Awkward Bioinformatics Conversations #1

Image from flickr user hades2k

Image from flickr user hades2k

Bob: Hi Sue, it's Bob. Got a favor to ask. Could you load up the UCSC Genome Browser site in your web browser please?

Sue: Hi Bob. So just to clarify…do you want me to load the UCSC Genome Browser homepage, or the UCSC Genome Browser website Genome Browser tool?

Bob: Wait, what?

Sue: UCSC Genome Browser is both the name of the website — as identified in their HTML metadata — and also the name of a tool on that website.

Bob: Er, just go to the main website first.

Sue: Done.

Bob: So it says that it's the UCSC Genome Browser website?

Sue: Yes. And no.

Bob: Huh?

Sue: The homepage identifies itself as the UCSC Genome Bioinformatics site but it also welcomes you to the UCSC Genome Browser website.

Bob: Okay, that sounds like you're looking at the right page then. So can you now please click on the Genome Browser link at the top of the page?

Sue: Which one?

Bob: What? Er, the one in the toolbar I guess.

Sue: Which one?

Bob: I just told you which one.

Sue: No, which toolbar?

Bob: There's more than one?

Sue: There's the horizontal toolbar that mostly contains dropdown menus with links that expose most of the site's functionality…and then there's the vertical toolbar which mostly offers links to items that also exist in sections of the horizontal toolbar.

Bob: But surely there's only one toolbar link which says 'Genome Browser'?

Sue: No, there are two.

Bob: But they go to the same place, right?

Sue: No. The horizontal toolbar link for 'Genome Browser' takes you into the Genome Browser tool with data loaded for the human genome assembly. The vertical toolbar link for 'Genome Browser' takes you to an intermediate page that lets you access the 'Human Genome Browser gateway'. Which one do you want? Bob? Hello???

Shining a light on more bogus bioinformatics acronyms

jabba logo.png

Courtesy of an anonymous tip off…

There is a new bioinformatics tool that was described in a recently published BMC Genomics article. Here is the full name of the tool with any capitalization removed:

  • automated tool for bacterial genome annotation comparison

So can you guess what acronym/name was extracted from this description?

  • ATBGAC?
  • AutoBGA
  • BGAC?

No. The JABBA-award-winning name of this tool is as follows:

This name really isn't helped by the fact that it is shown as follows in the journal article title (with the G of 'Genome' also capitalized):

  • BEACON: automated tool for Bacterial GEnome Annotation ComparisON

101 questions with a bioinformatician #31: Morgan Taschuk

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.

Morgan Taschuk is a Senior Manager for Genome Sequence Informatics at the Ontario Institute for Cancer Research (OICR). She manages the production sequence analysis team to analyse all of the sequence data sequenced at OICR, resulting in the generation of alignment files, variant calls, QC metrics and other bountiful amounts of sequence data for OICR researchers and collaborators.

She recently wrote a great blog post regarding the (sometimes contentious) issue of Biologists vs Bioinformaticians. Definitely worth a read. Morgan has also recently started to assemble a Twitter list of Women in Bioinformatics, now up to 179 members. I'm sure she would like to make that list even longer, so please let her know of any omissions.

You can find out more about Morgan by visiting her Modern Model Organism blog, or by following her on twitter (@morgantaschuk). And now, on to the 101 questions...



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

There's always something more to learn. I'm spending a lot of time with our genomics lab recently and learning about how lab processes impact our data fascinates me. Bioinformatics skills are usually in demand so I also get to work with a wide variety of people with different questions and problems and have to stretch my brain to apply myself.



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

Often people write their own scripts or software instead of looking for something that already exists out there. Not only is it wasted effort for very similar results, it sabotages any attempt to standardize across the field. Open-source software is there for everyone to change and improve. Why not build on a foundation instead of digging the hole yourself?



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

Since nobody can tell you what bioinformatics is, it's up to you to define it. I spent a long time fighting with imposter syndrome, not just because I felt inadequate but also because I was called a bioinformatician when I didn't fit the classical model. Nobody fits the classical model these days. Thinking about this question actually inspired me to write a blog post about the difference between bioinformaticians and computational biologists. Judging from the feedback on Twitter and the blog, the problem of defining what a bioinformatician is still really sticks in people's throats.



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

SAMtools. It's an amazing piece of very stable, utilitarian, open source code that forms the backbone of most sequencing pipelines.



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

I struggled the most with this question! Y, because 'pyrimidine' is a pretty word and so Y not.

~crickets~

The names of bioinformatics tools that help study evolution shouldn't feel that they also have to evolve

Thanks to Torsten Seemann for bringing this to my attention…

In 2003 a bioinformatics tool was published. A tool with a thoroughly sensible name and acronym:

A simple name with a simple, and not-too-bogus. initialism. Bravo. However, a subsequent update to BIBI brought about a change to the name:

  • le BIBI:

Where the 'le' refers to 'light edition'. It should be said that most references to this tool drop the superscript notation for 'le'. Let's move forward to the present day and the publication of another version of this tool:

The full expansion of this new name is as follows:

  • Light Edition Bioinformatics Bacterial Identification Tool Quick Bioinformatic Phylogeny of Prokaryotes

Quite a mouthful! Bonus points for including 'Bioinformatics' and 'Bioinformatic' as part of the same name, as well as the largely redundant inclusion of 'Bacterial' as well as 'Prokaryotes'.

Generally I find use of superscript in software names to be largely unnecessary. It can make the tool name harder to read and it is unlikely to reproduced verbatim by others who mention your software. Starting your software with a lowercase letter also means that this might appear in uppercase if used to start a sentence (as happens several times in the above paper). Not a terrible problem but it reduces the strength and consistency of your 'bioinformatics brand'.