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_posts/2007-03-29-genbugg.markdown

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+---
+author: einar
+comments: true
+date: 2007-03-29 19:29:42+00:00
+layout: post
+slug: genbugg
+title: GenBUGG
+wordpress_id: 205
+categories:
+- Science
+---
+
+This entry already shows what I think of a popular open source pathway analysis and visualization program, [GenMAPP](http://genmapp.org). 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](http://www.geneontology.org) 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](http://groups.google.com/group/GenMAPP/browse_thread/thread/655f3d515b7460fe/0f6afe0582df6b74?lnk=gst&q=MAPPFinder.cfg&rnum=1#0f6afe0582df6b74). 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"](http://www.nodalpoint.org/2006/12/01/software_fit_for_publication), but still a massive annoyance...