Improving the usability and archival stability of bioinformatics software

Serghei Mangul^{1

2}, Lana S Martin³, Eleazar Eskin^{4

5}, Ran Blekhman^{6

7}

Affiliations

¹ Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA, 90095, USA. smangul@ucla.edu.
² Institute for Quantitative and Computational Biosciences, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095, USA. smangul@ucla.edu.
³ Institute for Quantitative and Computational Biosciences, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
⁴ Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA, 90095, USA.
⁵ Department of Human Genetics, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
⁶ Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St SE, Minneapolis, MN, 55455, USA.
⁷ Department of Ecology, Evolution, and Behavior, University of Minnesota, 100 Ecology Building, 1987 Upper Buford Cir, Falcon Heights, MN, 55108, USA.

PMID: 30813962
PMCID: PMC6391762
DOI: 10.1186/s13059-019-1649-8

Editorial

Improving the usability and archival stability of bioinformatics software

Serghei Mangul et al. Genome Biol. 2019.

. 2019 Feb 27;20(1):47.

doi: 10.1186/s13059-019-1649-8.

Authors

Serghei Mangul^{1

2}, Lana S Martin³, Eleazar Eskin^{4

5}, Ran Blekhman^{6

7}

Affiliations

¹ Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA, 90095, USA. smangul@ucla.edu.
² Institute for Quantitative and Computational Biosciences, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095, USA. smangul@ucla.edu.
³ Institute for Quantitative and Computational Biosciences, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
⁴ Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA, 90095, USA.
⁵ Department of Human Genetics, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
⁶ Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St SE, Minneapolis, MN, 55455, USA.
⁷ Department of Ecology, Evolution, and Behavior, University of Minnesota, 100 Ecology Building, 1987 Upper Buford Cir, Falcon Heights, MN, 55108, USA.

PMID: 30813962
PMCID: PMC6391762
DOI: 10.1186/s13059-019-1649-8

Abstract

Implementation of bioinformatics software involves numerous unique challenges; a rigorous standardized approach is needed to examine software tools prior to their publication.

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Conflict of interest statement

Competing interests

The authors declare that they have no competing interests.

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Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

References

1. Wren JD. Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades. Bioinformatics. 2016;32:2686–2691. doi: 10.1093/bioinformatics/btw284. - DOI - PubMed
1. Markowetz F. All biology is computational biology. PLoS Biol. 2017;15:e2002050. doi: 10.1371/journal.pbio.2002050. - DOI - PMC - PubMed
1. List M, Ebert P, Albrecht F. Ten simple rules for developing usable software in computational biology. PLoS Comput Biol. 2017;13:e1005265. doi: 10.1371/journal.pcbi.1005265. - DOI - PMC - PubMed
1. Stodden V, Seiler J, Ma Z. An empirical analysis of journal policy effectiveness for computational reproducibility. Proc Natl Acad Sci U S A. 2018;115:2584–2589. doi: 10.1073/pnas.1708290115. - DOI - PMC - PubMed
1. Beaulieu-Jones BK, Greene CS. Reproducibility of computational workflows is automated using continuous analysis. Nat Biotechnol. 2017;35:342–346. doi: 10.1038/nbt.3780. - DOI - PMC - PubMed

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Improving the usability and archival stability of bioinformatics software

Affiliations

Improving the usability and archival stability of bioinformatics software

Authors

Affiliations

Abstract

Conflict of interest statement

Competing interests

Publisher’s Note

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources