In response to a recent post, I had a few emails and comments asking general questions about a career as a bioinformatician. So to answer these all at once here are my thoughts on what I think the background and future of a bioinformatician is.
In a month, I start the third and final year of my PhD. Usually it’s around this time that students begin thinking about what’s gone before and contemplate the future, and I’m never one to buck a trend.
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
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.
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For instance, if you have a set of data, you have to understand many things. First, you have to know the biological relevance. How was it produced, what does the data mean, and what is the significance? Lab biologists need to know this as well, but a bioinformatician must also know, in addition, how to store the data. What is the best method of representing it, given that the data needs to pulled out and manipulated within computer code. Next the bioinformatician needs to know what’s statistically feasible given what’s available. It’s going to be tricky to get answers from only three replicates of a noisy microarray experiment. Can you use a SVD to filter some of this noise? What about a microarray experiment with 10 different drug treatments. Where do you begin, can you use dimensionality reduction? How about using clustering? How many clusters? Did someone say probabilistic?
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.