Archive for the ‘Bioinformatics’ category

MATLAB R2008b is out!

ottobre 11, 2008

Yesterday Mathworks released the ultimate version of the widely used Matlab. Unfortunately the R2008b release doesn’t seem to provide major updates neither in the bioinformatics nor in the systems biology toolbox (where, in particular, support to critical points of SBML is still missing). I’ll wait for the new version in the lab and I’ll let you know the first impressions on that…even though the outlook doesn’t seem to be too encouraging!

A bunch of new papers from PLoS Comp Bio

giugno 28, 2008

PLoS Computational Biology Published published a some papers that could be of interest for someone out there. These are the links:

Ten Simple Rules for Organizing a Scientific Meeting

Regulation of Signal Duration and the Statistical Dynamics of Kinase Activation by Scaffold Proteins

Integrated Information in Discrete Dynamical Systems: Motivation and Theoretical Framework


BioBarCamp is real!

giugno 4, 2008

I recently noticed that BioBarCamp is now reality! You can get more information here:

Great job, guys!

Two papers from PLoS Computational Biology

maggio 31, 2008

Two very interesting papers appeared today in PLoS Computational Biology. The first is the sequel of the never ending series of “ten simple rules”:

Ten Simple Rules for Aspiring Scientists in a Low-Income Country

the second, instead, is more concerned in establishing links between computational neuroscience and systems biology:

Why Are Computational Neuroscience and Systems Biology So Separate?

Have a look at both and enjoy!

SBTOOLBOX2 v1.1 released!

marzo 21, 2008

Henning Schmidt has just sent this announcement about his well known simulation/analsysis package Systems Biology Toolbox 2. He has just released the version 1.1. This is the link and the changelog, check it out!

1.  SBML: Support for the following SBML features has been added:

* Arbitrary event trigger expressions
* Delays and delayed events
* Algebraic rules
* Fast reactions

2. Stoachstic simulation: Bugfix in the SBstochsim function.
Kinetic parameters are now correctly converted to stochastic rate

3. New stoachstic simulation function: I added the SBstochsim2 function that
is able to simulate not only single runs (as the above function) but
also multiple runs and thus can determine the mean values. Furthermore,
it is written completely in MATLAB, so it runs under Windows AND Unix.
It has been optimized for speed. The function uses the Gillespie

4. Minor bug-fixes: SBPDmanualtuning and SBexportSBML functions have been

5. Time varying compartments: The ODEs are built accordingly to take that
into account.

6. MEX File Generation: Updated the MinGW compiler in order to allow correct
C++ MEX file generation.

7. Forum: The Forum has been disabled, since there has been a large amount of

Great work Henning! 😉

Matlab R2008a is out

marzo 1, 2008

Mathworks has released today the latest version of its most famous software package, namely MATLAB R2008a (v 7.6). You can find it here. The feeling is that this release includes very few major updates (Mathworks lists 5 major updates, among the others the Optimization and Neural Networks Toolboxes have been changed).  It seems that this time the upgrade should not be compulsory!

Python 2.5.2 is out

febbraio 25, 2008

The latest version of Python is out and ready to be put on the road. This is one of the main releases waited for in the field of bioinformatics. Anyway we are still waiting for the 3.0 rel!

You can download the new version here.