Bioinformatics software names: the good, the bad, and the ugly

The Good

Given that I spend so much time criticising bad bioinformatics names, I probably should make more of an effort to those occasional flag names that I actually like! Here are a few:

RNAcentral: an international database of ncRNA sequences

A good reminder that a bioinformatics tool doesn't have to use acronyms or intialisms! The name is easy to remember and makes it fairly obvious as to what you might expect to find in this database.


KnotProt: a database of proteins with knots and slipknots

A simple, clever, and memorable, name. And once again, no acronym!


WormBase and FlyBase

Some personal bias here — I spent four years working at WormBase — but you have to admire the simplicity and elegance of the names. 'WormBase' sort of replaced it's predecessor ACeDB (A Caenorhabidtis elegans DataBase). I say 'sort of' because ACeDB was the name for both the underlying software (which continued to be used by WormBase) and the specific instance of the database that contained C. elegans data. This led to the somewhat confusing situation (circa 2000) of there being many public ACeDB databases for many different species, only one of which was the actual ACeDB resource with worm data.

The Bad

These are all worthy of a JABBA award:

The human DEPhOsphorylation database DEPOD: a 2015 update

I find it amusing that they couldn't even get the acronym correctly captitalized in the title of the paper. As the abstract confirms, the second 'D' in 'DEPOD' comes from the word 'database' which should be capitalized. So it is another tenuous selection of letters to form the name of the database, but I guess at least the name is unique and Google searches for depod database don't have any trouble finding this resource.


IMGT®, the international ImMunoGeneTics information system® 25 years on

It's a registered trademark and that little R appears at every mention of the name in the paper. This initialism is the first I've seen where all letters of the short name come from one word in the full name.


DoGSD: the dog and wolf genome SNP database

I have several issues with this:

  1. It's a poor acronym (not explicitly stated in the paper): Dog and wolf Genome Snp Database
  2. The word 'dog' contributes a 'D' to the name, but then you end up with 'DoG' in the final name. It looks odd.
  3. What did the poor wolf do to not get featured in the database name?
  4. The lower-case 'O' means that you potentially can read this as dog-ess-dee or do-gee-ess-dee.
  5. Why focus the name on just two types of canine species? What if they wanted to add SNPs from Jackals or Coyotes, are they going to change the name of the database? They could have just called this something like 'The Canine SNP Database' and avoided all of these problems.

The Ugly

Maybe not JABBA-award winners, but they come with their own problems:

MulRF: a software package for phylogenetic analysis using multi-copy gene trees

Sometimes using the lower-case letter 'L' in any name is just asking for trouble. Depending on the font, it can look like the number 1 or even a pipe character '|'. The second issue is concerns the pronouncability of this name. Mull-urf? Mull-ar-eff? It doesn't trip off the tongue.


DupliPHY-Web: a web server for DupliPHY and DupliPHY-ML

This tool is all about looking for gene duplications from a phylogenetic perspective, hence 'Dupli' + 'PHY'. I actually think this is quite a good choice of name, except for the inconsistent, and visually jarring, use of mixed case. Why not just 'Dupliphy'?


ChiTaRS 2.1—an improved database of the chimeric transcripts and RNA-seq data with novel sense–antisense chimeric RNA transcripts

It's not spelt out in detail, but one can assume that 'ChiTaRS' derives from the following letters: CHImeric Transcripts And Rna-Seq data. So it is not being a bogus bioinformatics acronym in that respect. But I find it visually unappealing. Mixed capitalization like this never scans well.


DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

The paper doesn't explicitly state how the word 'DoRiNA' is formed other than saying:

we have built the database of RNA interactions (doRiNA)

So one can assume that those letters are derived from 'Database Of Rna INterActions'. On the plus side, it is a unique name easily searchable with Google. On the negative side, it seems strange to have 'RNA' as part of your database name, only with an additional letter inserted inbetween.

Metassembler: Merging and optimizing de novo genome assemblies →

There's a great new paper in bioRxiv by Alejandro Hernandez Wences and Michael Schatz. They directly address something I wondered about as we were running the Assemblathon contests. Namely, can you combine some of the submitted assemblies to make an even better assembly? Well the answer seems to be a resounding 'yes'.

For each of three species in the Assemblathon 2 project we applied our algorithm to the top 6 assemblies as ranked by the cumulative Z-score reported in the paper…

We evaluated the correctness and contiguity of the metassembly at each merging step using the metrics used by the Assemblathon 2 evaluation…

In all three species, the contiguity statistics are significantly improved by our metassembly algorithm

Hopefully their Metassembler tool will be useful in improving many other poor quality assemblies that are out there!

My favorite bioinformatics blogs of 2014

Yeah, so I’m a little late in getting around to writing this! The following are not presented in any particular order…


Blog: In between lines of code
Creator: Lex Nederbragt (@lexnederbragt)
Frequency of updates: maybe 1 post a month on average (but it can vary)
Recommended blog post: Developments in next generation sequencing – June 2014 edition

This blog primarily focuses on developments in modern sequencing technology and genome assembly. Required reading if you have an interest in the state of current sequencing technologies, and more importantly, where they are heading.

Blog: Bioinformatician at large
Creator: Ewan Birney (@ewanbirney)
Frequency of updates: less than 1 post a month on average
Recommended blog post: A cheat’s guide to histone modifications

Ewan doesn’t update the blog very often, but when he does post, he usually takes the time to provide us with a very detailed look at some aspect of genomics. Many of his posts explore the underlying science that people are addressing through various genomics/bioinformatics approaches.

Blog: Loman Labs Blog
Creator: Nick Loman (@pathogenomenick)
Frequency of updates: 1–2 posts a month on average
Recommended blog post: The infinite lie of easy bioinformatics

Nick covers lots of material relating to metagenomics and sequencing in general. As a self-confessed Oxford Nanopore fan boy he has some interesting thoughts and observations to share about this nascent sequencing technology, but he writes about most modern sequencing technologies. He also likes the occasional rant from time to time (don’t we all?).

Blog: Living in an Ivory Basement Stochastic thoughts on science, testing, and programming
Creator: C. Titus Brown (@ctitusbrown), a.k.a. Chuck Norris
Frequency of updates: several posts a week
Recommended blog post: Some myths of reproducible computational research

Titus covers a lot of different material on his blog. Many posts see him ‘thinking out loud’ on an issue, keeping people updated with developments with his training courses, or frequently asking people for their thoughts or suggestions on a topic. There are also detailed scientific posts relating to his interests in kmer-based approaches relating to genome assembly. Being a keen advocate (and practitioner) of open and reproducible science, Titus also uses his blog to write on these topics.

Blog: Omics! Omics! A computational biologist’s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
Creator: Keith Robison (@omicsomicsblog)
Frequency of updates: 1–2 posts per month (but many more during AGBT!)
Recommended blog post: A Sunset for Draft Genomes?

This blog is predominantly focused on the latest developments in sequencing technology. Keith provides great insight into future developments in the world of sequencing, and also tries to make sense of the claims and marketing hype that sometimes surrounds the announcements of new technologies. During the annual Advancements in Genome Biology and Technology (AGBT) meeting, you can rely on Keith to provide great commentary on what is happening (and not happening) at the meeting.

Blog: Opiniomics: bioinformatics, genomes, biology etc. “I don’t mean to sound angry and cynical, but I am, so that’s how it comes across”
Creator: Mick Watson (@biomickwatson)
Frequency of updates: 1–2 posts per week
Recommended blog post: Why anonymous peer review is bad for science

Of all the blogs that I’m including here, this is probably my favorite. I greatly enjoy Mick’s writing; not so much for the detailed technical posts about sequencing technology — good though these are — but for the fantastic pieces he writes about the wider field of bioinformatics. Mick has insightful views on such topics as peer review, training of bioinformaticians, and reproducible science. I particularly like Mick’s frequently humorous — and sometimes slightly ranty — style of writing. Oh, I should also point out that Mick’s site is best viewed on an iPad.