I wrote a rudimental script to scrape the Uniprot Website and extract some information about a list of Uniprot entries. This may be useful as an example on how to query Uniprot (since I couldn’t find any public API nor library), or to get infos about a list a genes of your interest. NOTE: the
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Favorite command of the day: parallel from moreutils
Yesterday I have discovered a nice Unix tool to launch commands in parallel. It is called ‘parallel’ and it is very easy to use. I think it is the easiest way to parallelize things in a multi-core computer. You can install it from the ‘moreutils’ package in Linux, or from http://www.gnu.org/s/parallel/ the basic usage is:
Ten Simple Rules initiative entering the final phase
The initiative for the collaborative writing of a candidate ‘Ten Simple Rules’ paper, launched two weeks earlier this month from this blog, has been very successful. So successful that after only two weeks the manuscript is almost ready, in a state where further modifications may be more harmful than useful. For this reason, we are
new version of the collaborative Post-GWAS article published
There are some recent news about the initiative of the collaborative article on Post-GWAS analysis launched last December[1]. It seems that a new version of the manuscript has been published on Nature Precedings (link), a few weeks earlier this month. Well, in the end, with the exception of one figure, they did not include almost
update on the status of the ‘Ten Simple Rules’ initiative after the first 2 weeks
This is an update of the status of the ‘Ten Simple Rules for getting help from Mailing Lists and Online Scientific Communities’ initiative, after two weeks. I am posting it here, but if you want to follow the initiative you should better subscribe to the dedicated mailing list. First of all, I would like to
contribute to a candidate ‘Ten Simple Rules’ article
A few months ago I had the idea of writing an article in the style of the PLoS Computational Biology ‘Ten Simple Rules’ where to explain people how to use mailing lists and web forums to solve technical problems related to bioinformatics. Something on the style of ‘How To Ask Questions The Smart Way’ by
about my research: gene position and selective constraints
It is time I introduce a bit the research I am doing for my PhD, here at the Pompeu Fabra-CSIC university :-) The main area of our research is to study whether there is correlation between the position of a gene within a biological pathway and the strength of selective constraints on it. So, for
my Twitter account!
I have just created a twitter account. You can now follow me at: http://twitter.com/#!/dalloliogm I tried to resist joining Twitter for a long time, but now I need it to participate to a spare-time project of mine. I recognize that twitter can be a very useful tool for a researcher, but I am worried that
scripting Cytoscape to plot different Node Centrality measures
Finally I have made it: scripting and automatizing Cytoscape with python!! Below you can see a figure that I have automatically generated with Cytoscape, including legend and values distributions merged into a single file: Cytoscape is a software to visualize and analyze networks, widely adopted by the bioinformatics community and with a lot of plugins
colleague leaving the academia
Massimo Sandal is the person who introduced me to Linux. The people who know me in person will understand how much does this mean for me, since I totally am an hard core Linux Geek. Almost 6 or 7 years ago, second year of bachelor, I joined a group of geek-lous students in the Biotec