This entry already shows what I think of a popular open source pathway analysis and visualization program, GenMAPP. It’s quite used to map gene expression data coming from microarrays to metabolic pathways, and in addition to that you can also evaluate enrichment for both pathways and Gene Ontology terms. Last but not least you can create and contribute new metabolic maps.

So why the title of the post? Because, despite being actively developed and with conscious developers that don’t want to break the software with new features, it’s extremely buggy. Yesterday I spent a whole afternoon trying to get it to work. The program doesn’t work if you use the comma as the decimal separator OS-wide, or some applications crash completely if your regional settings (sadly it’s a Windows only program) aren’t set to USA. What’s worse is that such a “feature” has been reported two years ago. I can understand the limited resources and all, but please, those are really basic bugs. It’s not as bad as software “fit for publication”, but still a massive annoyance…