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

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<h1>Measurement</h1>
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<p>There are a lot of exciting parts in the Registry, but many parts have still not been characterized. Synthetic Biology needs great measurement approaches for characterizing new parts, and efficient new methods for characterizing many parts at once. If you've done something exciting in the area of Measurement, describe it here!</p>
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                  <img class = "Header-img" src="https://static.igem.org/mediawiki/2017/9/9a/MichiganSoftware_2017_overview.png" />
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                  <h1 id = "headerImageh1">Measurement</h1>
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<h3>Best Innovation in Measurement Special Prize</h3>
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<p>If you've done excellent work in measurement, you should consider nominating your team for this special prize. Designing great measurement approaches for characterizing new parts or developing and implementing an efficient new method for characterizing thousands of parts are good examples.
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To compete for the <a href="https://2017.igem.org/Judging/Awards">Best Innovation in Measurement prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>.
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You must also delete the message box on the top of this page to be eligible for this prize.
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            <h1 class="grey-text heading-weight" align = "center">Background</h1>
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<h5>Inspiration</h5>
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<p>You can look at what other teams did to get some inspiration! <br />
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Here are a few examples:</p>
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<li><a href="https://2016.igem.org/Team:Stanford-Brown">2016 Stanford-Brown</a></li>
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<li><a href="https://2016.igem.org/Team:Genspace">2016 Genspace</a></li>
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            <p id = "doubleSpace" class="p-font grey-text">Two years ago the Michigan Software 2014 team began development
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<li><a href="https://2015.igem.org/Team:William_and_Mary">2015 William and Mary</a></li>
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              of ProtoCat 1.0. Like many innovative ideas, ProtoCat began because of a problem.
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<li><a href="https://2014.igem.org/Team:Aachen">2014 Aachen  </a></li>
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              <a class="a-over" href="https://peerj.com/articles/148">Studies</a> have estimated
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              that only 10-25% of published scientific results are reproducible.  A 2014 survey conducted
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              by the Michigan Software team confirmed that the repeatability problem exists in synthetic
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              biology, with every scientist surveyed reporting prior struggles with replicating protocols.
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              The majority of these scientists indicated unclear language and missing steps are the greatest
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              contributors to the irreproducibility of synthetic biology protocols. A <a class="a-over"
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                  href="https://2015.igem.org/Team:Michigan_Software/Outreach">second study</a> conducted by last
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              year's Michigan Software team only further confirmed the sentiments of the first study. These
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              issues are what ProtoCat has been designed to solve.
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            </p>
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            <h1 class="grey-text heading-weight" align = "center">Solution</h1>
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            <p id = "doubleSpace" class="p-font grey-text">Every respondent of the second survey indicated that they
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              would use a database to browse and download protocols, with over 85% indicating that
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              they would upload and maintain their own protocols if such a site existed. ProtoCat 3.0
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              is a free database of crowd sourced protocols designed to make existing protocols more
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              repeatable and enable more accurate computational models of biological systems. We believe
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              this can most efficiently be accomplished with a commitment to open source protocols and a
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              broader more active community of digital troubleshooters. ProtoCat 3.0 works to establish
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              such a community by giving anyone with an internet connection or smartphone access to a
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              repository of synthetic biology protocols collected from all over the world. Additionally,
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              ProtoCat 3.0 encourages the development of higher quality, more repeatable protocols by
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              allowing users to document, rate, review, and edit existing methods.
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            <h1 class="grey-text heading-weight" align = "center">ProtoCat 4.0</h1>
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            <br>
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            <br>
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            <p id = "doubleSpace" class="p-font grey-text">ProtoCat 4.0 is optimized for collaboration among users
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              and offers the best user experinece we have developed. We've added features such as threaded comments,
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              notifications, protocol favoriting, and a new chat system called ProtoChat in this
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              years verions of ProtoCat. Now users can communicate through commenting and chatting
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              to make improvements on existing protocols or favorite one they like to quickly relocate
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              it. ProtoCat also recieved a password recover system, notifications, and a better search
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              algorithm to search more fields of a protocol. In addition, users can now create drafts
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              of a protocol which allows them to start and finish a new protocol at their convienience.
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              These are are all important features that contribute to a better user experience and our
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              best version of ProtoCat.
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            </p>
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      <footer id = "footer">
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                  <h3 id = "h3Header">Important Links:</h3>
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                      <tr>
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                        <td>
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                          <p><a href="https://2017.igem.org/Team:Michigan_Software/Overview">Overview</a></p>
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                        </td>
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                        <td>
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                          <p><a href="https://2017.igem.org/Team:Michigan_Software/Results">Results</a></p>
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                          <p><a href="https://2017.igem.org/Team:Michigan_Software/Installation">Installation</a></p>
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                        </td>
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                        <td>
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                          <p><a href="https://2017.igem.org/Team:Michigan_Software/Collaboration">Collaboration</a></p>
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                        <p><a href="https://2017.igem.org/Team:Michigan_Software/HP">HP Silver</a></p>
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                        </td>
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                        <td>
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                          <p><a href="https://2017.igem.org/Team:Michigan_Software/Attributions">Attributions</a></p>
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                        </td>
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                        <p><a href="https://2017.igem.org/Team:Michigan_Software/Demonstration">Demonstration</a></p>
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                    </td>
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Revision as of 00:11, 31 October 2017

Measurement







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.





ProtoCat 4.0




ProtoCat 4.0 is optimized for collaboration among users and offers the best user experinece we have developed. We've added features such as threaded comments, notifications, protocol favoriting, and a new chat system called ProtoChat in this years verions of ProtoCat. Now users can communicate through commenting and chatting to make improvements on existing protocols or favorite one they like to quickly relocate it. ProtoCat also recieved a password recover system, notifications, and a better search algorithm to search more fields of a protocol. In addition, users can now create drafts of a protocol which allows them to start and finish a new protocol at their convienience. These are are all important features that contribute to a better user experience and our best version of ProtoCat.