Top twitter talent: UC Davis genome scientists lead the way

The Next Gen Seq website has just published its 2013 list of the Top N Genome Scientists to Follow on Twitter. Over 10% of this International list of scientists are all staff or Faculty here at UC Davis, which says a lot about the quality of genomics talent here on campus:

It is also worth mentioning that there are so many other people at UC Davis who work in genomics and bioinformatics and who use twitter to effectively communicate their research and engage with the community. E.g.

  • @dr_bik - Holly Bik (Postdoc in Jon Eisen's lab)
  • @ryneches - Russel Neches  (Grad student in Jon Eisen's lab)
  • @theladybeck - Kristen Beck (Grad student in Ian Korf's lab)
  • @sudogenes - Gina Turco (Grad student in Siobhan Brady's lab...and winner of best twitter account name)

Great to see UC Davis recognized like this.

 

Update

Updated at 9:09 am to reflect that Next Gen Seq have now added Vince Buffalo to the list (he was apparently meant to be on the list anyway).

Another winner of the JABBA award for horrible bioinformatics acronyms

It's time to hand out another JABBA (Just Another Bogus Bioinformatics Acronym) award. Joining the recent recipients is a tool described in the latest issue of the Bioinformatics journal.

I don't have any problem with the acronym itself, and this is not a tool which is randomly adding or removing letters from the full name to produce the acronym. So what is my problem? Well the tool — which calculates a score to assess the local quality of a protein structure — is called The Local Distance Difference Test. And the acronym? Oh, the acronym is just 'lDDT' with a lower-case 'L'.

Now, this might not be so bad if it were not for the fact that all fonts used by the Bioinformatics journal (HTML & PDF versions) as well as the author's own website make this 'L' look like the letter I or the number 1.

From the HTML

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From the PDF

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From the author's website

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I can't help but imagine that people will only ever read this as IDDT and not LDDT...which of course doesn't bode well if someone ends up Googling for this tool at a later date. Compare a search for LDDT (which finds the correct tool) vs a search for IDDT (which doesn't:

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Congratulations on being the recipient of another JABBA award!

What's in a name? Better vocabularies = better bioinformatics?

About 7:00 this morning I was somewhat relieved because my scheduled lab talk had been postponed (my boss was not around). But we were still having the lab meeting anyway.

About 8:00 this morning, I stumbled across this blog post by @biomickwatson on twitter. I really enjoyed the post and thought I would mention in in the lab meeting. Suddently though that prompted me to think about some other topics relating to Mick's blog post.

Before I knew it, I had made about 30 slides and ended up speaking for most of the lab meeting. I thought I'd add some notes and post the talk on SlideShare.

What's in a name? Better vocabularies = better bioinformatics?

from

Keith Bradnam

I get very frustrated by people who rely heavily on GO term analysis, without having a good understanding of what Gene Ontology terms are, or how they get assigned to database objects. There are too many published anayses which see an enrichment of a particular GO term as some reliable indicator that there is a difference in datasets X & Y. Do they ever check to see how these GO terms were assigned? No.

New recipient of the Just Another Bogus Bioinformatics Acronym (JABBA) award

It was only a few weeks ago that I gave out the last JABBA award. One of the winning recipients that time was a database — featuring excessive use of mixed-case characters — called 'mpMoRFsDB'.

Well it seems that if you work on 'MoRFs' (Molecular Recognition Features) then you must love coming up with fun acronyms. This week in BMC Bioinformatics we have another MoRFs related tool that is worthy of a JABBA award:

The oh-so-catchy 'MFSPSSMpred' (Masked, Filtered and Smoothed Position-Specific Scoring Matrix-based Predictor) is the kind of name that requires you to first sit down and take a deep breath before attempting to pronounce it. Just imagine having to tell someone about this tool:

"Hi Keith, can you recommend any bioinformatics tools for identifying MoRFs?"

"Why certainly, have you tried em-eff-ess-pee-ess-ess-em-pred?"

Congratulations MFSPSSMpred, you join the ranks of former JABBA winners.