Bad bioinformatics software names revisited

I recently have been sorting through lots of old notes files, including many from my time as a genomics researcher at UC Davis. One note file I had was called ‘Strategies for naming bioinformatics software’ and I initially assumed it was one of the blog posts posted on this blog.

However, I couldn’t find it as an actual post and when I did a quick web search, I instead discovered this ‘Bioinformatics lab’ podcast from earlier this year:

I have been out of the field of genomics/bioinformatics for many years now and didn’t know about The Bioinformatics Lab podcast which describes itself as ‘ramblings on all things bioinformatics’.

The conversation between the hosts (Kevin Libuit and Andrew Page) is good and listening to it brought back lots of memories from the many things I’ve written about on this blog. At the end of the episode, Andrew concludes:

“It’s kind of hard. People should bit a bit of effort into it”

100% this! Naming software should definitely not be an afterthought. Andrew goes on:

“Before you do any development on anything, go and choose a really good name and make sure it doesn’t conflict with any trademarks or existing tools, you can Google it easily and it’s not offensive in any language.”

These are the types of things that I have written about extensively on this blog. If you are interested, perhaps start with

Then you can ready any one of the nearly forty posts I wrote which handed out ‘JABBA awards’ which stands for Just Another Bogus Bioinformatics Acronym.

This award series started all the way back in 2013 and the inaugural award went to a tool with the crazy capitalisation of 'BeAtMuSiC'.

There’s also a series of posts on duplicate names in bioinformatics where people haven’t checked whether their software name is stepping on someone else’s toes.

This includes a post about the audacious attempt to name a new piece of bioinformatics software BLAST. There is also a post about the five different tools that are all called ‘SNAP’.

Admittedly I’ve been out of the loop for so long there is the possibility of there being many more SNAPs out there now!

The moral of this blog post is that names are important and it is very easy to mess them up which could end up meaning that fewer people ever discover your tool in teh first place.

Three cheers for JABBA awards

jabba logo.png

These days, I mostly think of this blog as a time capsule to my past life as a scientist. Every so often though, I’m tempted out of retirement for one more post. This time I’ve actually been asked to bring back my JABBA awards by Martin Hunt (@martibartfast)…and with good reason!

There is a new preprint in bioRxiv…

I’m almost lost for words about this one. You know that it is a tenuous attempt at an acronym or initialism when you don’t use any letters from the 2nd, 3rd, 4th, or 5th words of the full software name!

The approach here is very close to just choosing a random five-letter word. The authors could also have had:

CLAMP: hierarChical taxonomic cLassification for virAl Metagenomic data via deeP learning

HOTEL: hierarcHical taxOnomic classificaTion for viral mEtagenomic data via deep Learning

RAVEN: hieraRchical tAxonomic classification for Viral metagenomic data via dEep learNing

ALIEN: hierArchical taxonomic cLassification for vIral metagEnomic data via deep learniNg

LARVA: hierarchicaL taxonomic classificAtion for viRal metagenomic data Via deep leArning

Okay, as this might be my only blog post of 2020, I’ll say CHEERio!

Hopping back for another JABBA award

jabba logo.png

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:

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!

jabba logo.png

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:

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)

jabba logo.png

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?

ANARCI in the UK: time for a new JABBA award

Time for a new JABBA award. This one comes from a group based at the Department of Statistics in Oxford, UK. The paper was published recently in the journal Bioinformatics:

I think they're trying a little too hard to make a clever acronym here:

ANARCI: Antigen receptor Numbering And Receptor ClassificatIon

It's fun but just a little too tenuous for my liking, and so it merits a JABBA award.

Finding bogus bioinformatics acronyms sometimes requires a laser-like focus

jabba logo.png

A new paper has been published in the journal BMC Research Notes:

This name is:

  1. Bogus — the word 'genome' doesn't contribute any letters to 'LASER' and two letters ('S' and 'R') are not derived from the initial letters of words.
  2. Duplicated — there are at least two other bioinformatics tools called LASER (see here and here).
  3. Undiscoverable — you really need to search Google for LASER genome assembly before you see this as a top result.
  4. Ambiguous — large is a very subjective term. The authors imply that LASER is suitable for human genomes. These are larger than some genomes but smaller than others.
  5. Inconsistent — the paper reveals that LASER is built on the code of QUAST (Quality Assessment Tool for Genome Assemblies). This means you end up with the somewhat bizarre documentation for how to run the program called LASER:

The example included with LASER installation can be run as:

./quast.py testdata/contigs1.fasta testdata/contigs2.fasta \ -R testdata/reference.fasta.gz -G testdata/genes.txt \ -O test_data/operons.txt

The output of LASER program can be viewed in file: ./quast_results/latest/report.txt

So to run LASER just type 'quast'!

Time to toggle the JABBA-award status of this bioinformatics software name

Give me a B.
Give me a O.
Give me a G.
Give me a U.
Give me a S.

What have you got?

Another BOGUS bioinformatics acronym! This time it is courtesy of the journal BMC Bioinformatics:

I think you can already see why this one is going to win a JABBA award. The name 'TOGGLE' derives from TOolbox for Generic nGs anaLysEs. Using their same strategy, they could have also gone for BOGGLE, BONNY, or even BORINGLY.

Welcome to the JABBA menagerie: a collection of animal-themed, bogus bioinformatics names…that have nothing to do with animals!

Bioinformaticians make the worst zookeepers:

A

B

C

D

E

F

G

H

I

J

K

L

M

N

O

P

Q

R

S

T

U

V

W

X

Y

Z

 

Other suggestions welcome! Only requirements are that:

  1. The name is bogus, i.e. not a straightforward acronym and worthy of a JABBA award
  2. The acronym is named after an animal (or animal grouping)
  3. The software/tool has nothing to do with the animal in question

In need of some bogus bioinformatics acronyms? Try these on for size…

Three new JABBA awards for you to enjoy (not that anyone should be enjoying these crimes against acronyms). Hold on to your hats, because this might get ugly.

 

1: From the journal Scientific Reports

The paper helpfully points out that the name of this tool is pronounced 'Cadbury'. I'm not sure if they are saying this to invite a trademark complaint but generally I feel that it is never a good sign when someone has to tell you how to pronounce something. The acronym CADBURE is derived as follows:

Comparing Alignment results of user Data Based on the relative reliability of Uniquely aligned REads

On the plus side, CADBURE mostly uses the initial letters of words. On the negative side, only six out of the fifteen words contribute to the acronym and this is why it earns a JABBA award.

 

2: From the journal BMC Bioinformatics

SPINGO is generated as follows:

Species-level IdentificatioN of metaGenOmic amplicons

So only two words contribute the initial letters, 'identification' donates its second N (but not its first), and 'amplicons' gives us nothing at all. Very JABBA-award worthy.

 

3: From the journal Bioinformatics (h/t to James Wasmuth)

It is very common for people to wait until the end of the Introduction before they reveal how the acronym/initialism in question came to be, but in this paper they don't waste any time at all…it's right there in the title.

It is the mark of a tenuously derived acronym when the initial letter of a word isn't used, but the same letter from a different position in the same word is used, e.g. the second 'R' of 'regression'.

While the code for HEALER is available online, none of the five C++ files contain the word HEALER in their name or anywhere in their code. Nor is there any form of README or accompanying documentation. This is all that you see…

Congratulations to our three worthy JABBA award winners!