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

 
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<h2> Project Results</h2>
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<h1> Project Results</h1>
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<p>
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Protocat 2.0 is a crowd sourced catalog of protocol. Non-registered users can only search for and access the protocols stored in our database. On the other hand, registered users have access to Protocat 2.0's full capabilities. In addition to searching for protocol, registered users can upload and edit protocol of their own their own. Registered users can also rate and comment on others' protocol, generating feedback for the author about the efficacy of his/her protocol.
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<center><img src="https://static.igem.org/mediawiki/2015/8/88/Team_Michigan_Software_Usage.png" width=500px /></center>
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<br><br>
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<div class="NEW">
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<h3> New Features in Protocat 2.0: </h3>
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<ul>
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<li>Refined search engine</li>
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<li>Protocol can be rated</li>
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<li>Protocol can be both sorted and reverse sorted</li>
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<li>Protocat users can register an account and have user pages</li>
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</ul>
  
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New features: sorting, sophisticated search engine, rating, user page, editing protocol
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<br>
  
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<h3> Future Improvements </h3>
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<ul>
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<li>Implement version control</li>
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<li>Implement variable protocol for limited supplies of reagents</li>
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<li>Implement experiment modeling</li>
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<li>Implement a timer for time-sensitive protocol</li>
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<li>Link users to reagent suppliers</li>
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<li>Grow protocat userbase and protocol repository</li>
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</ul>
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</div>
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<img src="https://static.igem.org/mediawiki/2015/8/83/Team_Michigan_Software_Improve.png" width=45%/>
  
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<p> The Future of ProtoCat
 
  
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<p> Future development of ProtoCat focuses on expanding our library of protocols by mining methods from other digital publishing sources (e.g. protocols.io and open wet ware) and aggregating them in one central location. The user interface will also be further developed to automate calculations of protocol parameters like (reagent volumes and reactant proportions). Other improvements to the user experience include direct links to safety and storage information about the materials used in the protocol as well as access to a platform for purchasing requisite materials and equipment from partnering vendors. Finally, the next geneation of ProtoCat incorporates modeling software to enable virtual trials for the purpose of optimizing experimental design. For example, ProtoCat could simulate a PCR of a specified target sequence using a variety of primers to see which primer produces the highest yield or run virtual ligations of two specified sequences at different proportions to discern the ratio which produces the highest plasmid yield.
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<h3> Medal Requirements</h3>
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<h4>Bronze</h4>
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<ul>
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<li>
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<i>Register for iGEM, have a great summer, and attend the Giant Jamboree.</i>
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<span class="list">DONE</span>
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</li>
  
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<h4> Project Achievements </h4>
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<li>
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<i>Complete the Judging form.</i>
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<span class="list">DONE</span>
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</li>
  
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<h4> Further Improvements </h4>
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<li>
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<p></p>
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<i>Create and share a Description of the team's project using the iGEM wiki, and document the team's parts (if any) using the Registry of Standard Biological Parts.</i>  
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Look to add: Version control, Timer, Variable protocols, Experiment Modeling, In app purchasing, grow both users/members
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<span class="list"><a href="https://2015.igem.org/Team:Michigan_Software/Description">DONE</a></span>
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<p> If we are to continue, what are things we are looking to improve> </p>
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</li>
  
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<h4>Inspiration</h4>
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<li>
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<p>See how other teams presented their results.</p>
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<i>Present a poster and a talk at the iGEM Jamboree. See the 2015 poster guidelines for more information.</i>  
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<span class="list">DONE</span>
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</li>
 +
 
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<li>
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<i>Create a page on your team wiki with clear attribution of each aspect of your project. This page must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services.</i>
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<a href="https://2015.igem.org/Team:Michigan_Software/Attribution">DONE</a>
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</li>
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<li>
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<i>Develop and make available, via the iGEM GitHub page, an open source software that supports Synthetic Biology based on Standard Parts or interacts with the Registry.</i>
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<a href="https://github.com/igemsoftware/Michigan15"> DONE</a>
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</li>
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</ul>
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<h4>Silver</h4>
 
<ul>
 
<ul>
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<li><a href="https://2014.igem.org/Team:TU_Darmstadt/Results/Pathway">2014 TU Darmstadt </a></li>
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<li>
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<li><a href="https://2014.igem.org/Team:Imperial/Results">2014 Imperial </a></li>
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<i>Provide a comprehensive, well-designed User Guide for your software and upload it to your wiki. Be creative! (An instructional video may work as well.)</i>
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<li><a href="https://2014.igem.org/Team:Paris_Bettencourt/Results">2014 Paris Bettencourt </a></li>
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<a href="https://2015.igem.org/Team:Michigan_Software/UserGuide">DONE</a>
 +
</li>
 +
 
 +
<li>
 +
<i>Develop a well documented library or API for other developers (rather than "only" a stand-alone app for end users.)</i>  
 +
<a href="https://2015.igem.org/Team:Michigan_Software/Documentation">DONE</a>
 +
</li>
 +
 
 +
<li>
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<i>Demonstrate that you followed best practices in software development so that other developers can modify, use, and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of test coverage, bug tracking facilities, and documentation of releases and changes between releases.</i>
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<span class="list">DONE <a href="https://github.com/igemsoftware/Michigan15">Code</a>and <a href="https://static.igem.org/mediawiki/2015/8/83/Team_Michigan_Software_TC.png">Test Coverage</a></span>
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</li>
 +
</ul>
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 +
 
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<h4>Gold</h4>
 +
<ul>
 +
<li>
 +
<i>iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, and intellectual property rights. We refer to these activities as Human Practices in iGEM. Demonstrate how your team has identified, investigated and addressed one or more of these issues in the context of your project.</i>
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<a href="https://2015.igem.org/Team:Michigan_Software/Practices">DONE</a>
 +
</li>
 +
 
 +
<li>
 +
<i>Address a problem that you would like to co-develop with a wetlab team. This should be a collaboration where the wetlab team posts a problem they are having and your team addresses the issue by creating an online software solution.</i>
 +
<span class="list">Protocat was designed based on a <a href="https://2015.igem.org/Team:Michigan_Software/Practices">survey</a> we sent to lab teams.</span>
 +
</li>
 +
 
 +
<li>
 +
<i>Re-use and further develop a previous iGEM software project (or parts thereof) and demonstrate how future teams can continue this trend through good code documentation, use of open source materials and creation of great instructional materials.</i>
 +
<span class="list">We expanded upon <a href="https://2014.igem.org/Team:Michigan_Software">Michigan Software 2014's project.</a></span>
 +
</li>
 +
 
 +
<li>
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<i>Demonstrate your software at the iGEM Giant Jamboree in the software demo suite. You should show a functional prototype that teams can use in following years.</i>
 +
<span class="list">DONE</span>
 +
</li>
 
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Latest revision as of 14:05, 18 September 2015


Michigan Software 2015

Project Results

Protocat 2.0 is a crowd sourced catalog of protocol. Non-registered users can only search for and access the protocols stored in our database. On the other hand, registered users have access to Protocat 2.0's full capabilities. In addition to searching for protocol, registered users can upload and edit protocol of their own their own. Registered users can also rate and comment on others' protocol, generating feedback for the author about the efficacy of his/her protocol.



New Features in Protocat 2.0:

  • Refined search engine
  • Protocol can be rated
  • Protocol can be both sorted and reverse sorted
  • Protocat users can register an account and have user pages

Future Improvements

  • Implement version control
  • Implement variable protocol for limited supplies of reagents
  • Implement experiment modeling
  • Implement a timer for time-sensitive protocol
  • Link users to reagent suppliers
  • Grow protocat userbase and protocol repository

Medal Requirements

Bronze

  • Register for iGEM, have a great summer, and attend the Giant Jamboree. DONE
  • Complete the Judging form. DONE
  • Create and share a Description of the team's project using the iGEM wiki, and document the team's parts (if any) using the Registry of Standard Biological Parts. DONE
  • Present a poster and a talk at the iGEM Jamboree. See the 2015 poster guidelines for more information. DONE
  • Create a page on your team wiki with clear attribution of each aspect of your project. This page must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services. DONE
  • Develop and make available, via the iGEM GitHub page, an open source software that supports Synthetic Biology based on Standard Parts or interacts with the Registry. DONE

Silver

  • Provide a comprehensive, well-designed User Guide for your software and upload it to your wiki. Be creative! (An instructional video may work as well.) DONE
  • Develop a well documented library or API for other developers (rather than "only" a stand-alone app for end users.) DONE
  • Demonstrate that you followed best practices in software development so that other developers can modify, use, and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of test coverage, bug tracking facilities, and documentation of releases and changes between releases. DONE Codeand Test Coverage

Gold

  • iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, and intellectual property rights. We refer to these activities as Human Practices in iGEM. Demonstrate how your team has identified, investigated and addressed one or more of these issues in the context of your project. DONE
  • Address a problem that you would like to co-develop with a wetlab team. This should be a collaboration where the wetlab team posts a problem they are having and your team addresses the issue by creating an online software solution. Protocat was designed based on a survey we sent to lab teams.
  • Re-use and further develop a previous iGEM software project (or parts thereof) and demonstrate how future teams can continue this trend through good code documentation, use of open source materials and creation of great instructional materials. We expanded upon Michigan Software 2014's project.
  • Demonstrate your software at the iGEM Giant Jamboree in the software demo suite. You should show a functional prototype that teams can use in following years. DONE