On the ruffus mailing list[1] I am participating in a discussion on whether a pipeline should contain ‘if‘ conditions and loops. I don’t like to see conditions in a pipeline. In the real pipelines, the ones with pipes and water in them, there is no equivalent of ‘if‘ conditions. The tubes can be either be
Category: Uncategorized
a discussion about node centralities with G.Scardoni
Last week we hosted the visit of G.Scardoni, the author of Centiscape, a Cytoscape plugin to calculate different measures for Node Centralities in a network. I recommend you to read the supplementary material 1 of his paper (it’s a pdf), because it has a good description of many measures of node centralities and their possible
links, resources, games, tools (January 2011)
These are links that I have collected in the past two months. I am copying them in a pseudo-random order. PhD students life / becoming a better PhD student English Communication for Scientists – Nature has published a very nice manual on how to improve English Communication skills for young researchers. Check it out! The
Apps and videogames for bioinformatics/genetics geeks (January 2011)
Apps and Games FreePub is a mind-mapping software to organize scientific materials. Check also this presentation After the games about protein folding and multiple alignments, a new geeky bioinformatics game has been published on Internet. Check out EteRNA!
For N-Glycosylation freakies
If you are a N-Glycosylation geek, check out this interview with Ajit Varki, a guru of the field: Interview with A. Varki on the importance of studying post-translational modifications
The analogy between Blast and Google
A way to explain what Blast is to young students or non-scientists is to say that ‘Blast is the equivalent of Google for searching sequences‘. This analogy is controversial and not all the bioinformaticians would agree on it: but it is one of my favorite ways to explain what is Blast to people outside science,
Should I start putting my slides on Nature Precedings?
After the experience with the Post-GWAS article on WikiGenes I started looking at the resources on Nature Precedings, which is where the original idea of that collaborative article came from. Nature Precedings is a Nature Network website where researchers can post drafts, ideas, presentations about work that can be published. This is exactly what I
technical problems solved!
These days I have been having problems with the DNS services, which should have been solved by now. For approximately one week, this blog has not been reachable from all the world, depending on which DNS servers you were using. Instead, an older version of the site was shown, at least here in Spain and
published a geekish paper on reporting errors to scientific databases
We have published a commentary paper about reporting annotation errors to scientific databases. In this work we discussed the fact that the work of reporting annotation errors to a database is usually not acknowledged and not considered as a scientific activity, while in our opinion it should. Let’s say that you encounter an error in
The best question to ask in a bioinformatics seminar is..
I have opened a new discussion on Biostar, on ‘What is the best question that you have asked, or heard asking, in a bioinformatics seminar?‘ For a scientist, it is very important to be able to make good questions; seminars are a good place to practice. In my case, I am lucky because in the