Bioinformatics Zen

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

In my opinion, great coding skills, a thorough knowledge of statistics, and Shakespearian writing ability do not make a great bioinformatician. They help, but the most important things are a relevant scientific question and a good understanding of the literature. If you’re like me, the path to scientific enlightenment begins with typing keywords into PubMed until you get the results you were after - the same way you use Google. However the are other options besides PubMed, here are six other options you might not have heard of, worth a look perhaps?

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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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The recent release of the bio::blogs “tips & tricks” special has proved popular and comments from three readers suggested continuing it further. But I’d like to know what kind of interest there would be in this. And how to carry it out.

One possibility is to aim for regular release cycles, for example every 4/6 months. Each issue would be on a specific topic, such as sequence analysis, network analysis, etc. This could be co-ordinated and set up on a wiki site.

Another idea I had is to set up a semantic wiki, the aim to create both a human and machine readable resource. This would be particularly useful for categorising the tools and databases available in bioinformatics.

These are just two examples, but I be really interested to hear your suggestions. Posting an idea here isn’t a commitment, it could just be something you’d like to see. Like most amateur web ideas, it would probably just be me initially, and if it was useful, other people would naturally become interested in helping.

Of course the other suggestion is that this is just a successful one of a kind that should be left so.