What's in a name? Some thoughts on the 'exSPAnder' assembly tool

This week a new tool was published in the Bioinformatics journal:

ExSPAnder: a universal repeat resolver for DNA fragment assembly

The tool's name really refers to the name of an algorithm that is implemented as part of the SPAdes genome assembler. I don't think that this is particularly obvious from the title of the paper. The results section in the paper further complicates this somewhat. E.g. this is how the comparative assembler results are reported in Table 2 of the paper:

The entry called 'SPAdes 2.4' refers to a version of the SPAdes assembler that doesn't use the exSPAnder algorithm, whereas the entry marked 'EXPANDER" refers to a newer version of the SPAdes assembler that does include the algorithm. I find this confusing and it is one of three issues that I have concerning the use of the exSPAnder name:

1. Do we really need to start giving names to algorithms that are part of another tool? This has the potential to create a lot more confusion for people. Particularly when there is no tool called 'exSPAnder' that you can download from anywhere. If somebody implemented the algorithm as part of another piece of software would they be expected to retain the exSPAnder name somewhere (MegaAssembler featuring exSPAnder)?

2. You would hope that the website that the paper links to gives you more information about exSPAnder. But that's not the case:

  • Number of mentions of exSPANder in the publication: 35
  • Number of mentions of exSPAnder in the linked software web page: 0
  • Number of mentions of exSPAnder in the latest SPAdes v3.1.0 manual: 0

Again, I think this can only lead to confusion. The mention of exSPAnder as if it was its own separate tool suggests that this is software that you can download. E.g. this is from the Conclusion section of the paper:

Benchmarks across eight popular assemblers demonstrate that exSPAnder produces high-quality assemblies for datasets of different types.

But exSPAnder is not an assembler that anyone can download and use at the moment. Rather you can download the SPAdes assembler which may or may not feature the exSPAnder algorithm (I don't know because the website and the manual doesn't say).

3. My final issue is perhaps the most minor one and it relates to this horrible trend of using mixed capitalization for bioinformatics tool names. If you are going to do this, please be consistent and please realize that journal formatting conventions may mess up your planned use of capitalization. Here are the different ways you can see 'exSPAnder' referred to in this paper:

  • ExSPAnder: 1
  • exSPAnder: 1
  • EXPANDER: 1
  • EXSPANDER: 28

So I'm assuming that the latter format is the one that the authors are really using and the other variations are due to problems of the journal formatting the article. Using small caps like this is a great way to guarantee that no-one else will bother to format the name like this. Okay, time to finish this post as I need to go and work on my new assembly tool:

MaSSEMbLerXL— an assembler that assigns different font sizes to each DNA base

 

101 questions with a bioinformatician #11: Ewan Birney

This post is part of a series that interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.

This is a special 'If we need that extra push over the cliff' edition of '101 questions with a bioinformatician'.

This week's interviewee is the Associate Director of the European Bioinformatics Institute and also the head of CTTV (the Centre for Therapeutic Target Validation). Furthermore, he is a winner of the prestigious Benjamin Franklin Award, a winner of the Overton Prize, and he was recently elected as a Fellow of the Royal Society. He helped found Ensembl, was an early supporter/developer of BioPerl, and has contributed to an improbably large number of genomics and bioinformatics projects.

And yet, these are not the accomplishments of Ewan Birney that I am most impressed by. Rather, I am in awe that he helped define life to Douglas Adams (a very special kind of DNA). And most impressively, his entry on Wikipedia lists one of his roles/accomplishments as follows: 

[Ewan] acted as a bookmaker to the genomics community, taking bets on different estimates of the total number of genes in the human genome.

Ewan Birney, a man who will help satisfy your genomic gambling needs! You can find out more about Ewan by following him on twitter (@ewanbirney), or reading his blog (Bioinformatician at large), or attending any bioinformatics conference (he asks all the questions at all the conferences…it's in his contract).

And now, on to the 101 questions...

 

 

001. What's something that you enjoy about current bioinformatics research?

Learning new stuff. My research is heading towards leveraging outbred genetics to understand basic biological processes in a variety of metazoans (fly, medaka, human). I’m learning about statistical genetics (population structure, other stuff…), fly development, medaka anatomy and human physiology along with my students. It’s great.

 

010. What's something that you *don't* enjoy about current  bioinformatics research?

Broadening this out to life sciences, not just bioinformatics, it’s about a chronic set-point problem in our collective investment into information infrastructure. Fundamentally, biology is an information science; we need to understand how things work and we need to pass data, information and knowledge both on in the future and between people now. Writing papers is part of this, but other parts — just as important (perhaps more?) — are both raw and derived sets of information. To do this we need robust information infrastructures. Collectively we are happy that multiple billions are spent on data generation/experiments/analysis and yet we often agonise on the millions spent on aggregating (over space) and propagating (over time) this information. This is a fundamental mindset that we need to change.

 

011. If you could go back in time and visit yourself as an 18 year old, what single piece of advice would you give yourself to help your future bioinformatics career?

  1. Get your head around statistics — frequentists, bayesian, etc. You will really need this.
  2. Be open (the few times I’ve not been, I’ve regretted it).

 

100. What's your all-time favorite piece of bioinformatics software, and why?

 Hmmm. Tough one.

 Perl? (though the cool kids do Python now)

 R? (though the insanity of the function conventions drive me mad…)

 

101. IUPAC describes a set of 18 single-character nucleotide codes that can represent a DNA base: which one best reflects your personality?

I’ve always had a soft spot for Y. Perhaps thats because I first got into bioinformatics through splicing and the 3’ splice sites have the polypyrimindine tract beforehand. Or that T and C seem like the underdogs in the nucleotide world…

This JABBA-award-winning bioinformatics tool should be 'detonated'

Another week, another JABBA award for Just Another Bogus Bioinformatics Acronym. The title of the paper — published on bioRxiv.org — that describes this tool, does not reveal the name:

Neither does the abstract, but when you get to the end of the Introduction, it is finally revealed:

We improve upon the state-of-the-art in transcriptome assembly evaluation by presenting DETONATE: DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation 

Wow. Three of the eight letters in this name do not come from the initial letters of words, and five out of eleven words in the full name of the tool do not contribute to the acronym at all. I particularly like the 'with or without' part.

While I can understand why they didn't want to use the full acronym (DNTRAWOWTTE), I'm sure that they could have come up with something else instead  — how about TETRA: Truth Evaluation Transcriptome RNAseq Assembler? But really, this is yet another example where you don't need to make an acronym! Just call the tool 'Detonate' and be done with it.

MIRA, MIRA on the wall: the problem of duplicated names in bioinformatics

So in addition to lots of bioinformatics tools that use bogus acronyms for their names, or which have very unpronounceable names, we now have a new problem…duplicate names. Rachel Glover (@rach_glover) tweeted this today:

The new MIRA tool (Mutual Information-based Reporter Algorithm for metabolic networks) is entirely unrelated to the existing MIRA tool which is a genome assembler that's been around for over 15 years.

It is not uncommon to need to search online for a bioinformatics tool. This can be complicated by the fact that many tools have names that are more commonly associated with other things (e.g. SHRiMP, ICEberg, HAMSTeRS, Pigeons, MOUSE, INSECT etc.). The first three examples also highlight that using mixed capitalization to help distinguish your bioinformatics tool from other things doesn't really help when you use a web search engine. 

One solution to this problem has always been to add the word 'bioinformatics' to your web search. However, if we start seeing more tools that share the same name, then this might not be that useful either.

Following Rachel's tweet, Torsten Seemann (@torstenseemann) had a suggestion:

I can't imagine that this would be an easy undertaking, but Alastair Kerr (@alastair_kerr) made a good follow-up point:

I think this is a great suggestion. Bioinformatics journals should perhaps state in their author guidelines that people should not duplicate the name of an existing (published) bioinformatics tool. Reviewer guidelines could also prompt the reviewer to check if this has happened (a simple web search of '<tool name> bioinformatics|genomics' would probably suffice).