Samuel's Tech Blog

SBML, the "Systems Biology Markup Language", has reached over 500 citations, reports physorg.com, indicating the success of the standard. Congrats!

Very good review on Semantic Web technologies in the Life Sciences:

• Biological knowledgemanagement: the emerging role of the Semantic Web technologies

Interestingly they talk some on "Semantic Systems biology" as well, concluding that Systems biology has been predicted, and shown, to be one of the main adopters of semantic technologies within the life sciences, due to it's high need of integration of knowledge from diverse scientific fields.

Surprisingly they are not mentioning any of the projects of the BioModels initiative, of which I just blogged, such as the Systems Biology Ontology. Should be essential?!

I've had the idea that I'd like to model the embryologic process with semantics (combined with simulations, which would be wrapped in semantics), into a general query answering system for the developmental process of a given species, but having thought that too many ontologies etc. are still missing, such as for expressing time and space.

Well, in addition to realizing that there are ontologies for describing systems biology models, simulations, and simulation results, already (see blog post), I now also realize that work on the above mentioned ontologies (for time and space e.g.) are there as well, and that tons of work along the line of integrate biological knowledge and systems level simulations, is already done (though they don't seem to address embryology specifically, so far).

Gotta think of what that means. Most probably somebody will soon address the embryology process as well, using the mentioned groundwork, and so I don't have to do it! =P

I was at EBI last week for PhD interview (though I unfortunately failed the IAA test, and did not enter), but in addition to the opportunity to see EBI, I got to know some interesting stuff.

Agent based simulation seems highly interesting for biological and/or molecular systems, which are too complex and "high dimensional" to be successfully simulated solely by mathematical means.

Stochastic simulation use to be the way to go then, but it seems agent based computing provide an even more general, and powerful paradigm for simulating this kind of systems.

In light of this, I was delighted to find Mason, a free (how does the "academic free licence" compare against LGPL etc.?) Java based software for agent based simulations, seemingly with many characteristics that make it good for integration in other software (Of course I'm pondering bioclipse integration here)

It seems to be quite working ... see the Conway's "Game Of Life" implementation, further down on the page :)

And, in case MASON is not the right answer to every question, they provide a shortlist of other interesting agent-based simulation software.

While reading up before the UU Cheminformatics journal club, initiated thanks to Egon Willighagen, I stumbled on this ... which seems to be something for Bioclipse, whenever it's time for extending it into the systems biology direction:

• http://www.bio.ifi.lmu.de/FERN (Original article)

A LGPL licenced, Java based, Stochastic biological system simulator, designed with ease of integration and interoperability in mind. (Stochastical simulations seems to be the ones which currently captures biological behaviour the best).