Archive for the ‘Systems Biology’ 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!


Systems Biology Graphical Notation v1.0 is out

agosto 26, 2008

Finally the systems biology group did it and published the v1.0 specifications of the graphical notation standard for systems biology. This is a quite relevant step forward in this field since the lack of standardization and the ever growing amount of information to be coded were generating an unbearable situation. If you want to take a look at the new stadard you should check this link.


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


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! 😉

Biological complexity: from molecules to systems

febbraio 23, 2008

On the 12-13 of June the Imperial College in London will host an amazing event on the topic “Biological Complexity”. This is a very interesting area of research in systems biology and I believe this is one of the points in which biology and engineering are closer. Several well known researchers will participate to this event and young researchers are invited to participate, the fee is only 30£ for students.

You can check it here

libSBML 3.1.0 released

febbraio 21, 2008

The libSBML 3.1.0 have been recently released and they are available at this site.

LibSBML is a library designed to help you read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with many example programs), but rather a library you can embed in your own applications.

LibSBML 3.1 understands:

  • SBML Level 1 Versions 1 and 2
  • SBML Level 2 Versions 1, 2 and 3
  • The draft SBML Layout Proposal (experimental)

LibSBML is written in ISO C and C++ but as a library it may be used from all the programming languages listed to the left. In fact, we strive to adhere to the natural idioms of each particular language to make the libSBML programming experience seamless. For example, SBML <listOf> elements behave like lists and sequences in Python, but vectors in Matlab. Also, the C and C++ interfaces are completely distinct (it’s possible to program in pure C), but in C++ the C APIs may be called without sacrifcing type safety.

The LibSBML code is very portable and is supported on Linux, Windows (native), and Mac OS X.

Here it is even an amazing report from the SBML Hackaton. Enjoy!