Category: bioinformatica

Sumatra and git support

Sumatra is very cool idea which I felt the need from a long time. Andrew started the development of it and released the version 0.1 few days ago. The idea was great: record all the details about your simulation, storing the parameters, why you have launched it, what was the outcome. Tagging on top for categorization as well.

There was only one problem: Sumatra was not supporting git so I was unable to use it. Therefore, giving the fact was opensource I just baked a series of patches which were integrated in the tool and now sumatra has a git support 🙂

If you want to have a feel about it and want to try with git there is an example repository on github which you can use.

This is the results of the webinterface (sumatra stores everything in the django ORM system) showing the tables of the simulations:

If you click on the single record you can access the details of the simulation:

Using sumatra you will be able to:

  • search your simulations’ results
  • describe the results of the simulation on the simulation record itself, keeping everything very compact and ordered.
  • retrieve all the tiny details when you will need (papers hopefully..)

Storing all this informations is done automatically for you (except the analysis’ results of course), so you can focus more on your science, without worrrying on loosing your results.

Soon I’ll integrate sumatra in Neuronvisio.

P.S.: The patch for git integration (second part) is on its own way and it should be integrated soon in the tree, so you will need to run the bleeding edge and integrate the patch yourself if it’s not yet there (and you can’t wait 🙂 )

Have Fun

Pylab quick intro

You can find some slides about pylab and some code as well on this presentation.

It is very basic, quick and dirty. But maybe it’s useful to someone.

[slideshare id=2512270&doc=pylab-091116123248-phpapp02]

For the code highlights I used pygments, which rocks.

A small discovery

I just discovered that in using pylab you can plot an array or list of number vs the list lenght by default.

Let’s say we have a list of point like [2,2,3,4,5,5,6,10, 23,45,58,42,12]
points = [2,2,3,4,5,5,6,10,23,45,58,42,12]
well to plot this you just have to

and this is the results:

pylab example

pylab example

The whole script in python
import pylab
points = [2,2,3,4,5,5,6,10,23,45,58,42,12]

The last one is needed to show the window, which will happen automatically if you are running the script using ipython with the pylab option.

I just discovered by chance. I always thought that to plot you need x and y, but of course it’s possible to infer the x if you just one to plot only the points, cause each point in the list has a “Cartesian coordinates” embedded, i.e. [0,2];[1,2];[2,3];[3,4];… etc.

Mendeley: manage your papers and sync them

If you are in research you read a huge amount of papers, which you would like to retrieve later according to a keyword, author name, or any other method that works for you.

Right now it’s plenty of this tool around, starting from Papers, to Referencer which is my choice right now. However having your papers available when you don’t have your laptop and having them from an on-line resources is also a good idea and CiteUlike is my solution for now.

One thing that I am really keen to have is a synchronized way to manage this two worlds. Right now SyncUThink is a tool developed to do just that. We even have interviewed the developer some time ago.

mendeley logo

Today a new guy is coming up and it’s called Mendeley. One of the innovative features that this software is able to offer is the automatic synchronization between the offline and the online world.

The software consist of two part, the desktop client and the website. On the website you can have the classical social soul and on the desktop you can use the software to search your papers and find that piece of information that you are looking for.

The Desktop client (Qt based in my case) has a pretty neat interface and the search for authors is one of my favourite tool to search the articles. And the synchronization is only one click away. Pretty slick, isn’t it?

It’s worth to give a shoot.

Note: I discovered this software directly from an e-mail sent to me by Victor. He found this blog when he googled for open science. This made me quite happy :).

Bioinformatics survey is over

The bioinformatics survey proposed by Bioformatics zen during july is over.


As expected the USA is the country with the numerous entries, but France in second place looks to me as a surprise.

As usual Italy is one of the last country for number of entries (but at least is there :))

Into macro regions the Europe is rocking!

macro regions

Have a look the other initial charts here.

More to come.

Bioinformatics… getting the (people) data

So it seems that Bioinformatic Zen has launched another interesting idea:

Why we don’t get the data about all the bioinformaticians around ad see what they are doing, to have at least a snapshot of what’s going on in the bioinformatics field?

So, to do that, a survey has been developed. The data gathering has started the 1st of July and it will be on up to the 1st of August. The data will be analyzed by all the people that want to do it and the result are going to be made available on the (proposed date) 1st of September.

For your convenience also YANNB will post the result.
Fill it if you have 5 mins :).

Another blog about bioinformatics

So, some of my friends has set up another blog on Bioinformatics.
The address is phdblog
and the subtitle it’s just true.

70% of what we do doesn’t work

I would just increase the percentual, but hey, we should trust us and hope for the best.

It’s just a new born blog, few articles right now, but it’s growing well.
Keep on eye on it, you wouldn’t regret.