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Bioconductor: open software development for computational biology and bioinformatics

Robert C Gentleman1*, Vincent J Carey2, Douglas M Bates3, Ben Bolstad4, Marcel Dettling5, Sandrine Dudoit4, Byron Ellis6, Laurent Gautier7, Yongchao Ge8, Jeff Gentry1, Kurt Hornik9, Torsten Hothorn10, Wolfgang Huber11, Stefano Iacus12, Rafael Irizarry13, Friedrich Leisch9, Cheng Li1, Martin Maechler5, Anthony J Rossini14, Gunther Sawitzki15, Colin Smith16, Gordon Smyth17, Luke Tierney18, Jean YH Yang19 and Jianhua Zhang1

Author Affiliations

1 Department of Biostatistical Science, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA

2 Channing Laboratory, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA

3 Department of Statistics, University of Wisconsin-Madison, 1210 W Dayton St, Madison, WI 53706, USA

4 Division of Biostatistics, University of California, Berkeley, 140 Warren Hall, Berkeley, CA 94720-7360, USA

5 Seminar for Statistics LEO C16, ETH Zentrum, Zürich CH-8092, Switzerl

6 Department of Statistics, Harvard University, 1 Oxford St, Cambridge, MA 02138, USA

7 Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, Lyngby 2800, Denmark

8 Department of Biomathematical Sciences, Mount Sinai School of Medicine, 1 Gustave Levy Place, Box 1023, New York, NY 10029, USA

9 Institut für Statistik und Wahrscheinlichkeitstheorie, TU Wien, Wiedner Hauptstrasse 8-10/1071, Wien 1040, Austria

10 Institut für Medizininformatik, Biometrie und Epidemiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Waldstraße6, D-91054 Erlangen, Germany

11 Division of Molecular Genome Analysis, DKFZ (German Cancer Research Center), 69120 Heidelberg, Germany

12 Department of Economics, University of Milan, 23 Via Mercalli, I-20123 Milan, Italy

13 Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St E3035, Baltimore, MD 21205, USA

14 Department of Medical Education and Biomedical Informatics, University of Washington, Box 357240, 1959 NE Pacific, Seattle, WA 98195, USA

15 Statistisches Labor, Institut für Angewandte Mathematik, Im Neuenheimer Feld 294, D 69120, Heidelberg, Germany

16 Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC-28, La Jolla, CA 92037, USA

17 Division of Genetics and Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia

18 Department of Statistics and Actuarial Science, University of Iowa, 241 Schaeffer Hall, Iowa City, IA 52242, USA

19 Center for Bioinformatics and Molecular Biostatistics, Univerisity of California, San Francisco, 500 Parnassus Ave, San Francisco 94143-0560, USA

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Genome Biology 2004, 5:R80  doi:10.1186/gb-2004-5-10-r80

Published: 15 September 2004

Abstract

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.