Two papers from PLoS Computational Biology

Pubblicato maggio 31, 2008 di fmenolascina
Categorie: Bioinformatics, Systems Biology

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!


BioBarCamp: that’s a good idea!

Pubblicato aprile 30, 2008 di fmenolascina
Categorie: Uncategorized


I learned from Attila’s blog. It seems a quite interesting idea…let’s see how it will evolve!

Good job, guys!

This is why being an engineering student doesn’t suck!

Pubblicato marzo 26, 2008 di fmenolascina
Categorie: Engineering

I recently read this post on Rod’s blog discussing this article. I do think this thesis is absolutely misleading and I’ll explain why. Let’s sum up the points of the article:

5. Awful Textbooks

Absolutely false…try to read a serious math book and an equivalent engineering book. Everyone will notice the difference. There should be some reason for all the jokes describing mathematicians complaining with engineers about their simplistic way of approximating complex processes in order to come up with a solution at any cost.

4. Professors are Rarely Encouraging

False in general. It significantly depends on the professors you have to do with. There are many highly qualified and much stimulating researchers among professors. Moreover laziness doesn’t only affect engineering professors.

3. Dearth of Quality Counseling

This depends on the university you attend and its management. This could be true for some situations but it’s sure that engineering is one of those universities which is more in touch with real life problems and students usually find their work some weeks after they got their degree.

2. Other Disciplines Have Inflated Grades

This is true but this doesn’t depend on the engineering but on the other universities! However there are similar situations even in the various curricula in engineering.

1. Every Assignment Feels the Same

This is probably the more absurd statement about engineering classes. Assignments are usually difficult, challenging but of course not all the same.

SBTOOLBOX2 v1.1 released!

Pubblicato marzo 21, 2008 di fmenolascina
Categorie: Bioinformatics, Systems Biology

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

Pubblicato marzo 1, 2008 di fmenolascina
Categorie: Bioinformatics, Programming, Software

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

Pubblicato febbraio 25, 2008 di fmenolascina
Categorie: Bioinformatics, Programming

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.

Zotero: this is what I was looking for!

Pubblicato febbraio 24, 2008 di fmenolascina
Categorie: Bioinformatics, Lavoro, Software, Web 2.0

Some months ago I get acquainted with latex and I was no more able to leave it. I think that bibtex is one of the most intelligent things researchers have done in order to give a systematic appearance to their activity (which is far from systematic, indeed 😀 ). Unfortunately the way bibtex works and the support it has in some relevant fields like computational biology prevents it from reaching a real spread. Some days ago I came across this tool, it’s named Zotero, I thought: “What a strange name for a citation manager…should I take it seriously!?!”. I should have! Zotero is one of the best REALLY INTEGRATED citation manager I’ve ever seen, with the most powerful functionalities (and, among them, the capability to export citations in a number of different formats, bibtex included!). Zotero allows you to take notes on your documents, to store pdfs and it is able to integrate itself with most commong document editors and blogging platforms. Moreover future developments announced on the official site include bibliographic content sharing and all the stuff that a real research 2.0 application should have. Amazing, isn’t it? You should give it a try!