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

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                   <h1 id = "headerImageh1">Attributions</h1>
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                   <h1 id = "headerImageh1">Overview</h1>
 
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            <h1 class="grey-text heading-weight" align = "center">Background</h1>
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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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              of ProtoCat 1.0. Like many innovative ideas, ProtoCat began because of a problem.
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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
 +
              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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             <h1 class="grey-text heading-weight" align = "center">The People Behind The Cat</h1>
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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
 +
              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.
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            </p>
 
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                    <h3 class="name-tag">Ali Turfah</h3>
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                    <p class="desc">Hello, I'm Ali Turfah. I'm a junior studying Data Science, and am the current president of the Michigan Software 2017 team. In my free time I like to program, read, and play pokemon. I have a cat, so I thoroughly enjoy the branding of our project as well as the ProtoCat mascot.</p>
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             <h1 class="grey-text heading-weight" align = "center">ProtoCat 4.0</h1>
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                    <p class="teamText">Attributions:</p>
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                    <ul class="teamTextList">
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                        <li>Team president</li>
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                        <li>Front end development</li>
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                        <li>Presentation chair stand-in</li>
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                    </ul>
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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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                  </div>
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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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                  <div class="front">
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              notifications, protocol favoriting, and a new chat system called ProtoChat in this
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                    <img class="center-block vertical-center board-img" src="photos/Ali.jpg">
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              years verions of ProtoCat. Now users can communicate through commenting and chatting
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                  </div>
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              to make improvements on existing protocols or favorite one they like to quickly relocate
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              </div>
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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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             <div class="col-xs-12 col-sm-6 col-md-4 top-buffer">
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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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                    <h3 class="name-tag">Dan Dineen</h3>
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            </p>
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                    <p class="desc">Hi! My name is Daniel Dineen. I am the current webmaster of the team. I am from Connecticut and am a sophomore at the University of Michigan. I am studying computer science and enjoy playing piano and guitar when not working.</p>
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                    <p class="teamText">Attributions:</p>
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                    <ul class="teamTextList">
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                        <li>Team Webmaster</li>
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                        <li>Lead wiki designer</li>
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                    <img class="center-block vertical-center board-img" src="photos/Dan.jpg">
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                    <h3 class="name-tag">Drew Manson</h3>
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                    <p class="desc">Hello! My name is Drew Manson, the Public Relations Officer for the team! Currently I'm a German and Biomolecular Science dual-major, with plans for pharmacy school in the future. This is my first year on the team, and my iGEM experience has been really cool so far!</p>
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                    <p class="teamText">Attributions:</p>
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                        <li>Public Relations Chair</li>
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                    <img class="center-block vertical-center board-img" src="photos/Drew.jpg">
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                    <h3 class="name-tag">Kyle Cochrane</h3>
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                    <p class="desc">Hi! My name is Kyle Cochrane. I am from southwest Michigan and am currently a Junior at the University of Michigan. I study computer science and spanish, and in my free time I enjoy playing Quidditch (go UMQ!), browsing reddit, and hiking. Photo credit goes to Christina Oh Photography!</p>
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                    <p class="teamText">Attributions:</p>
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                    <ul class="teamTextList">
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                        <li>Team Secretary</li>
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                        <li>Front end development</li>
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                  <div class="front">
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                    <img class="center-block vertical-center board-img" src="photos/Kyle.png">
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                    <h3 class="name-tag">Sir Thomas Oliver</h3>
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                    <p class="desc">I'm Tommy Oliver and am from Brighton, Michigan. I am a sophomore studying computer engineering and computer science. Outside of all school and all this fun stuff, I spend time with my friends, playing Pokemon Go, and watching superhero shows on Netflix.</p>
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                    <p class="teamText">Attributions:</p>
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                        <li>Project Manager</li>
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                        <li>Back end development</li>
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                        <li>Front end development</li>
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                    <img class="center-block vertical-center board-img" src="photos/Tommy.jpg">
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              <h1 class="grey-text heading-weight" align = "center">Advisors</h1>
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                    <h3 class="name-tag">Dr. Marcus Ammerlaan</h3>
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                    <p class="desc">Dr. Marcus Ammerlaan is affiliated with the Department of Molecular, Cellular, and Developmental Biology at the University of Michigan. He is in charge of labs and graduate student instructors for the department’s introductory courses. He received his Ph.D. from the University of Texas-Austin in 1994.</p>
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                        <li>Team biology adviser</li>
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                        <li>Primary iGEM contact</li>
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                    <h3 class="name-tag">Dr. Santiago Schnell</h3>
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                    <p class="desc">Dr. Santiago Schnell is a Professor of Molecular &amp; Integrative Physiology and Computational Medicine &amp; Bioinformatics at the University of Michigan Medical School. He is also a Willliam K. Brehm Investigator at the Brehm Center for Diabetes Research. He received his License in Biology from Universidad Sim&oacute;n Bol&iacute;var and then his doctorate in Mathematical Biology from the University of Oxford.</p>
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                        <li>Team software adviser</li>
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                        <li>Department Representative</li>
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Revision as of 23:38, 30 October 2017

Overview







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.