Protocol Model Development
Prior to beginning the development of ProtoCat 3.0, we did research on currently used protocol models. 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.
Standard Protocol Format
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. In order to begin working towards a standardized protocol format format, we reached out to OpenWetWare and Protocols.io, two well known protocol repositories. We have began discussing how we will reconcile our respective protocol models in order to get the best protocol model. The first steps have been taken to build a cooperative relationship and create a standard protocol that will help make protocols even easier to use, test, review, and design.