Difference between revisions of "Team:Michigan Software/HP/Silver"
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<p>Prior to begining the development of ProtoCat 3.0, we did research on <em>something</em>. We began by brainstorming with members of our team who had lab experience to get a foundation upon which we could improve. We tested the robustness of this initial model by trying to represent the protocols uploaded to ProtoCat 2.0 with our new model, tweaking and updating it along the way. Once we felt our model could adequately handle the protocols we anticipated in ProtoCat 3.0, we met with our adviser, Dr. Santiago Schnell, and ran our protocol model by him. Taking his feedback, we went back and further refined our model to the one that we use in our current implementation of ProtoCat 3.0.</p> | <p>Prior to begining the development of ProtoCat 3.0, we did research on <em>something</em>. We began by brainstorming with members of our team who had lab experience to get a foundation upon which we could improve. We tested the robustness of this initial model by trying to represent the protocols uploaded to ProtoCat 2.0 with our new model, tweaking and updating it along the way. Once we felt our model could adequately handle the protocols we anticipated in ProtoCat 3.0, we met with our adviser, Dr. Santiago Schnell, and ran our protocol model by him. Taking his feedback, we went back and further refined our model to the one that we use in our current implementation of ProtoCat 3.0.</p> | ||
<h3>OpenWetWare</h3> | <h3>OpenWetWare</h3> | ||
| − | <p> | + | <p>Standardization in synthetic biology has gained a lot of traction, such as the BioBrick and Registry of Standardized Biological Parts. However, the procedures used to generate them tend to be diverse in nature, with a bacterial transformation protocol likely requiring different information than a ligation protocol. Online protocol repositories must account for such differences when creating their data models, which will usually require either a simplified model (such as solely text-based) or a more arduous upload process. These different models become a problem when trying to share protocols between the repositories, because the formats that the protocols are stored in are not compatible and require an external conversion tool to get from one format to the other.</p> |
| − | <p> | + | <p>Description of the thing.</p> |
<p>Our protocol database is not the only one out there. OpenWetWare and protocols.io are some of the most popular alternatives. Since there are so many different databases, our team wanted to find a way to ensure that no matter which database someone decides to use, they can upload their protocol to all of them the same way. We reached out to OpenWetWare and began discussing how to standardize the file format of protocol to be uploaded. Our format is based on the JSON format, and we gave them an example of one of our protocols to begin the collaboration. The first steps were taken to build a cooperative relationship and create a standard protocol that will help make protocols even easier to use, test, review, and design.</p> | <p>Our protocol database is not the only one out there. OpenWetWare and protocols.io are some of the most popular alternatives. Since there are so many different databases, our team wanted to find a way to ensure that no matter which database someone decides to use, they can upload their protocol to all of them the same way. We reached out to OpenWetWare and began discussing how to standardize the file format of protocol to be uploaded. Our format is based on the JSON format, and we gave them an example of one of our protocols to begin the collaboration. The first steps were taken to build a cooperative relationship and create a standard protocol that will help make protocols even easier to use, test, review, and design.</p> | ||
Revision as of 00:12, 18 October 2016
Michigan Software Team
Protocat 3.0 - Human Practices
Protocol Model Development
Prior to begining the development of ProtoCat 3.0, we did research on something. We began by brainstorming with members of our team who had lab experience to get a foundation upon which we could improve. We tested the robustness of this initial model by trying to represent the protocols uploaded to ProtoCat 2.0 with our new model, tweaking and updating it along the way. Once we felt our model could adequately handle the protocols we anticipated in ProtoCat 3.0, we met with our adviser, Dr. Santiago Schnell, and ran our protocol model by him. Taking his feedback, we went back and further refined our model to the one that we use in our current implementation of ProtoCat 3.0.
OpenWetWare
Standardization in synthetic biology has gained a lot of traction, such as the BioBrick and Registry of Standardized Biological Parts. However, the procedures used to generate them tend to be diverse in nature, with a bacterial transformation protocol likely requiring different information than a ligation protocol. Online protocol repositories must account for such differences when creating their data models, which will usually require either a simplified model (such as solely text-based) or a more arduous upload process. These different models become a problem when trying to share protocols between the repositories, because the formats that the protocols are stored in are not compatible and require an external conversion tool to get from one format to the other.
Description of the thing.
Our protocol database is not the only one out there. OpenWetWare and protocols.io are some of the most popular alternatives. Since there are so many different databases, our team wanted to find a way to ensure that no matter which database someone decides to use, they can upload their protocol to all of them the same way. We reached out to OpenWetWare and began discussing how to standardize the file format of protocol to be uploaded. Our format is based on the JSON format, and we gave them an example of one of our protocols to begin the collaboration. The first steps were taken to build a cooperative relationship and create a standard protocol that will help make protocols even easier to use, test, review, and design.
