[Esip-preserve] Fwd: PLOS Computational Biology: Ten Simple Rules for Reproducible Computational Research

[Curt Tilmes]

-------- Original Message --------
Subject: 	PLOS Computational Biology: Ten Simple Rules for Reproducible 
Computational Research
Date: 	Sun, 27 Oct 2013 07:54:56 -0600
From: 	Steve Aulenbach <saulenbach at usgcrp.gov>


*PLOS Computational Biology: Ten Simple Rules for Reproducible 
Computational Research*
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003285;jsessionid=4AFC0E022E4769E5856CC5BB897EF6F9 


"Replication is the cornerstone of a cumulative science [1]. However, 
new tools and technologies, massive amounts of data, interdisciplinary 
approaches, and the complexity of the questions being asked are 
complicating replication efforts, as are increased pressures on 
scientists to advance their research [2]. As full replication of studies 
on independently collected data is often not feasible, there has 
recently been a call for reproducible research as an attainable minimum 
standard for assessing the value of scientific claims [3]. This requires 
that papers in experimental science describe the results and provide a 
sufficiently clear protocol to allow successful repetition and extension 
of analyses based on original data [4].

[...]

We here present ten simple rules for reproducibility of computational 
research. These rules can be at your disposal for whenever you want to 
make your research more accessible---be it for peers or for your future 
self."


  * Rule 1: For Every Result, Keep Track of How It Was Produced
    <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003285#s2>
  * Rule 2: Avoid Manual Data Manipulation Steps
    <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003285#s3>
  * Rule 3: Archive the Exact Versions of All External Programs Used
    <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003285#s4>
  * Rule 4: Version Control All Custom Scripts
    <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003285#s5>
  * Rule 5: Record All Intermediate Results, When Possible in
    Standardized Formats
    <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003285#s6>
  * Rule 6: For Analyses That Include Randomness, Note Underlying Random
    Seeds
    <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003285#s7>
  * Rule 7: Always Store Raw Data behind Plots
    <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003285#s8>
  * Rule 8: Generate Hierarchical Analysis Output, Allowing Layers of
    Increasing Detail to Be Inspected
    <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003285#s9>
  * Rule 9: Connect Textual Statements to Underlying Results
    <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003285#s10>
  * Rule 10: Provide Public Access to Scripts, Runs, and Results
    <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003285#s11>


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