Appistry Pipeline Contest

The Appistry Pipeline Challenge: Translating NGS Data into Clinical Action

What are today’s most challenging NGS analysis problems? Do you have a pipeline that could address one of those problems—but lack the resources to bring the pipeline into production?

The Appistry Pipeline Challenge will reward and support one winning proposal for a creative pipeline that will make a difference in clinical research and precision medicine. We’ll provide the winner with a complete NGS analysis package valued at $70,000 including commercial-grade bioinformatics tools for variant calling and somatic mutation analysis, software and hardware for developing and executing pipelines at scale, and a year’s worth of support so that you can make your idea a reality. In addition, the individual submitting the winning entry will receive a MacBook or iPad to facilitate his/her personal research.

Whether you’re an academic or commercial researcher, working for a large lab or a start-up—we challenge you to take NGS data to the next level. Take the Appistry Pipeline Challenge today—and may the best pipeline win!

Contest Details

Entry Guidelines

Contest open from July 7–September 12, 2014

Appistry will accept submissions to the Pipeline Challenge from July 7–September 12, 2014. In addition to completing the contest submission form, you should provide an abstract outlining

  • The overall scientific objective of your pipeline
  • High-level project details
  • Which bioinformatics tools your pipeline will include
  • The experience and expertise of your project team
  • How your pipeline will make an impact on clinical research and precision medicine

(New) Your proposal should be no less than 500 words and no more than 1,500 words. Read more about our expectations for entries here. DEADLINE EXTENDED. Contest now closes September 12, 2014!

In addition to your formal submission, we invite you to introduce your team and workspace and have fun making the case for your pipeline by shooting a short video with your mobile phone or device. Upload your video to Facebook or Twitter, tagging Appistry and #pickmypipeline. Videos should be between 60-90 seconds, and creativity is appreciated!

Judging Criteria

Leading life science innovators will select a winner

All entries will be reviewed by a judging panel of leading life science innovators, who will evaluate the entries based on the following criteria:

  • The overall quality of the submission
  • The need for a solution to the problem addressed by the pipeline
  • Innovation in the choice of tools and their use in the pipeline
  • The impact the solution will have on clinical research or precision medicine

The judging panel will announce the winner on September 25, 2014. The winner will be the subjective decision of the judges and all decisions are final.

The Prize

Tools, software, and hardware valued at $70,000 and a MacBook or iPad for the submitter of the winning proposal!

The winning project will receive one-year licenses for research analysis tools and an implementation package of software, hardware and support valued at $70,000. The package includes 

  • Industry-leading NGS analysis tools  from the Broad Institute and Appistry for integration into the winning pipeline, including the Genome Analysis Toolkit (GATK), MuTect, ContEst, and Somatic Indel Detector
  • The Ayrris® On Ramp Program for NGS analysis, which consists of a developer workstation capable of processing up to 200 Gbases per day; Appistry’s Ayrris software environment for pipeline development and execution; and preconfigured analysis tools and starter pipelines so that you can get started on development fast
  • Full support for the NGS analysis tools for one year and eight hours of training and services for implementing the On Ramp Program
  • A MacBook Air or iPad Air to the submitter of the winning entry. The individual making the submission will be given the choice of a 128 GB system to facilitate his/her personal research.

The Judges

Callum Bell

President, National Center for Genome Resources

judge-callumDr. Bell’s 25 years of experience in genetics, genomics and bioinformatics, with research, development, and management experience spanning human, plant, and microbial kingdoms, gives him a unique view of bioinformatics products as both a consumer and producer. He brings to the judging team significant experience working in technology startups, having received two Phase 2 SBIR awards for software and algorithm development. Prior to NCGR, which he joined in 2008, Dr. Bell held positions at Emergen, the women’s health genomics company; Sequana Therapeutics, where he ran an interdisciplinary team involved with mapping type 2 diabetes and obesity genes; and Children’s Hospital of Philadelphia, where he led the program to map human chromosome 22 in one of the first Human Genome Project centers. Dr. Bell holds a Ph.D. in Arabidopsis from the University of Edinburgh. 

Neil Miller

Director of informatics, Children’s Mercy Hospitals and Clinics of Kansas City

judge-millerMr. Miller has over 15 years of experience in the field of bioinformatics analysis and software development, with research interests in HPC, data visualization, and high throughput genome analysis. Prior to joining Children’s Mercy in 2011, he held positions at the National Center for Genome Resources, iXL, Inc., and Genome Therapeutics Corporation. Mr. Miller has led the development of multiple software applications for high throughput analysis of genomic data, including the SSAGA, RUNES, and VIKING system for enabling nucleotide variant detection, characterization, and interpretation in a clinical environment.  Mr. Miller also architected the Alpheus software system for nucleotide variant detection with NGS data, which in 2009 received a Bio-IT World Best Practices award and was named a finalist in the Computerworld Honors program. Mr. Miller holds a bachelor’s degree from Tufts University.

Dr. Rich Mazzarella

Chief Scientific Officer, Appistry, Inc.

judge-richDr. Mazzarella has more than three decades of experience in diverse fields including biochemistry, cell and molecular biology, immunology, genetics, computational biology, and bioinformatics. Prior to Appistry, Dr. Mazzarella accumulated a range of genomics research expertise, including advancing the human genome project at Washington University, St. Louis, and patenting progressive findings in cancer research while at Pfizer. He has edited a computational and systems book, authored four book chapters and 40 scientific journal articles, and sat on the editorial board of several peer-reviewed journals. Mazzarella holds a Ph.D. in microbiology from Saint Louis University School of Medicine and has served as an instructor at the Institute for Biomedical Computing and the Center for Genetics in Medicine at Washington University.

Dr. John Begemann

Director of product management, Appistry, Inc.

judge-johnDr. Begemann has 30 years of experience in scientific sales, software development, project management, and product management in both academic and small company environments. Dr. Begemann’s career began doing post-doctoral work in the application of novel data processing techniques to NMR data, which was spun into a company where he held a variety of positions including pre-sales, sales, marketing, development, and management. Dr. Begemann spent many years at Tripos involved in the definition, development, and support of their flagship software product, SYBYL, along with several other software products. Since joining Appistry, he has been involved in specification and development of genomics research products including Appistry’s release of the GATK. Dr. Begemann holds a Ph. D. in physical chemistry from Northwestern University.

Contest Submission Form