Hopping back for another JABBA award

So I was meant to have retired myself from handing out JABBA awards to recognise instances of ‘Just Another Bogus Bioinformatics Algorithm’. However, I saw something this week which clearly merits an award.

And so, from a new paper recently published in PLoS ONE I give you:

• GRASShopPER—An algorithm for de novo assembly based on GPU alignments

The three lower-case letters signal that there is going to be some name wrangling going on…so let’s see how the authors arrive at this name:

GRASShopPER: GPU overlap GRaph ASSembler using Paired End Reads

That’s how it is described in the paper, so I guess it could have also been called ‘GOGAUPER’? I find this is another example of a clumsily constructed acronym that could have been avoided altogether.

‘Grasshopper’ is a cool, and catchy, name for any software tool and it doesn’t really need to be retconned into making an awkward acronym.

It does, however, give me one new animal for the JABBA menagerie!

Back from the dead…time for a new JABBA award!

I really wasn't intending to hand out any more JABBA awards. The last time I gave out an award for a bogus bioinformatics acronym was back in February 2016 and that was meant to be that.

However, I recently saw something that sent a shiver down my spine and I felt obliged to dust off the JABBA award one more time (for now anyway).

Let's get straight to the point. Published in bioarXiv is a new preprint:

• BURRITO: An interactive multi-omic tool for visualizing taxa-function relationships in microbiome data

Now don't get me wrong, I love burritos and I think it's kind of a fun name for a piece of software. I just happen to think that in this case it is a somewhat tenuous acronym. So how do you get to make BURRITO the name of your tool?

Browser Utility for Relating micRobiome Information on Taxonomy and functiOn

It's the inclusion of 'O' from 'functiOn' that gets me.I guess 'BURMITF' didn't have such a good ring to it.

What else is on the menu?

Note that BURRITO shouldn't be confused with the QIIME application controller code called burrito-fillings or the electronic lab notebook software for computational researchers known as Burrito.

Also, you get bonus points if you can use BURRITO with SALSA. Of course, if BURRITO doesn't work out for you, then maybe try TACO or…er, TACO.

The last ever awards for Just Another Bogus Bioinformatics Acronym (JABBA)

All good things come to an end…and, more importantly, all bad things come to an end. For that reason, I have, with some sadness, decided to bring my series of JABBA awards (Just Another Bogus Bioinformatics Acronym) to an end.

This is partly because my new job means that I am no longer a bioinformatician. It is also partly because it seems that the flood of bogus bioinformatics acronyms will never cease.

I've tried campaigning to raise awareness of why these acronyms are often awkward, tenuous, and generally unhelpful to the wider community. Hopefully, I've made some of you think about naming your software just a little bit.

I can't go without presenting you with a bumper crop of recently minted JABBA awards…

1. Kicking us off, from BMC Bioinformatics we have a paper titled SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis. This is not excessively bogus, but omitting any contributions to the acronym from the words 'reference-based bacterial' is what gets this earns a tool a JABBA award. Oh, and don't confuse this tool with the 2014 bioinformatics tool called sPARTA. Who would make that mistake?

2. From Nucleic Acids Research we have the following paper…DIDA: A curated and annotated digenic diseases database. DIDA is derived from DIgenic diseases Database. Never a good sign when an acronym only takes letters from two of the three words. Also never a good sign when there is a completely different piece of bioinformatics software that uses the same name (although I think the software mentioned here may have been around first).

3. From Genome Research we have a new paper: SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. SCRaMbLE is derived from Synthetic Chromosome Rearrangement and Modification By LoxP-mediated Evolution. They really could have just gone for 'SCRAMBLE' (all upper-case) as it would be a legitimate acronym. However, my dislike of this name is because it is just a little too tenuous. Oh, and the fact that is already a bioinformatics tool called Scramble.

4. Next up, from the journal BMC Bioinformatics we have NEAT: a framework for building fully automated NGS pipelines and analyses. NEAT derives from NExt generation Analysis Toolbox. Leaving aside the general issue of how I feel about NGS as a phrase, this name is bogus for taking two letters from 'next' and none from 'generation'. Oh, and there is also a bioinformatics tool called NeAT.

5. From the journal Bioinformatics we have…ParTIES: a toolbox for Paramecium interspersed DNA elimination studies. Let's break that acronym down: PARamecium Toolbox for Interspersed dna Elimination Studies. As I've always said, ain't no party like a Paramecium party.

6. Okay, are you sitting down? Next we have a paper published in the journal Bioinformatics. The title is going to make you very curious…SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. Surely nobody was seriously going to try to make an acronym called SUPER-FOCUS? Oh wait they have…SUbsystems Profile by databasE Reduction using FOCUS. Any time you have the word 'database' as part of your software name and you choose to use just the last letter of this word…that's a bogus acronym, or should I say SUPER-BOGUS?

That is your lot. I reserve the right to maybe come back with one more JABBA-related post to present my top 10 JABBA awards. I'll end with a brief summary of the advice that I've tried to impart many times before:

1. Not all software needs to have an acronym…you could choose to call your novel transcriptome validator 'Keith' rather than tenuously coming up with KEITH: Kmer-Enriched Inspection of Transcript deptH.
2. Preferably, do not name your acronym after animals …especially when your software has no connection with that animal.
3. Check: has anyone else has used that name before? Search Google with your intended name plus the word 'bioinformatics'.
4. Check: is your name pronounceable? Tell the name to your parents over the phone and ask them if they can spell it correctly.
5. Check: are you using random capitalisation to be cool (or 'KeWL' even)? Will other people who reference your software likely bother to use the italicised superscript font that you unwisely chose to use for every other letter in your software name?