The Open2Dprot project is “a community effort to create an open source n-dimensional (n-D) protein expression data analysis system”. It looks very promising and has a lot of interesting thoughts about how a 2D (nD) gel analysis should be done. It has a modular approach (each step will be caried by a specific tool or “subproject”; I think this is a good thing, à-la-Unix), it’s based on an old but functional version of Gellab-II and will be using Java (for the disponibility of the proprietary-JVMs under many operating systems), R (for the stats), SVG for graphics and MySQL/PostgreSQL for storing data. They even have plans to extend the use of Open2Dprot to n dimensions, incorporating tools for microarrays, liquid chromatography, mass spectrometry. When it will be finished, it will be a cool and useful tool, from the beginning of the proteome(s) analysis to its end. And we won’t be dependent on proprietary – and costly – software from big companies anymore.

But this is the problem: “when it will be finished” … Although they have plenty of good ideas, I modestly think that they are lacking practical stuff. Some subprojects already have released files but some of the functions are not functional (I didn’t succeeded segmenting a .tiff and a .gif images with Seg2Dgel). I think that the goals are too high and too theorical to be achieved soon. Maybe it’s time to have another short, small, practical project, just for segmenting 2D gels. Later, it could perhaps be integrated in the Open2Dprot project …

• Proteomics