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

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               <h1 class="grey-text heading-weight" align = "center">Protocol Model Development</h1>
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               <h1 class="grey-text heading-weight" align = "center">Protocols.io & ProtoCat</h1>
 
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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"> 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. The tool takes protocol of their format and converts it to that of format, and vice versa. 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.
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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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              <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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Revision as of 21:55, 31 October 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. The tool takes protocol of their format and converts it to that of format, and vice versa. 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.