The authors of programming4scientists have published a nice blog post with several tips on how to avoid distractions while programming:
programming4scientitst – Stay on target!
I think this is a major issue for all people working in bioinformatics, because compared to the classical computer scientist, we bioinformaticians have less culture on this topic, and generally there is [...]
I would like to point to you ruffus, an alternative to Make as a tool to define pipelines, with a python syntax and many good things.
Here it is a link to the project:
ruffus – a tool to define scientific pipelines with a python syntax
and here it is also its home page at google/code:
ruffus google/code page
I [...]
I am writing a parser for the kegg KGML format, the dialect of XML used to store kegg pathways.
I couldn’t find any existing module to do this in python. There is a similar library for R (KEGGgraph), maybe something for perl (I didn’t find it), but apparently nothing for python.
Here it is the code, hosted [...]
I am back in Barcelona after the italian Pycon.it, and I can finally publish the slides of my talk on ‘Python and Bioinformatics’:
I am sorry that the slides are in Italian. I could have written them in English, but I was too tired
The talk went well, and I have been asked many questions. [...]
I have found some useful links on databases and bioinformatics.
First, you must be introduced to the debate ‘Flat files against databases’:
nodalpoint – databases or flat files?
bioinformaticszen post on databases
what is a database, a flat file, etc..
Usually, people in bioinformatics start with using flat files for doing most of the things. Later, they learn relational databases [...]
I would like to wish you all an Happy San Jordi, which is one of the most important National Feasts here in Catalunya.
Today (well, it was the 23th of April), boys are used to give a rose to their girlfriends, while girls use to give a book to their boyfriends.
What does this have to do [...]
In the last post, I forgot to put some thoughts I had when preparing the slides.
it is true that it is better to have a lot of slides, at least one or two per minute. When you show the same slide for too much time, like two or three minutes, you start seeing people in [...]
Here in the prbb, we organize a series of talks called ‘PRBB technical seminars‘.
This time, it was my turn to present something, so I have prepared an introduction to python for bioinformatics in general.
Have a look at it here:
I have talked about a bit of everything, insisting on three things:
python has a very good syntax [...]
PyCon.it is the yearly conference on python in Italy, usually yeld in the beatiful city of Firenze (Florence). This year, the keynote talk will be given by Guido Van Rossum himself.
Earlier I proposed a talk on python and bioinformatics for the pycon3, and I have just been told that it has been accepted.
So, now I [...]
I am really horryfied by a mail that I have just received from Riccardo Fallini, Molecularlab.it’s founder and former owner.
Molecularlab is a open web italian scientific community, and this is a pretty reductive description to say that it is the community where I have learned everything I know about e-science and the importance of communication [...]
