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Appistry Seeks Submissions for NGS Analysis Pipeline Challenge

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NEW YORK (GenomeWeb) – Through the newly launched Appistry Pipeline Challenge, bioinformatics firm Appistry is seeking to support the development and execution of a single next-generation sequencing analysis pipeline that addresses a need in the clinical research or precision medicine market.

Appistry began accepting proposal submissions for the challenge and will continue to do so until August 15, 2014. It is accepting 500-word abstracts that articulate the overall scientific objectives of the proposed pipeline, high-level project details, bioinformatics tools that will be part of the pipeline, the experience and expertise of the development team, and the expected impact of the pipeline. In addition, participants can also submit short videos – 60 – 90 seconds long — that introduce their teams and present their pipelines.

Entries will be judged by a panel of four judges — two internal and two external — who will evaluate the quality of the submissions, the need for the proposed pipeline, innovation in the choice of tools and their use in the pipeline, and the expected impact. They'll announce the winner on August 28, 2014.

The authors of the selected proposal will then receive a one-year license to Appistry's software and hardware which include tools such as the Broad Institute's Genome Analysis Toolkit, MuTect, ContEst, and Somatic Indel Detector; and Appistry's Ayrris On Ramp Program for NGS analysis which provides a developer workstation; installed software for managing tools, data, and pipelines; preconfigured analysis tools and starter pipeline;— that's about $70,000 worth of software and hardware according to the company — as well as eight hours of Appistry training.

Over the next year, the winner will use these resources, along with other open source or commercial products of their choice, to build the pipeline they proposed with Appistry's help and support, Kevin Haar, Appistry's president and CEO, told BioInform. "Our hope is that this goes well and spurs a lot of creativity, and then we can make it an annual program."

There are no limits on the research or clinical questions that participants choose to address, nor is the challenge restricted to a specific disease area. That's not the goal of the challenge as far as Appistry is concerned. "We want to foster innovation in the industry," Rich Mazzarella, Appistry's chief scientific officer and one of the challenge judges, told BioInform. "You can have a great idea but to actually implement it in a good NGS pipeline is actually pretty difficult, especially if you want it to run fairly quickly … "We want to relieve that burden" by providing the tools and expertise needed to build and implement the pipeline, he said.

Appistry will discuss the challenge and answer interested participants' questions on July 13 during a session at the Intelligent Systems for Molecular Biology conference which starts this week. It will also host a webinar on July 24 to discuss the challenge.

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