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Managing Reproducible Computational Experiments with Curated Proteins in KINARI-2

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Bioinformatics Research and Applications (ISBRA 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9096))

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Abstract

KINARI-2 is the second release of the web server KINARI-Web for rigidity and flexibility of biomolecules. Besides incorporating new web technologies and making substantially improved tools available to the user, KINARI-2 is designed to automatically ensure the reproducibility of its computational experiments. It is also designed to facilitate incorporating third-party software into computational pipelines and to simplify the process of large scale validation of its underlying model through comprehensive comparisons with other competing coarse-grained models. In this paper we describe the underlying architecture of the new system, as it pertains to experiment management and reproducibility.

This project is supported by NSF CCF-1319366, NSF UBM-1129194 and NIH/NIGMS 1R01GM109456.

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Author information

Authors and Affiliations

  1. School of Computer Science, University of Massachusetts, Amherst, MA, USA

    John C. Bowers, Rose Tharail John & Ileana Streinu

  2. Department of Computer Science, Smith College, Northampton, MA, USA

    Ileana Streinu

Authors
  1. John C. Bowers
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  2. Rose Tharail John
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  3. Ileana Streinu
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Corresponding author

Correspondence to John C. Bowers .

Editor information

Editors and Affiliations

  1. Georgia State University, Atlanta, USA

    Robert Harrison

  2. Old Dominion University, Norfolk, USA

    Yaohang Li

  3. University of Connecticut, Storrs, Connecticut, USA

    Ion Măndoiu

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© 2015 Springer International Publishing Switzerland

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Bowers, J.C., John, R.T., Streinu, I. (2015). Managing Reproducible Computational Experiments with Curated Proteins in KINARI-2. In: Harrison, R., Li, Y., Măndoiu, I. (eds) Bioinformatics Research and Applications. ISBRA 2015. Lecture Notes in Computer Science(), vol 9096. Springer, Cham. https://doi.org/10.1007/978-3-319-19048-8_7

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  • DOI: https://doi.org/10.1007/978-3-319-19048-8_7

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-19047-1

  • Online ISBN: 978-3-319-19048-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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