---
author: einar
comments: true
date: 2007-03-29 19:29:42+00:00
layout: page
slug: genbugg
title: GenBUGG
wordpress_id: 205
categories:
- Science
header:
    image_fullwidth: banner_other.jpg
---

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...