over" href="https://peerj.com/articles/148">Studies</a> have estimated that only 10-25% of published scientific results are reproducible.  A 2014 survey conducted by the Michigan 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 indicated unclear language and missing steps are the greatest contributors to the irreproducibility of synthetic biology protocols. A <a class="a-over" href="https://2015.igem.org/Team:Michigan_Software/Outreach">second study</a> conducted by last year's Michigan Software team only further confirmed the sentiments of the first study. These issues are what ProtoCat has been designed to solve.</p>
  
 
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<h3>Solution</h3>
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<p><h3 class="grey-text heading-weight">Solution</h3></p>
  
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<p>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 3.0 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 3.0 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 3.0 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.</p>
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<p class="p-font grey-text">Every respondent of the second survey 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 3.0 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 3.0 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 3.0 encourages the development of higher quality, more repeatable protocols by allowing users to document, rate, review, and edit existing methods.</p>
  
 
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<h3>Whats new in Protocat 3.0?</h3>
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<p><h3 class="grey-text heading-weight">What's new in ProtoCat 3.0?</h3></p>
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<p class="p-font grey-text">ProtoCat 3.0 is a complete re-imagining of the ProtoCat software that has been in development for the last two years. By making dramatic changes to how we store protocols, we have been able to add new features that would have been impossible before. These features include variable reagent calculations, allowing users to scale the amounts in a protocol to their liking, and timers on a per-step basis. We have also made it possible to link to specific reagents so that users can immediately learn more about the reagents used in the protocol. Another benefit to the new protocol model is that the user is able to upload fully customized steps and, unlike in previous versions of ProtoCat, add warnings to necessary steps. ProtoCat also supports full version control of uploaded procedures, where a user can track the revisions made and access previous versions. Additional benefits include a brand new category system, a better and more dynamic user interface, more sorting and filtering options, and a more advanced user page.</p>
  
 
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<h5>Advice on writing your Project Description</h5>
 
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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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<h5>References</h5>
 
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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 thought about your project and what works inspired you.</p>
 
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<h5>Inspiration</h5>
 
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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 02:14, 19 October 2016

Michigan Software Team
ProtoCat 3.0 - Project Description


Background

Two years ago the Michigan Software 2014 team began development of ProtoCat 1.0. Like many innovative ideas, ProtoCat began because of a problem. Studies have estimated that only 10-25% of published scientific results are reproducible. A 2014 survey conducted by the Michigan 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 indicated unclear language and missing steps are the greatest contributors to the irreproducibility of synthetic biology protocols. A second study conducted by last year's Michigan Software team only further confirmed the sentiments of the first study. These issues are what ProtoCat has been designed to solve.


Solution

Every respondent of the second survey 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 3.0 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 3.0 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 3.0 encourages the development of higher quality, more repeatable protocols by allowing users to document, rate, review, and edit existing methods.


What's new in ProtoCat 3.0?

ProtoCat 3.0 is a complete re-imagining of the ProtoCat software that has been in development for the last two years. By making dramatic changes to how we store protocols, we have been able to add new features that would have been impossible before. These features include variable reagent calculations, allowing users to scale the amounts in a protocol to their liking, and timers on a per-step basis. We have also made it possible to link to specific reagents so that users can immediately learn more about the reagents used in the protocol. Another benefit to the new protocol model is that the user is able to upload fully customized steps and, unlike in previous versions of ProtoCat, add warnings to necessary steps. ProtoCat also supports full version control of uploaded procedures, where a user can track the revisions made and access previous versions. Additional benefits include a brand new category system, a better and more dynamic user interface, more sorting and filtering options, and a more advanced user page.