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.

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.

Bio::Blogs is a monthly round up of what’s being discussed on bioinformatics blogs. In addition, to next month’s edition at NodalPoint, there will also be a special edition here at Bioinformatics Zen. The aim, a community generated article of tips for computational biologists.

I hope that the text of the article will be generated by submissions from the bioinformatics community. That’s means you reading this now. What would be your best piece of advice you would offer someone starting out in bioinformatics? Databases, coding, organisation?

Send your suggestions, with your website if you have one, to the Bioinformatics Zen email address. Everything will be compiled and posted with the next edition of Bio::Blogs, on June 1.