Free Access
Issue
Biologie Aujourd'hui
Volume 211, Number 3, 2017
Page(s) 233 - 237
Section La biologie computationnelle parle à la biologie expérimentale
DOI https://doi.org/10.1051/jbio/2017029
Published online 7 février 2018
  • Allison, D.B., Brown, A.W., George, B.J., Kaiser, K.A. (2016). Reproducibility: A tragedy of errors. Nature, 530, 27-29. [CrossRef] [PubMed] [Google Scholar]
  • Baker, M. (2016). Muddled meanings hamper efforts to fix reproducibility crisis. Nature News. DOI: 10.1038/nature.2016.20076. [Google Scholar]
  • Belmann, P., Dröge, J., Bremges, A., McHardy, A.C., Sczyrba, A., Barton, M.D. (2015). Bioboxes: standardised containers for interchangeable bioinformatics software. Gigascience, 4, 47. [CrossRef] [PubMed] [Google Scholar]
  • Blankenberg, D., Von Kuster, G., Bouvier, E., Baker, D., Afgan, E., Stoler, N; Galaxy Team, Taylor J., Nekrutenko, A. (2014). Dissemination of scientific software with Galaxy ToolShed. Genome Biol, 15, 403. [Google Scholar]
  • Bray, N. L., Pimen tel, H., Melsted, P., Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol, 34, 525-527. [CrossRef] [PubMed] [Google Scholar]
  • Byron, S.A., Van Keuren-Jensen, K.R., Engelthaler, D.M., Carpten, J.D., Craig, D.W. (2016). Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet, 17, 257-271. [CrossRef] [PubMed] [Google Scholar]
  • Di Tommaso, P. (2016). A curated list of Nextflow pipelines. Available at: https://github.com/nextflow-io/awesome-nextflow/ (Accessed: 18th May 2016). [Google Scholar]
  • Di Tommaso, P., Chatzou, M., Floden, E.W., Prieto Barja, P., Palumbo, E., Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nat Biotech, 35, 316-319. [CrossRef] [Google Scholar]
  • Garijo, D., Kinnings, S., Xie, L., Xie, L., Zhang, Y., Bourne, P.E., Gil, Y. (2013). Quantifying reproducibility in computational biology: the case of the tuberculosis drugome. PLoS One, 8, e80278. [CrossRef] [PubMed] [Google Scholar]
  • Goecks, J., Nekrutenko, A., Taylor, J. (2010). Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol, 11, R86. [CrossRef] [PubMed] [Google Scholar]
  • Goodman, S. N., Fanelli, D., Ioannidis, J.P.A. (2016). What does research reproducibility mean? Sci Transl Med, 8, 341ps12. [CrossRef] [PubMed] [Google Scholar]
  • Hosny, A., Vera-Licona, P., Laubenbacher, R., Favre, T. (2016). AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms. Bioinformatics, 32, 2396-2398. [CrossRef] [PubMed] [Google Scholar]
  • Koster, J., Rahmann, S. (2012). Snakemake-a scalable bioinformatics workflow engine. Bioinformatics, 28, 2520-2522. [CrossRef] [PubMed] [Google Scholar]
  • Kurs, J.P., Simi, M., Campagne, F. (2016). NextflowWorkbench: Reproducible and reusable workflows for beginners and experts. bioRxiv, 041236. DOI: 10.1101/041236. [Google Scholar]
  • LeVeque, R.J., Mitchell, I.M., Stodden, V. (2012). Reproducible research for scientific computing: Tools and strategies for changing the culture. Comput Sci Eng, 14, 13-17. [CrossRef] [Google Scholar]
  • Loman, N., Watson, M. (2013). So you want to be a computational biologist? Nat Biotechnol, 31, 996-998. [CrossRef] [PubMed] [Google Scholar]
  • Masca, N.G., Hensor, E.M., Cornelius, V.R., Buffa, F.M., Marriott, H.M., Eales, J.M., Messenger, M.P., Anderson, A.E., Boot, C., Bunce, C., Goldin, R.D, Harris, J., Hinchliffe, R.F., Junaid, H., Kingston, S., Martin-Ruiz, C., Nelson, C.P., Peacock, J., Seed, P.T., Shinkins, B., Staples, K.J., Toombs, J., Wright, A.K., Teare, M.D. (2015). RIPOSTE: a framework for improving the design and analysis of laboratory-based research. Elife, 4. DOI: 10.7554/eLife.05519. [CrossRef] [Google Scholar]
  • Moreews, F., Sallou, O., Ménager, H., Le Bras, Y., Monjeaud, C., Blanchet, C., Collin, O. (2015). BioShaDock: a community driven bioinformatics shared Docker-based tools registry. F1000Res, 4, 1443. [PubMed] [Google Scholar]
  • Perkel, J. (2016). Democratic databases: science on GitHub. Nature News, 538, 127. [CrossRef] [Google Scholar]
  • Piccolo, S.R., Frampton, M.B. (2016). Tools and techniques for computational reproducibility. Gigascience, 5, 30. [CrossRef] [PubMed] [Google Scholar]
  • Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690. [CrossRef] [PubMed] [Google Scholar]
  • Steinbiss, S., Silva-Franco, F., Brunk, B., Foth, B., Hertz-Fowler, C., Berriman, M., Otto, T.D. (2016). Companion: a web server for annotation and analysis of parasite genomes. Nucleic Acids Res, 44, W29-34. [CrossRef] [PubMed] [Google Scholar]
  • Vivian, J. (2016). Rapid and efficient analysis of 20, 000 RNA-seq samples with Toil. bioRxiv, 062497. DOI: 10.1101/062497. [Google Scholar]

Current usage metrics show cumulative count of Article Views (full-text article views including HTML views, PDF and ePub downloads, according to the available data) and Abstracts Views on Vision4Press platform.

Data correspond to usage on the plateform after 2015. The current usage metrics is available 48-96 hours after online publication and is updated daily on week days.

Initial download of the metrics may take a while.