Team:Michigan Software/Description

Michigan Software Team
ProtoCat 3.0 - Project Description


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.


What's new in ProtoCat 3.0?

ProtoCat 3.0 is a complete re-imagining of the ProtoCat software that has been in development for the last two years. By making dramatic changes to how we store protocols, we have been able to add new features that would have been impossible before. These features include variable reagent calculations, allowing users to scale the amounts in a protocol to their liking, and timers on a per-step basis. We have also made it possible to link to specific reagents so that users can immediately learn more about the reagents used in the protocol. Another benefit to the new protocol model is that the user is able to upload fully customized steps and, unlike in previous versions of ProtoCat, add warnings to necessary steps. ProtoCat also supports full version control of uploaded procedures, where a user can track the revisions made and access previous versions. Additional benefits include a brand new category system, a better and more dynamic user interface, more sorting and filtering options, and a more advanced user page.

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