This is the February edition of Bio::Blogs, an aggregation of bioinformatics posts from the past month. This issue has a particular focus on Open Notebook Science - researchers sharing their work as they produce it.
For this edition, with the help of Cameron Neylon, Jean-Claude Bradley, and Pedro Beltrao, I’ve tried to write a short essay on open science as well as the open notebook variety. I’ve posted this on my research website.
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.
Short and to the point - the tips & tricks supplement to this month’s bio::blogs edition has been compiled. The link to the pdf is at the end of this post. But first I want to thank those who contributed.
Thanks to Dan Swan, Pierre Lindenbaum and Konrad Forstner, who contributed particularly large articles covering every aspect of being a bioinformatian.
Euan Adie (Stew) wrote about revision control, creating applications and blogging. Bertalan Meskó sent in a list of genetic disorder databases. Roland Krause offers tips on managing and searching data sets. Ryan Castillo wrote about his experiences in bioinformatics. Paras Chopra offers advice for undergraduates on how to use their summers. Pedro Beltrao, editor of bio::blogs, discusses the importance of keeping up to date on the literature. Also, Duncan Hull whose observations I was unable to add due to lack of time and space (read: my poor organisational skills)
And finally, special thanks go to Neil Saunders whose entry, on recreating code from bioinformatics papers, was so large I couldn’t fit it in the pdf, but you should definitely go and take a look.
Enjoy.
