Anthony Scopatz

I think, therefore I amino acid.

inSCIght Episode 5: Reproducibility in Scientific Computing

This was originally published at inSCIght.

Listen to the podcast

On episode 5, by popular demand, we discuss the theme of reproducibility in scientific computing. Today we hit on a lot of topics, but don’t be saddened by the current state-of-affairs! We also cover tools, standards, and attitudes that provide new hope for a brighter future.

The moral: Conversations on reproducibility need to continue.

If we were to record this episode again its hosts would include:

  • Neil Best (special guest)
  • Katy Huff (inspiration from episode 1)
  • Luis Ibanez (special guest)
  • Anthony Scopatz (moderator)

Joining us this week is Luis Ibanez, who is a Technical Leader at Kitware, Inc. He has been one of the main developers of the Insight Toolkit (ITK) for the past ten years of the project. He is one of the Editors of the Insight Journal, the only Journal with reproducible papers in the medical imaging field.

Additionally, in a special double-guest treat, we also have Neil Best on the show.  Neil is a database manager at the University of Chicago’s Computation Institute and a graduate student in Geography & Environmental Studies at Northeastern Illinois University. He is applying the reproducible research paradigm to the creation of a hybrid land-use/land-cover data set from multiple geospatial data sets using R and Sweave. The product of this work will initialize models of economy/agriculture/climate change interactions that will run in high-performance computing environments at the CI.

Intro/Outro Music: ‘Ten Thousand Strong’ -Iced Earth

Show Links:

  1. CDE (http://www.stanford.edu/~pgbovine/cde.html)
  2. Elsevier Executable Paper Challenge (http://www.executablepapers.com/)
  3. Sumatra, which we forgot to talk about (http://neuralensemble.org/trac/sumatra/wiki)
  4. PASS: Provenance Aware Storage Systems (http://www.eecs.harvard.edu/syrah/pass/)

Open Access / Reproducible Research Journals You Should Know About:

  1. Reproducible Research (http://reproducibleresearch.net/index.php/RR_links)
  2. Insight Journal (http://www.insight-journal.org/)
  3. Open Research Computation (http://www.openresearchcomputation.com/)
  4. Journal of Statistical Software (http://www.jstatsoft.org/)
  5. Theory of Computing (http://theoryofcomputing.org/)

inscight

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