Archivio per febbraio 2008

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.

Zotero: this is what I was looking for!

febbraio 24, 2008

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!

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

A Top-Down Approach to Network Modelling in Systems Biology

febbraio 22, 2008

Trey Ideker has recently presented an interesting overview of the various strategies his group at the NIH Systems Biology Special Interest Group has been developing in the recent years in order to integrate multiple types of large scale datasets. During his talk he has gone through these points:

  • mapping of transcriptional response pathways
  • functional mapping of protein complexes
  • disease diagnosis and stratification

Trey presented the study recently published in Molecular Systems Biology (Chuang et al, 2007) where the information provided by microarray expression profiling is superposed to a protein-protein physical interaction network to identify ‘subnetwork’ biomarkers that classify metastatic vs non-metastatic breast tumors.

From: the seven stones

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!

An Engineer’s Perspective on Biology

febbraio 20, 2008

Drew Endy gave, some time ago, a quite interesting interview on his view of engineering life. Drew Endy is one of the most appreciated professors at the MIT and one of the most active researchers in the field of synthetic biology. I found his ideas an highly dense but reasonable summary of what bioengineers think about their activity. Here it is an excepert of the interview you can find at;

“Engineers hate complexity. I hate emergent properties. I like simplicity. I don’t want the plane I take tomorrow to have some emergent property while it’s flying.
How do you manage the information going into a DNA synthesizer so that you can construct some useful object that’ll help you do genetics? […] I think George Church and Craig Venter have a lot to contribute to it, which will be terrific. It will be part of synthetic biology, but it will be synthetic biology impacting science, which is the worst case scenario for synthetic biology.
Five years from now, we may have just begun to make some good progress on reliable functional composition of standard biological parts. Nobody knows how expensive solving that problem will be, but because biology works there’s plenty of existence proofs. […] If I had to guess, I’d say we’ll have a collection of tens of thousands of genetic objects that support reliable functional composition between ten and 15 years from now.”

On the Concepts of Modularity and Retroactivity in Systems Biology

febbraio 18, 2008

Modularity and retroactivity are two highly recurrent concepts in the recent research in systems biology. There could be many interpretations for these two concepts. As Sauro says in his recent paper in Nature Molecular Systems Biology a bioinformatician with an eye on graph theory will view modules as loosely linked islands of densely connected nodes, on the other hand a geneticist might see modules as groups of coexpressed genes. In engineering, instead, a module is defined as a functional unit that is capable of maintaining its intrinsic properties irrespective of what it is connected to.