Software Carpentry

Helping scientists make better software since 1997

Archive for March 2007

Sign Error => Five Papers Retracted

Via Genome Biology (free registration for trial access required), news that scientists from the Scripps Institute have to retract five papers published in various prestigious journals because of a sign error in a computer program. As Gregory Petsko says in the article:

Their mistake has consequences beyond the damage to the unfortunate young investigator and his team. For five years, other labs have been interpreting their biophysical and biochemical data in terms of the wrong structures. A number of scientists have been unable to publish their results because they seemed to contradict the published X-ray structures. I personally know of at least one investigator whose grant application was turned down for funding because his biochemical data did not agree with the structures. One could argue that an entire sub-field has been held back for years…

If I was a twenty-something working toward my PhD, I’d be thinking very hard about how I was going to validate the programs I was writing—the odds are growing steadily that journal editors and granting agencies are going to start demanding some sort of due diligence, sooner rather than later.

Written by Greg Wilson

2007/03/19 at 14:46

Posted in Opinion

SciPy’07 Dates Announced

According to, The SciPy 2007 Conference will be on August 16-17 this year; tutorials and sprints will run on the 14th, 15th, and 18th.  I won’t be able to attend (new baby), but I’d like to organize a half-day or one-day session to update and extend the Software Carpentry notes.  Lots of modules need writing, both on Python-specific stuff and on general software engineering skills for scientists and engineers.  I’d particularly like to see:

  • A lecture or two on NumPy (used to have one, it fell behind Travis Oliphant’s coding, and it’s probably now the biggest gap in the lectures)
  • A whole lecture on the subprocess module, job control, and remote execution
  • A second lecture on security
  • Some screencasts on Python IDEs (Wing 101, IDLE, Eclipse, and Komodo)
  • A lecture on connecting to C and Fortran
  • A lecture on design patterns
  • A lecture on professional ethics and responsibilities
  • And stuff on requirements, traceability, data lineage, and, oh, what else do you want?

If you’re interested, please let me know…

Written by Greg Wilson

2007/03/11 at 09:50

Posted in Community

Reproducibility of Computational Results

Via Titus Brown, a link to the Insight Journal, an open access online publication covering medical image processing. They have a very interesting process requirement: your source code must compile & be verifiable by an automatic system. I’ve been expecting something like this for a long time; glad to see it happening.

Later: and, via Gary Bader, Source Code for Biology and Medicine.  Anyone know of a journal or journals like this for physics, chemistry, geology, and other non-life-science areas?  Or (wistfully) computer science?

Written by Greg Wilson

2007/03/10 at 16:41

Posted in Content


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