BioContainers: an open-source and community-driven framework for software standardization

Author:

da Veiga Leprevost Felipe1,Grüning Björn A23,Alves Aflitos Saulo4,Röst Hannes L5,Uszkoreit Julian6,Barsnes Harald78,Vaudel Marc91011,Moreno Pablo12,Gatto Laurent13,Weber Jonas2,Bai Mingze12,Jimenez Rafael C12,Sachsenberg Timo14,Pfeuffer Julianus15,Vera Alvarez Roberto16,Griss Johannes1217,Nesvizhskii Alexey I118,Perez-Riverol Yasset12

Affiliation:

1. Department of Pathology, University of Michigan, Ann Arbor, MI, USA

2. Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany

3. Albert-Ludwigs-University, Department of Computer Science, Bioinformatics Group, Freiburg, Baden-Württemberg, Freiburg, Freiburg

4. Wageningen Plant Research, Cluster Bioinformatics, Wageningen, AD, Gelderland, Netherlands

5. Department of Genetics, Stanford University, USA

6. Medizinisches Proteom-Center, Ruhr-University Bochum, Germany

7. Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway

8. Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway

9. KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway

10. KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway

11. Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway

12. EMBL Outstation, European Bioinformatics Institute, Proteomics Services, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

13. Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK

14. Universität Tübingen, Wilhelm Schickard Institut für Informatik, Applied Bioinformatics Group, Tübingen, Germany

15. Eberhard-Karls-Universität Tübingen, Department of Computer Science, Applied bioinformatics, Tübingen

16. Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

17. Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria

18. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA

Funder

NIH

Swiss National Science Foundation

EMBO

BMBF

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Reference7 articles.

1. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update;Afgan;Nucleic Acids Res,2016

2. Bioboxes: standardised containers for interchangeable bioinformatics software;Belmann;GigaScience,2015

3. On best practices in the development of bioinformatics software;Leprevost;Bioinf. Comput. Biol,2014

4. BioShaDock: a community driven bioinformatics shared Docker-based tools registry;Moreews;F1000Research,2015

5. Open source libraries and frameworks for mass spectrometry based proteomics: a developer’s perspective;Perez-Riverol;Biochim. Biophys. Acta (BBA) Proteins Proteomics,2014

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