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Cost of Irreproducible Research

Published Material

 

Better reporting for better research: a checklist for reproducibility

Mesirov JP. Accessible Reproducible Research. Science Vol 327 22 January 2010.

  • http://dx.doi.org/10.1126/science.1179653
  • Nice, succinct (2 pages) overview of the issues in reproducible and accessible research, has paragraph with good description of the complicated, modern data analysis pipeline, coins the RRS term (not sure?), GenePattern-Word RRS, author is PI of GenePattern project.

Goecks et al.: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology 2010 11:R86.

  • http://dx.doi.org/10.1186/gb-2010-11-8-r86
  • Makes reference to Ioannidis paper, compares Galaxy to GenePattern and Mobyle (other RRSs), also compares Galaxy to Bioconductor and Taverna, mentions participation in Genomespace.

Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, Falchi M, Furlanello C, Game L, Jurman G, Mangion J, Mehta T, Nitzberg M, Page GP, Petretto E, van Noort V. Repeatability of published microarray gene expression analyses. Nat Genet. 2009 Feb;41(2):149-55. Epub 2008 Jan 28. PMID: 19174838.

An invitation to reproducible computational research

  • Donoho DL.Department of Statistics, Stanford University, Stanford, CA 94305, USA. donoho@stanford.edu

DERIVING CHEMOSENSITIVITY FROM CELL LINES: FORENSIC BIOINFORMATICS AND REPRODUCIBLE RESEARCH IN HIGH-THROUGHPUT BIOLOGY

Koenker, Roger and Zeileis, Achim (2007) Reproducible Econometric Research. A Critical Review of the State of the Art. Research Report Series / Department of Statistics and Mathematics, 60. Department of Statistics and Mathematics, WU Vienna University of Economics and Business, Vienna.

Gentleman, R., Lang, D., Statistical Analyses and Reproducible Research, Berkeley Electronic Press, 2004.

Gentleman, R., Reproducible Research: A Bioinformatics Case Study, Berkeley Electronic Press, 2004.

Peng, R., Dominici, F., Zeger S., Reproducible Epidemiologic Research, American Journal of Epidemiology, Vol. 163, No. 9, 2006.

Lane, P., Gobet, F., Developing reproducible and comprehensible computational models., Artificial Intelligence 144 (2003) 251-263.

Buckheit, J., Donoho, D., Wavelab and Reproducible Research, 1995.

This is a short but handy page on what should 'go in' for a reproducible research paper.

Nice wiki page on following guidelines on scientific citations

Enabling Reproducible Research: Open Licensing For Scientific Innovation

Reproducible Research in R : Talks about how you should record (The way you downloaded data).

Evidence that sharing research data improves the citation of a publication

Reproducible Research in Genome Technology:

Nature news feature on importance of data sharing for reproducible research

Reproducible Statistical Research in Practice
http://www.r-bloggers.com/RUG/2010/08/user-2010-conference-videos/

Reproducible Research Systems (RRS)

Galaxy

GenePattern

Taverna

Mobyle

Case Study

Update on Myth Busting: Number of Grants per Investigator. May 13, 2011 by Sally Rockey

Blog Posts Discussing Reproducible Research in Genomics

http://johnhawks.net/weblog/topics/metascience/timmer-biology-computer-replication-2010.html

http://arstechnica.com/science/2010/01/keeping-computers-from-ending-sciences-reproducibility/

http://sciblogs.co.nz/code-for-life/2010/01/24/reproducible-research-and-computational-biology/

http://blog.openhelix.eu/?p=5164

Tutorials

Workflows for reproducible research in computational neuroscience

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