The latest issue of the journal Bioinformatics was released today and as with most issues, it features a large number of bioinformatics tools and resources. Many of these tools feature questionable use of acronyms and initialisms and so it is time to hand out some new JABBA awards.
A quick reminder, JABBA stands for 'Just Another Bogus Bioinformatics Acronym'. I recently gave out the inaugural JABBA award and have since discovered that JABBA is not the only game in town (if the game is critically evaluating the overreaching use of acronymns in science). Step forward ORCA - the Organisation of Really Contrived Acronyms, a blog that was started by an old bioinformatics colleague of mine. I highly recommend checking this out to see more acronym-derived-crimes.
Anyway, here are the several nominations for JABBA awards from the latest issue of Bioinformatics:
- MaGnET: Malaria Genome Exploration Tool - My main issue with this one is the ungainly capitalization. There is also the issue that the tool is in no way related to magnets so if you don't remember the fact that it is called MaGnET then it it hard to find. A Google search for malaria tool doesn't feature MaGnET on the first page of hits.
- MMuFLR: missense mutation and frameshift location reporter - Okay, so part of me thinks that this is probably meant to be pronounced 'muffler'? If this is not the case, then it doesn't really roll of the tongue. "Oh you're looking to find missense and frameshift mutations? Then you should try em-em-yoo-ef-el-ar". It doesn't help when you follow the link in the article to find the resource (a Galaxy workflow) only to find no mentions of MMuFLR on the resulting page (unless you search for it).
- mRMRe: an R package for parallelized mRMR ensemble feature selection - Some of the same reasons that applied to MMuFLR also apply to mRMRe. Try saying this three times fast and you'll see what I mean. It seems that mRMRe is an 'ensemble' implementation of something called mRMR (minimum redundancy maximum relevance). Still not sure why the first 'm' is free from the need of capitalization (or the 'e' for 'ensemble').
- TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference - Aways a bit suspicious when you have a tool name that features 15 words but somehow gets reduced to 5 letters for the abbreviated name. Could equally make a case that this tool should be called TIRBI. In any case, TIGAR is quite an unusual spelling and you might think that a Google search for TIGAR would put this resource near the top of the results. However it also seems that TIGAR is the The Inland Gateway Association of Realtors as well as The International Gymnastics Academy of the Rockies. But perhaps more importantly, TIGAR already has a scientific connection as it also the name of a gene (TIGAR: TP53-induced glycolysis and apoptosis regulator00762-8)).
Thanks to Bioinformatics journal for providing some new JABBA recipients.