And the award for needless use of subscript in the name of a bioinformatics tool goes to…

The following paper can be found in the latest issue of Bioinformatics:

MoRFs are molecular recognition features, and the tool that the authors developed to identify them is called:

MoRFCHiBi

So the tool's name includes a subscripted version of 'CHiBi', a name which is taken from the shorthand name for the Center for High-Throughput Biology at the University of British Columbia (this is where the software was presumably developed). The website for MoRFCHiBi goes one step further by describing something called the MoRFChiBi,mc predictor. I'm glad that they felt that some italicized text was just the thing to complement the subscripted, mixed case name.

The subscript seems to serve no useful purpose and just makes the software name harder to read, particularly because it combines a lot of mixed capitalization. It also doesn't help that 'ChiBi' can be read as 'kai-bye' or 'chee-bee'. I'm curious whether the CHiBi be adding their name as a subscripted suffix to all of their software, or just this one?

A great slide deck about how to put together the new format NIH Biosketch

This is a little bit off-topic, but I found it useful…

Earlier this year, Janet Gross and Gary Miller from the Rollins School of Public Health at Emory University put together a very useful guide on how to put together the new format NIH Biosketch:

There is also a nice page of grant writing tools available. I liked how they highlight the important point that cramming as many words as possible into the five pages should not be the goal. Aesthetics and layout matter!

101 questions with a bioinformatician #27: Michael Barton

Michael Barton is a Bioinformatics Systems Analysis at the Joint Genome Institute (that makes him a JGI BSA?). His work involves developing automated methods for the quality checking of sequencing data and evaluating new bioinformatics software. He may introduce himself as Michael, but as his twitter handle suggests, he is really Mr. Bioinformatics.

His nucleotid.es website is doing amazing things in the field of genome assembly by using Docker containers to try to parcel up genome assembly pipelines. This is enabling the ‘continuous, objective and reproducible evaluation of genome assemblers using docker containers’. Related to this is the bioboxes project — a great name by the way — which may just succeed in revolutionizing how bioinformatics is done. From the bioboxes manifesto:

Software has proliferated in bioinformatics and so have the problems associated with it: missing or unobtainable code, difficult to install dependencies, unreproducible workflows, all with terrible user experiences. We believe a community standard, using software containers, has the opportunity to solve these problems and increase the standard of scientific software as a whole.

You can find out more about Michael by visiting his Bioinformatics Zen blog or by following him on twitter (@bioinformatics). And now, on to the 101 questions…

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Registration is now open for the UK 2015 Genome Science meeting

Registration for the 2015 Genome Science meeting is now open. This is the meeting formally known as Genome Science: Biology, Applications and Technology, which in turn was formally known as The UK Next Generation Sequencing Meeting. I expect that next year it will just be known as Genome.

It's a fun meeting which all the cool kids go to, and it's in Brum so you will at least be able to get a decent curry.

The scientific sessions will be as follows:

  • 20 years of bacterial genomics: Dr Nick Loman, University of Birmingham
  • Environmental genomics: Dr Holly Bik, University of Birmingham
  • Functional genomics: Associate Professor Aziz Aboobaker, University of Oxford
  • New technologies: Dr Mike Quail, Wellcome Trust Sanger Institute
  • Plant and animal genomics: Mr Mick Watson, Edinburgh Genomics
  • Novel computational methods: Professor Chris Ponting, University of Oxford
  • Single cell genomics, Professor Neil Hall, University of Liverpool

It is not altogether inconceivable that evening entertainment will be provided by The Nick & Mick Show, where Messrs. Loman and Watson might showcase their latest venture — Nanopore: the musical.