Bioinformatics Zen

All emails have been put on the Nodalpoint wiki. Here’s a brief summary of each.

Nature’s response came from the always helpful Maxine Clarke, who regularly appears on their publishing blog. Nature encourages the discussion of work by scientists prior to publication, such as the established practices of preprint servers and presenting at conferences, but blogs and wikis are also covered under this. Nature is however very strict about discussing work with the media until the peer review process is complete.

I contacted Matt Hodgkinson at BMC, after reading about a discussion with Heather on her blog. Publishing data and figures on personal websites is considered by BMC to be similar to informal preprint circulation, and therefore does not prevent the inclusion of the data in an article submitted to the journal. Matt also has a blog where he discusses issues related to journals and publishing.

Matt Patterson replied regarding PLoS’s attitude to open notebook science. Currently PLoS have no clear policy, but they’ve had several enquiries so plan to review their stance with regards to this. Matt kindly said he would send me a follow up email when this was clearer

Bio::Blogs special edition

I’m still aiming to get this special edition finished in time for the August 1 edition of Bio::Blogs. The response from the journals has been good, and we’ve got four in total. I’m hoping to get a few more in future, but I think we need to keep the momentum going, so I’m going start lobbying for people interested in open science to contribute an opinion piece. So if you’ve got an opinion on open notebook science, you could, if you’re feeling generous, write a short piece of text then email me or post it on the Nodalpoint wiki page.

Creative Commons
The photo used in this post is taken from Today is a good day on flickr and used under a creative commons licence.

Computers and the Internet have made things great for scientists, particularly for us, since our jobs are sitting in front of them analysing data all day. Imagine being a bioinformatician without a computer, multivariate statistics is more of a pain than usual, genome sequence alignments need large pieces of paper. There would however be an upside to this analog dystopia - no more powerpoint presentations. Computers have arguably had a detrimental effect on the presentation of research, they allow the easy creation of big, text heavy slide sets. The emphasis of a talk leans towards the slides, and not the speaker.

Being asked to give a talk is viewed as a dull task: time taken away from research plus the discomfort of public speaking. If you’ve already decided beforehand that it’s going to be a dull, pointless exercise then don’t bother, not only will you be wasting your own time but also the time of everyone watching. It’s true that this is a very critical attitude to express; boring presentations are symptom of our scientific culture rather than the fault of the individual, but how many times have you been sat in conference and thought that you could have been using your time much more usefully? Now imagine, for a second time, a world where we have both computers and great presentations. The chance to give a presentation is greeted with enthusiasm, as an opportunity to teach the world about what you commit most of your time to, and to get valuable feedback on it. But we don’t need to imagine this place, we’re the generation of scientists coming through: the professors and PI of the next 30 years, we can start this revolution now.

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Previously I wrote about journal polices towards preprint servers. Since, Dave Robertson contacted me to highlight the Romeo database, which contains a list of journals and their publishing policies. A quick 10 minute search produced this list of archiving guidelines, I’ve updated this on the Nodalpoint wiki. Each journal also has some additional conditions, follow the links to Romeo to read more.

Supports preprint and postprint

BMC
PLOS
National Academy of Sciences
Elsevier excluding Cell

Supports preprint only

OUP
Nature

Supports postprint only

Science
Elsevier - Cell

Continuing the theme of open science, I think one of the most important issues that needs clarification is the position of journals to making your research available prior to publication. One example of this is preprint servers, of which Nature has recently launched their own. Coincidently, a year ago today, Pedro discussed this issue on his blog. With the aim of including it in the next issue of the bio::blogs special edition, I repeated Pedro’s search - the results were consistent with his, except for two cases.

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Traditional science is carried out by experimentation, interpreting the results in respect to the hypothesis, and repeating this until publication. Publication is everything, and as such it’s important to keep your research secret, lest anyone publish something similar which undermines the opportunity to publish in a high impact journal.

An open science philosophy says that this closed approach slows scientific advancement. Results should be made available as soon as possible, then everyone in the field can benefit from them sooner. There is no delay for peer review and publication.

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