Team:Michigan Software/Outreach

Michigan Software 2015

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Outreach

Reproducibility is one of the pillars of science, it allows separate groups of scientists to perform the same experiments and come to the same conclusions. Despite the importance of reproducibility, studies 1 and 2 have shown that oftentimes the conclusions published in high-impact science journals are not reproducible. Our project, ProtoCat, is designed with the intent to tackle the problem of reproduction by providing scientists with a collection of user submitted and reviewed protocols with which they can perform experiments.

Before we started building ProtoCat, we reached out to scientists to ask for their thoughts on reproducibility, and whether or not an online protocol database would help to increase reproducibility in science. The survey was emailed to 155 recipients, the majority of whom were iGEM advisors and student participants. A link to the survey was also posted on the iGEM facebook page. In total, 55 responses were received, and were used to aid our design of ProtoCat.

The papers cited above reveal the lack of reproducibility in drug development, but as iGEM is a synthetic biology competition, we wanted to find out if the problem is also encountered by synthetic biologists. We asked participating teams about their experiences with the protocols that iGEM provides on their website. Surprisingly, 78% of teams encountered issues with, or had to make adjustments to one or more of the iGEM-provided protocols that they used. We believe that this result illustrates the issue that ProtoCat is designed to address. Even though the iGEM-provided protocols are classic molecular biology protocols, and among the most used in the field, a large majority of users had problems with them.

With this information in mind, we wanted to gauge the appeal of a software like ProtoCat. We asked scientists whether or not they could see themselves using a multidisciplinary, online protocol database. The responses were generally favorable, with 30 yes’s 0 no’s and 11 maybe’s.

Given the positive responses, we felt certain the ProtoCat would be appealing to scientists searching for protocols. The next step for our team was determining what features to implement in ProtoCat. Luckily, respondents provided plenty of ideas like giving users the ability to review protocols. We implemented both a comment system, and a way for users to rate protocols on a scale of 0 to 5. We believe these tools will assist many users in finding the best protocols for the experiments they performing. We also saw from our survey that in many people’s minds, the search tool was one of the most important parts, as a result we spent a large amount of time developing an efficient and easy to use search tool. Although we were able to implement many of the features suggested to us by survey respondents, project deadlines did not allow us to get to all of them. Some future improvements we hope to make to ProtoCat include illustrations, links to reagents, and a time-breakdown feature which would show users how long they could expect to spend on each step.