I am a bioinformatician. My background is as a traditional geneticist, my PhD was in the fields of molecular biology (and a little phylogenetics and domain analysis). I only entered the domain of bioinformatics during my Post doctoral years when I worked as a genome annotator for the first green eukaryotic genome project. During this time I learned a lot of PERL, moved into Python and integrated a load of stuff to link my needs with a relational database and distributed jobs across a large cluster to run the typical InterPro / UniProt / nonred type tasks. GUI was never considered (or attempted) and code remained ad hoc until broken.
Now 10 years on from these heady days, I am now writing code in C, Java, R and a little Python. During my few years as an adjunct professor at a Finnish research centre I rewrote the whole software pipeline that I imagined in Java as a rather monolithic beast and have reimplemented the whole stack as something a little more abstracted and perhaps useful over the last few years as a distraction on the daily commute to the capital city. The whole software environment is now several hundred thousand lines of code, we have a rich GUI delivered over HTML and through Java WebStart and things are finally beginning to look how they should have when I first starting planning the project back in 2004.
Critical at this point is how is a self-taught informatician supposed to handle this code? I work alone, there is no code audit and no one works with me to validate, correct or comment on my code! I maintain a single code tree and this is at least within a code versioning system (subversion for bioinformatics is great …), so I am hopefully not completely inept at doing my work.
My question is how should I really manage the long list of non-specific issues, bugs and problems that I routinely encounter. A campaign to resolve an issue that has been introduced through feature creep can take hours if not days, and during this time I undoubtedly discover many more bugs and issues…
At the moment bugs are documented within a text file of problems, issues and events. I have a todo list, and this seems rather inefficient and trivial. I know that something like Bugzilla could work, but this seems rather more complex than is absolutely needed. I also work on a train, and therefore don’t have web access for much of the commute – a client side project that can be synced through SVN would be ideal. I also work on Linux, OSX and Windows, so ideally something that is cross-platform would be great…
This seems like a tall order, and something that there is no simple answer for. What bug tracking software do other bioinformaticians use?