My very old, new blog.
06 September 2013
24 August 2013
The real advantage of a "human readable" model definition format
A colleague of mine wanted to submit a model along with a paper that they had published and had somehow converted from their native format into SBML, unfortunately this had not been entirely successful and I was asked to diagnose the problem after COPASI reported a serious error in the file.
Using PySCeS I converted the file to the PySCeS model format where some translation errors were immediately apparent, could be compared to the original equation and fixed. Reloading the file, testing the steady-state solution and re-exporting it to SBML was a piece of cake.
Not bad going for a Friday afternoon ;-)
Using PySCeS I converted the file to the PySCeS model format where some translation errors were immediately apparent, could be compared to the original equation and fixed. Reloading the file, testing the steady-state solution and re-exporting it to SBML was a piece of cake.
Not bad going for a Friday afternoon ;-)
25 July 2013
Funky Amsterdam promotional video
This is a new advertisement for Amsterdam as a cool tourist destination ... and why its nice to live there ;-)
15 July 2013
Finally registered on GitHub
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.
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.
- 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:
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.
- 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.
Subscribe to:
Posts (Atom)