Why I twitter →

I cannot sit on the fence. I like twitter and what it offers. I have learned things I never would, built genuine relationships with international people who I would have perhaps have only met over a quick coffee at a conference. And I have changed the way I speak about science.

This post by Mark Brandon sets out nine great reasons as to why he finds Twitter so useful, many of which relate to science communication.

I believe twitter is a strong positive for science, and it is a worthwhile investment of your time.

I completely agree with just about everything he has to say. It's a good list.

101 questions with a bioinformatician #15: Karyn Meltz Steinberg

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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Karyn Meltz Steinberg is a staff scientist at The Genome Institute at Washington University ('TGI' to those in the know, but it will forever be the GSC to some of us). Prior to joining, Karyn was a postdoc in Evan Eichler's lab at the University of Washington (perhaps she is destined to head here, here, or here when time comes to move on?).

Her current position sees her work as part of the Genome Reference Consortium to improve the human reference assembly. In particular, she is involved with characteHrizing and resolving the particularly 'messy' regions of the genome that have complex genomic architecture.

You can find out more about Karyn by following her on twitter (@KMS_Meltzy). And now, on to the 101 questions...

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

I enjoy the collaborative community of bioinformatics. Although we are all working on our own research questions, the basic issues of how to process sequence data and report and annotate variants are the same. I've attended some workshops recently and have been impressed with how much people want to work together to solve these problems particularly with respect to the new reference assembly and dealing with the alternative loci.

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

File formats. Can we please agree on something, friends? (KB: see Law's First Law!)

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?

I actually love the fact that I was not a bio major and that I did tons of non-sciencey activities as an undergrad. My non-traditional journey has definitely shaped who I am as a researcher. I would advise my 18 year old self to not be afraid of the command line and to learn a programming language earlier.

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

BEDTools. Full stop.

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

I was going to say '.' because I work on filling gaps in the human genome, but Deanna Church already took that. So, I will go with 'S' as I like a GC-rich challenge and the flexibility of being either a purine or pyrimidine.

Data access for the 1,000 Plants (1KP) project →

From the abstract of a new paper in GigaScience:

The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees.

The paper doesn't provide a link to what seems to be the actual project website. They mention directories within the iPlant Collaborative project where you can access data. The project website reveals that this project can be referred to either '1000 plants', 'oneKP' or '1KP' (but not '1000P'?).

Being a pedantic kind of guy, I was curious by the paper's vague mention of 'over 1,000 plant species'. How many species exactly? The paper doesn't say. But if you go to one of the iPlant pages for 1KP, you will see this:

Altogether, we sequenced 1320 samples (from 1162 species)

So this project seems to have exceeded the boundaries suggested by its name. How about the '1.2KP' project?

Identical Classifications In Science: Some advice for Jonathan Eisen

Jonathan Eisen — a colleague at the UC Davis Genome Center — has a quandary. He came up with a name for one of his projects but now needs to consider renaming it. The problem is that ICIS (Innovating Communication in Scholarship) sounds a bit like…well you all know what it sounds like. So Jon has appealed for suggestions on how to rename their project.

He should take comfort that he may not be the only one facing this dilemma. After all, the International Cooperative ITP Study Group (ICIS) has been an ongoing collaboration between hematologists since 1997. I wonder whether they are considering a name change? Maybe Jon could also ask the folk at the International Conference on Information Systems (ICIS) who have been meeting since 1980. Or they could talk to the people that came up with the Intelligent Coin Identification System (ICIS), or the The Intensive Care Infection Score (ICIS), or the Integrated Crate Interrogation System (ICIS), or the 20 year old International Crop Information System (ICIS), or the people who named this gene.

These are just some of the academic uses of ICIS that I could find from a couple of quick searches. I expect that there are more out there. This is a reflection on one of the most primal desires of all scientists…the need to come up with an acronym or initialism for their project. This urge is all too commonly associated with the additional need to make the name 'fun' (particularly a desire to name things after animals). Acronyms can also backfire for other reasons, such as when you don't fully appreciate how it might sound in other countries.

The shorter your acronym, the more likely that it has been used by other people before you (even within the same field). My suggestion would be to consider the shocking alternative of not using an acronym at all! After all, sometimes people can come up with new names that seem to catch on.