16 June 2013

Open source and free-to-use

I've just returned from a trip to Latvia and after discussions there was reminded of the value of open source, freely available/usable software. Of course while working in South Africa I was acutely aware of this but after living in the Netherlands for a while one gets spoilt (and lazy). What do I mean? Unless your definition of Science is such that it is restricted to the "wealthier western world" e.g.

  • Windows is not free

  • MATLAB (and especially it's toolboxes) are not free

  • academic access to commercial software is not free

  • publishing in open access journals is not free

Even though it is more difficult, takes more time and could even be career counter productive, I believe that development in Life Science software (a foundation/basic activity) should be as unrestricted (widely available) as possible.

The question of course is how does one try to convey this to funders, reviewers etc - who are embedded in a more affluent environment - that this is a valid consideration.

A more general question is whether it is worth the effort of developing a freely available tool when one can quickly whip up the code in something like MATLAB (or any other software based on a commercial platform)? In the end this starts to look like more like an ethical question e.g. "Science and Society"  than a practical one. of course whether practicing research Scientists should be concerning themselves with this sort of dilemma is up to the individual.

05 June 2013

PySCeS 0.9.0 has been released

Finally, after far too long, I'm happy to release a new version of PySCeS. This release has many bug fixes and provides a diverse range of new features, including:

  • parallel parameter scanning

  • generalized supply demand analysis

  • exporting simulations as SED-ML (including COMBINE archives)

  • support for scanning moiety totals

  • compatbility support for the latest versions of scipy/numpy

  • enhanced plotting support e.g. users may now choose the Matplotlib backend

This hopefully is the start of a whole new development/maintenance cycle, more news on the PySCeS website (http://pysces.sf.net) and thanks to Che for helping to debug an irritating Windows issue.