A new JABBA award for a particularly bogus bioinformatics acronym

JABBA is an acronym for 'Just Another Bogus Bioinformatics Acronym'. JABBA awards are given when people publish bioinformatics tools that have names which are tenuously derived acronyms (or initialisms). There have been many JABBA award winners, but this one might take some beating. This software tool was published earlier this year in the journal 'Microarrays'. Here is the title of the journal article: 

Pigeons: A Novel GUI Software for Analysing and Parsing High Density Heterologous Oligonucleotide Microarray Probe Level Data

So now the million dollar question is…what is 'Pigeons' an acronym of? Please sit down as  you might feel faint when you read this:

Photographically InteGrated En-suite for the OligoNucleotide Screening

Wow. This rates an 11 on the Bogus Scale (a scale that only goes up to 10).

What is the extent of gender bias in bioinformatics? Please help me find out.

I've been drawing up a short-list of people to interview for my 101 questions with a bioinformatician series, and I've realized that this list is skewed towards males (maybe 2:1). This partly reflects my own biases in choosing people that I know through work and from people that I follow on twitter. 

However, it probably also reflect underlying biases in the bioinformatics field as a whole. The existence of gender biases is STEM subjects is hardly a new concept (see here or here for some recent studies into this area) and anyone who follows Jonathan Eisen's blog will know that there is an all-too-common bias towards male speakers at scientific meetings. In a great blog post from last year (The Magnifying Glass Ceiling: The Plight of Women in Science), Jane Hu discusses the topic of gender bias in science. I encourage everyone to read this post, but I'll highlight one sentence here (emphasis mine):

It is true that women are underrepresented…but not because women aren’t interested in it or can’t handle the work.

Although projects like Girls Who Code and App Camp for Girls are doing a great job at increasing female participation in some STEM subjects, these projects will not help remove the discrimination against women that occurs later in their careers. Fortunately, other fantastic projects like Tools for Change: Boosting the retention of women in the STEM pipeline are helping raise awareness about these problems, and are offering solutions (e.g. encouraging more family friendly policies).

So I'm curious as to the extent of gender bias in bioinformatics. Please help me find out more by completing the really short form (below) and feel free to share this form with others (the Google form can be accessed separately via this link). I will report on the results in a future blog post. Also, I will make more effort to address any gender biases in my 101 questions with a bioinformatician series.

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Ewan Birney's EBI press conference on being elected to the Royal Society

Speaker: And that concludes this EBI press conference to congratulate Ewan Birney on being elected to the Royal Society. We just have time for one or two questions. Ah okay...the first question goes to…Ewan Birney.

Ewan: Hi Ewan. Just wanted to say that this is all great and I've found your work to be really interesting. Can I just ask whether you've looked at the opportunity of widening this effort by joining other Royal Societies as well? This would allow for a much better comparative analysis of the scope and impact of Royal Society members? The Royal Statistical Society may be a good choice to begin with, or maybe the Royal Society of Marine Artists.

Ewan: Thanks Ewan, that's a really good question. It is something that I'm considering and I think there is a lot to gain from such a comparative approach. But to do this properly I think it needs to be part of a much larger effort. So I'm hopeful of trying to join every Royal Society and then see what can be learned from a cross-societal analysis of such memberships. Furthermore I'm hopeful that Her Majesty could be persuaded to start a new Royal Society for the Promotion of Questions by People Named Ewan at Academic Conferences…something that is very near and dear to my heart.

Speaker: Okay, I think we have time for just one more question. Oh, Ewan…again.

Ewan: Just to follow up Ewan, given the advanced age of many Royal Society members, have you thought about trying to assess what fraction of the Royal Society is functional?

Ewan: That's a fantastic question Ewan, very perceptive of you. This is something else that I have a strong interest in. I am currently involved in some preliminary discussions with various people to form a new pan-European working group that will investigate how much of the Royal Society is functional. This effort will hopefully be called ENCODEMBLIXIR…or something snappy like that. 

Jesting aside, congratulations Ewan this is great news!

101 questions with a bioinformatician #5: Laura Clarke

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.

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Laura Clarke is the Project Coordinator for Resequencing Informatics, part of the Vertebrate Genomics team led by Paul Flicek at EMBL-EBI. Before joining the EBI, she was applying her considerable bioinformatics skills at the Wellcome Trust Sanger Institute (a move ranked #1 on the annual list of Easiest-employers-to-transition-between). 

Her role sees her help with the analysis and coordination of high throughput genomics efforts such as the 1000 Genomes project, BLUEPRINT (deciphering the epigenome of blood cells), and HipSci (the Human Induced Pluripotent Stem Cells Initiative). If you're wondering what this actually entails, I'll hand you over to Laura:

"This work boils down to making sure that data gets into and out of the sequence archives; running primary analysis and QC; and then making sure the resulting analysis makes it out to the community".

You can find out more about Laura by following her on twitter (@laurastephen), and of course you can also follow @blueprint_eu and @hipsci. And now, on to the 101 questions...

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

The possibility. With modern sequencing technologies, computation techniques have the ability to draw together these new data types and massive volumes of data, allowing us to get much closer to a proper understanding of cellular biology, which of course brings us closer to understanding organismal biology.

Add to that the diverse range of species being sequenced and what that can teach us about evolution and the forces which drive evolution.

That is of course before you consider how it might impact medicine or food security or any real world applications.

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

Extracting data from people. My life would be easier if people weren't so begrudging about sharing data and describing the data they do share well. I work with many people who do share data freely and easily but there are still too many people who are too reticent or reluctant to make data publicly available from within a consortium.

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?

For data coordination purposes we produce a lot of tab-delimited text files, cut is a wonderful Unix command for making those easier to work with and manipulate, learning about cut sooner would have at least made mucking about with various types of GFF files easier I suspect.

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

I have to say I did enjoy pairedends.com, very funny

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

R: this is because Adenine and Guanine are the same molecule type (purines) as both Theobromine and Caffeine, both of which are quite important to me and at least influence my personality.