precisionFDA’s Next Challenge? Conduct an App-a-Thon!

Posted on October 3, 2016 by FDA Voice

By: Zivana Tezak, Ph.D., and Elaine Johanson

FDA is increasingly harnessing the power of supercomputers, the creative and collaborative culture of the scientific community, and novel approaches to technology to help achieve advances in diagnostics, therapeutics, and analytics that will ultimately benefit patients.

Zivana Tezak, Ph.D., is Associate Director for Science and Technology at FDA’s Office of In Vitro Diagnostics and Radiological Health, Center for Devices and Radiological Health

Perhaps no program personifies these efforts more than the online research portal precisionFDA, which was developed by FDA scientists with the help of leading minds from Silicon Valley as part of President Obama’s Precision Medicine Initiative (PMI).

The goal of the PMI is to help translate scientific knowledge about genomics into clinical care. As part of this initiative, precisionFDA’s task is to advance the use of a core technology behind the PMI known as next generation sequencing or NGS, which is capable of mapping the entire human genome. To achieve that, precisionFDA is drawing upon the latest computing and storage technologies to provide an open source cloud-based space where experts can share data, ideas, and methodologies. Today, it boasts more than 1,600 participants, including researchers, test developers, industry, academics, statisticians, and clinicians.

One way we’ve been learning and growing is through contests designed to spark the creative thinking of members on behalf of important NGS questions about data, analytics, and sequencing tools.

We are happy to announce the next challenge: an “App-a-Thon,” inviting software developers to get together with their peers, collaborators, and friends to add NGS software apps to the precisionFDA app library. Apps in this case are executable commands using the Linux operating system that are “wrapped” around NGS software.

Elaine Johanson, is precisionFDA Project Manager and Deputy Director of FDA’s Office of Health Informatics

Apps can be existing, modified, or completely new. Ultimately this challenge, which closes Oct. 28, 2016, is a contest to engage the NGS community in the development of new genome sequencing analytical tools for use on precisionFDA. These apps can do a variety of useful activities such as simulations, benchmarking, data integration, mapping portions of the genome, or identifying genetic variants. Members of precisionFDA are encouraged to try out these apps by running them on the platform.

Our goal is to build a robust reference library of apps and files so that precisionFDA can provide developers with everything they need to support development work on their software pipeline or tests.

If you’d like to set up an App-a-Thon, FDA provides the framework and all the materials, storage, and compute capacity to hold an App-a-Thon on precisionFDA. We encourage you to choose a timeframe, invite your researcher/developer friends, and follow the directions in FDA’s ‘App-a-Thon in a Box’ toolkit. This toolkit even contains video and results from a precisionFDA App-a-Thon held at Stanford University.

The results of this challenge will be highlighted by FDA Commissioner Robert Califf at the World Precision Medicine Congress on Nov. 14, 2016 in Washington D.C. Participating will benefit the entire NGS community, but most importantly, it will advance public health and benefit the patients we collectively serve.

Zivana Tezak, Ph.D., is Associate Director for Science and Technology at FDA’s Office of In Vitro Diagnostics and Radiological Health, Center for Devices and Radiological Health

Elaine Johanson, is precisionFDA Project Manager and Deputy Director of FDA’s Office of Health Informatics