Bioinformatics Zen

While away in Madrid, I received two replies to my open science question to journals, from Elsevier and from BMC.

In short summary, Elsevier’s point of view, excluding Cell and Lancet, was quite positive with “watch, test and learn from examples”. BMC’s response was slightly negative, with “we only publish original research articles”. I’ve put both these emails on the nodalpoint wiki here, so that you can go and read them yourself and make up your own mind.

I’m very grateful that these two publishers replied, but I’m a bit disappointed by the lack of response from the other journals. Particularly PNAS, Nature, and PLoS which seem to be the most open science friendly. Any thoughts on this would be appreciated. I could get on the telephone and give them a call? Or bit pushy perhaps?

I still want to move forward with this open science issue special edition, I think getting it done for the September 1 edition of bio:blogs would be a good goal, since it’s been going for a while. I guess the next step would be to try and get scientists already participating in open science to write a short piece on their experiences. It would also be interesting to get funding bodies opinions on this too, since open science can generally lead to a better quality of research.

I think journal policies towards preprint servers are covered by the data from the Romeo database, outlined previously. For the next stage of the open science edition of tips and tricks I think I need to include clarification of journal positions towards publication and discussion of data on blogs, wikis, and such like.

I spent a while trying to come up with a suitably clever letter, but this is the best I could do.

Dear Sirs,

I’m compiling, with the bioinformatics blogging community, a guide to open science. I believe one of the one of most important points on in this issue are journal editorial polices towards sharing and discussing research, prior to publication. The use of preprint servers is becoming accepted, however the position of journals towards the use of blogs and wikis to discuss results is less clear.

I am writing to ask for your policy regarding this. I would like to permission to include your reply in the finished guide. You can find wiki page for this at wiki.nodalpoint.org/open_science.

As you might expect, I’ve put this on a nodal point wiki page. If you’ve got any corrections or suggestions, you can leave them here in the comments or edit the letter yourself. I’ll load up them into the SPAM bot and send them out on Friday.

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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