What is Reproducibility?

• Blog post (C TItus Brown): ivory.idyll.org
  • Basic reproducible paper HOWTO
• 10 Simple Rules for RR: plosone
• Open Access: A researcher's perspectice (Karl Broman): pdf
  • "OA is about money"
• Replicability is not Reproducibility: pdf
• Lior Pachter: 'Reproducibility vs. usability': liorpachter.wordpress.org
• David Stern's 'prescription' for reproducibility in science: bmc blog
• Protocol-based approach: khmer protocols
  • blog post: ivory.idyll.org
  • Trinity RNAseq protocols (Broad Inst.): nature
  • Idea: provide general protocols (software to use, suggested parameters, expected outputs) rather than pipelines
  • Less prone to bitrot / compat issues / platform isssues; diff programs can be substituted when obsolete
• Victoria Stodden: Computational Sci. Best Practices: scholar.google.com
• Measuring RR in Computer Systems Research: pdf
  • Summary: most papers are not reproducible
• Robert Gentleman views on Reproducible Research
  • A very nice an concise presentation Reproducible Research (2011)
  • Statistical Analyses and Reproducible Research
  • Reproducible Research: A Bioinformatics Case Study (2004)
• Reproducible Research and Programming

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