Brussels / 2 & 3 February 2013


Packaging mass spectrometry software in Debian

Mass spectrometry is a scientific field that has revolutionized the way we look at biochemical objects, and thus also at cells and organs, leading to enormous advances in biology these last 10-15 years. Mass spectrometry is a rather recent field in biology (converse to other fields, like genetics, genomics). Therefore, awareness about Free Software is very low among mass spectrometrists. Only since the last few years are people starting to develop on Free Software systems (Ubuntu, for example). But the mentality still has to progress a bit, as for the moment people develop software and keeps that soft in their lab without thinking about packaging it for their platform. I want to develop a project similar to NeuroDebian, that would bring to the mass spectrometrists a Debian platform for developing software and building mass data analysis workflows all based on Free Software.

One other aspect of software in mass spectrometry is related to the fact that mass spec vendors are trying hard the MS strategy to lock-in users in black-box data formats. We need to force them to open the formats or at least to force them to write proper full-featured converters to open standard formats. Free software must be a way to force vendors to behave properly. There are thousands of terabytes of biological data at stake.


Filippo Rusconi