Difference between revisions of "Team:Michigan Software/HP/Gold Integrated"

 
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                   <h1 id = "headerImageh1">Human Practices - Gold</h1>
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                   <h1 style = "color: #01407c;"id = "headerImageh1">Human Practices - Gold</h1>
 
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               <h1 class="grey-text heading-weight" align = "center">Protocols.io & ProtoCat</h1>
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               <h1 class="grey-text heading-weight" align = "center">Protocol Model Development</h1>
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               <p id = "doubleSpace" class="p-font grey-text">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Our relationship with protocols.io has grown into a very rewarding partnership over the course of this last year. In the 2016 season we took the first steps to build a relationship with the company, having several meetings with their head of outreach, and out of those meetings came the idea for a project that we have been developing since the summer. This iGEM season we have created a conversion tool that easily imports protocols between protocols.io and ProtoCat. This tool takes the output of the protocols.io API, and generates a ProtoCat protocol with the same content. This makes the gap between the two services just a bit smaller, as the major overhead of leveraging the benefits of both services was in the re-upload process.</p>
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               <p id = "doubleSpace" class="p-font grey-text">Prior to beginning the development of ProtoCat 3.0, we did research
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<p id = "doubleSpace" class="p-font grey-text">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Our organizations share the goal of improving protocol reproducibility, and the creation of this tool breaks through the biggest technical barrier that our common goal faces. Easy transfer of protocol across repositories will make it even easier for scientists to share their protocol and improve their experiments. This relationship not only helps ProtoCat and Michigan Software grow, providing a valuable opportunity for our team members to interact with industry professionals, but also removes the possibility of tensions arising in the future between our two organizations. In fact, when we send protocols.io the news that the conversion tool was up and running, their response was "This is cool!" and were happy to see people making use of their APIs.
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                  on currently used protocol models. We began by brainstorming with members of our team who had
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                  lab experience to get a foundation upon which we could improve. We tested the robustness of
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                  this initial model by trying to represent the protocols uploaded to ProtoCat 2.0 with our new
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                  model, tweaking and updating it along the way. Once we felt our model could adequately handle
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                  the protocols we anticipated in ProtoCat 3.0, we met with our adviser, Dr. Santiago Schnell,
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                  and ran our protocol model by him. Taking his feedback, we went back and further refined our
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                  model to the one that we use in our current implementation of ProtoCat 3.0.
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<td><img src="https://static.igem.org/mediawiki/2017/thumb/8/89/Michigan_software_pio_protocol.png/1599px-Michigan_software_pio_protocol.png" alt="protocols.io view" /></td>
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<td><img src="https://static.igem.org/mediawiki/2017/6/64/Michigan_software_import_tool.png" alt="protocat import" /></td>
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<td><img src="https://static.igem.org/mediawiki/2017/thumb/d/d0/Michigan_software_pcat_protocol.png/1599px-Michigan_software_pcat_protocol.png" alt="protocat view" /></td>
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<td>A protocol on protocols.io</td>
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<td>The ProtoCat Import Tool</td>
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<td>That protocol on protocat.org</td>
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              <h1 class="grey-text heading-weight" align = "center">Standard Protocol Format</h1>
 
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              <p id = "doubleSpace" class="p-font grey-text">Standardization in synthetic biology has gained a lot of traction,
 
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                  such as the BioBrick and Registry of Standardized Biological Parts. However, the procedures
 
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                  used to generate them tend to be diverse in nature, with a bacterial transformation
 
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                  protocol likely requiring different information than a ligation protocol. Online protocol
 
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                  repositories must account for such differences when creating their data models, which will
 
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                  usually require either a simplified model (such as solely text-based) or a more arduous
 
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                  upload process. These different models become a problem when trying to share protocols between
 
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                  the repositories, because the formats that the protocols are stored in are not compatible and
 
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                  require an external conversion tool to get from one format to the other. In order to begin
 
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                  working towards a standardized protocol format format, we reached out to OpenWetWare and
 
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                  Protocols.io, two well known protocol repositories. We have began discussing how we will
 
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                  reconcile our respective protocol models in order to get the best protocol model. The first
 
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                  steps have been taken to build a cooperative relationship and create a standard protocol that
 
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                  will help make protocols even easier to use, test, review, and design.
 
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Latest revision as of 19:53, 1 November 2017

Human Practices - Gold



Protocols.io & ProtoCat


     Our relationship with protocols.io has grown into a very rewarding partnership over the course of this last year. In the 2016 season we took the first steps to build a relationship with the company, having several meetings with their head of outreach, and out of those meetings came the idea for a project that we have been developing since the summer. This iGEM season we have created a conversion tool that easily imports protocols between protocols.io and ProtoCat. This tool takes the output of the protocols.io API, and generates a ProtoCat protocol with the same content. This makes the gap between the two services just a bit smaller, as the major overhead of leveraging the benefits of both services was in the re-upload process.

      Our organizations share the goal of improving protocol reproducibility, and the creation of this tool breaks through the biggest technical barrier that our common goal faces. Easy transfer of protocol across repositories will make it even easier for scientists to share their protocol and improve their experiments. This relationship not only helps ProtoCat and Michigan Software grow, providing a valuable opportunity for our team members to interact with industry professionals, but also removes the possibility of tensions arising in the future between our two organizations. In fact, when we send protocols.io the news that the conversion tool was up and running, their response was "This is cool!" and were happy to see people making use of their APIs.




protocols.io view protocat import protocat view
A protocol on protocols.io The ProtoCat Import Tool That protocol on protocat.org