Archive for the 'Uncategorized' Category

Greg Wilson has a new blog post Legal Frameworks for Reproducible Research.

I just found out about  coNCePTuaL, a project that promotes reproducible research in the context of performance measurements for high-speed computer networks.  (The capitalized letters in the name stand for Network Correctness and Performance Testing Language.)

The project is located at  http://conceptual.sourceforge.net/ and is described in the paper Reproducible network benchmarks with coNCePTuaL by Scott Pakin of Los Alamos National Laboratory.

Some of the highlights of coNCePTuaL:

• Performance tests (timed network-communication patterns) are described in a precise but English-like “executable pseudocode” designed for basic readability, even by someone not familiar with coNCePTuaL.
• Output files produced by coNCePTuaL-based performance tests include not only the measurements but the code describing the  test itself and a detailed description of the experimental platform on which the code ran.  This enables a third party to see exactly what was run, how it was run, and what the results were, all in one file.
• coNCePTuaL can automatically produce space-time diagrams of the communication pattern for additional clarity of presentation.

Sweave has been discussed here many times, but here’s a brief description for those just joining the discussion. Sweave is a tool for embedding R code inside LaTeX files, analogous to the way web development languages such as PHP or GCI embed scripting code in HTML. When you compile an Sweave file, the R code executes and the results (and optionally the source code) are inserted into the LaTeX output.

Sweave has the potential to make statistical analyses more reproducible. But I doubt many realize its vulnerabilities. The Sweave files are likely to have implicit dependencies on R session state or data located outside the file. You don’t really know that the output is reproducible until it’s compiled by someone else in a fresh environment.

My proposal is a service that lets you submit an Sweave file and get back the resulting LaTeX and PDF output. An extension to this would allow users to also upload data files along with their Sweave file so not all data would have to be in the Sweave file itself. For good measure, there should be some checksums to certify just what input went into producing the output.

Here’s one way I see this being used. Suppose you’re about to put a project on the shelf for a while. For example, you’re about to submit a paper to a journal.You may need to come back and make changes six months later. You think about the difficulty you’ve had in the past with these sorts of edits and want to make sure it doesn’t happen again. So you submit your Sweave document to the build server to verify that it is self-contained.

Here’s another scenario. Suppose you’ve asked someone whom you supervise to produce a report. Instead of letting them give you a PDF, you might insist they give you an Sweave file that you then run through the build service to make your own PDF. That way you can have the whole “but it works on my machine” discussion now rather than having it months later after the person who make the report has a new computer or a new job.

Michael Neilsen posted an excellent article this morning Three myths of scientific peer review. He points out that peer review has only become common in the last 40 or 50 years. Maybe a few years from now someone will write an article looking back at how reproducible research came to be de rigueur. No one questions whether peer review is a good thing, though many people have complaints about the current system and argue about ways to make it better. Maybe the same will be said for reproducible research some day.

Computing in Science and Engineering has just come out with a special issue on reproducible research.  (When you first visit the link, you need to click on “vol 11.” The page is doing some fancy JavaScript that makes it impossible to link directly to the issue.)

The following articles on RR are included.

Guest Editors’ Introduction: Reproducible Research

Sergey Fomel, University of Texas at Austin
Jon F. Claerbout, Stanford University

Reproducible Research in Computational Harmonic Analysis
David L. Donoho, Stanford University
Arian Maleki, Stanford University
Inam Ur Rahman, Apple Computer
Morteza Shahram, Stanford University
Victoria Stodden, Harvard University

Python Tools for Reproducible Research on Hyperbolic Problems
Randall J. LeVeque, University of Washington

Distributed Reproducible Research Using Cached Computations
Roger D. Peng, Johns Hopkins Bloomberg School of Public Health
Sandrah P. Eckel, Johns Hopkins Bloomberg School of Public Health

The Legal Framework for Reproducible Scientific Research: Licensing and Copyright
Victoria Stodden, Harvard University