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Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq

Ben Busby, Allissa Dillman, Claire L. Simpson, Ian Fingerman, Sijung Yun, David M. Kristensen, Lisa Federer, Naisha Shah, Matthew C. LaFave, Laura Jimenez-Brown, Manjusha Pande, Wen Luo, Brendan Miller, Cem Mayden, Dhruva Chandramohan, Kipper Fletez-Brant, Paul W. Bible, Sergej Nowoshilow, Alfred Chan, Eric JC Galvez, Jeremy Chignell, Joseph N. Paulson, Manoj Kandpal, Suhyeon Yoon, Esther Asaki, Abhinav Nellore, Adam Stine, Robert Sanders, Jesse Becker, Matt Lesko, Mordechai Abzug, Eugene Yaschenko
doi: https://doi.org/10.1101/018085
Ben Busby
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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  • For correspondence: ben.busby@gmail.com
Allissa Dillman
2Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
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Claire L. Simpson
3Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America
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Ian Fingerman
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Sijung Yun
4Laboratory of Cell Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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David M. Kristensen
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Lisa Federer
5NIH Library, Division of Library Services, Office of Research Services, National Institutes of Health, Bethesda, Maryland, United States of America
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Naisha Shah
6Systems Genomics and Bioinformatics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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Matthew C. LaFave
7Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Laura Jimenez-Brown
8Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
9Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
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Manjusha Pande
10Bioinformatics Core, University of Michigan, Ann Arbor, Michigan
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Wen Luo
11Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland, United States of America
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Brendan Miller
12Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
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Cem Mayden
13Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
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Dhruva Chandramohan
13Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
14Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York, United States of America
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Kipper Fletez-Brant
15Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
16McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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Paul W. Bible
17Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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Sergej Nowoshilow
18Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
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Alfred Chan
19Translational Immunology, John Wayne Cancer Institute at Saint John’s Health Center, Santa Monica, California, United States of America
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Eric JC Galvez
20Microbial Immune Regulation Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Jeremy Chignell
21Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, United States of America
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Joseph N. Paulson
22Graduate Program in Applied Mathematics & Statistics, and Scientific Computation, University of Maryland, College Park, Maryland, United States of America
23Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
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Manoj Kandpal
24Division of Health and Biomedical Informatics, Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
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Suhyeon Yoon
25Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Esther Asaki
26Bioinformatics and Molecular Analysis Section, Center for Information Technology, National Institutes of Health, Bethesda, Maryland, United States of America
27SRA International, Fairfax, Virginia, United States of America
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Abhinav Nellore
15Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
28Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
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Adam Stine
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Robert Sanders
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Jesse Becker
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Matt Lesko
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Mordechai Abzug
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Eugene Yaschenko
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Abstract

We assembled teams of genomics professionals to assess whether we could rapidly develop pipelines to answer biological questions commonly asked by biologists and others new to bioinformatics by facilitating analysis of high-throughput sequencing data. In January 2015, teams were assembled on the National Institutes of Health (NIH) campus to address questions in the DNA-seq, epigenomics, metagenomics and RNA-seq subfields of genomics. The only two rules for this hackathon were that either the data used were housed at the National Center for Biotechnology Information (NCBI) or would be submitted there by a participant in the next six months, and that all software going into the pipeline was open-source or open-use. Questions proposed by organizers, as well as suggested tools and approaches, were distributed to participants a few days before the event and were refined during the event. Pipelines were published on GitHub, a web service providing publicly available, free-usage tiers for collaborative software development (https://github.com/features/). The code was published at https://github.com/DCGenomics/ with separate repositories for each team, starting with hackathon_v001.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 16, 2015.
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Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq
Ben Busby, Allissa Dillman, Claire L. Simpson, Ian Fingerman, Sijung Yun, David M. Kristensen, Lisa Federer, Naisha Shah, Matthew C. LaFave, Laura Jimenez-Brown, Manjusha Pande, Wen Luo, Brendan Miller, Cem Mayden, Dhruva Chandramohan, Kipper Fletez-Brant, Paul W. Bible, Sergej Nowoshilow, Alfred Chan, Eric JC Galvez, Jeremy Chignell, Joseph N. Paulson, Manoj Kandpal, Suhyeon Yoon, Esther Asaki, Abhinav Nellore, Adam Stine, Robert Sanders, Jesse Becker, Matt Lesko, Mordechai Abzug, Eugene Yaschenko
bioRxiv 018085; doi: https://doi.org/10.1101/018085
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Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq
Ben Busby, Allissa Dillman, Claire L. Simpson, Ian Fingerman, Sijung Yun, David M. Kristensen, Lisa Federer, Naisha Shah, Matthew C. LaFave, Laura Jimenez-Brown, Manjusha Pande, Wen Luo, Brendan Miller, Cem Mayden, Dhruva Chandramohan, Kipper Fletez-Brant, Paul W. Bible, Sergej Nowoshilow, Alfred Chan, Eric JC Galvez, Jeremy Chignell, Joseph N. Paulson, Manoj Kandpal, Suhyeon Yoon, Esther Asaki, Abhinav Nellore, Adam Stine, Robert Sanders, Jesse Becker, Matt Lesko, Mordechai Abzug, Eugene Yaschenko
bioRxiv 018085; doi: https://doi.org/10.1101/018085

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