I'm attending ICSB 2004 , a conference on Systems Biology here in Heidelberg. I attended two tutorials over the weekend, one on Petri-Nets and one on Virtual Cell.
The petri nets presentation was too much math centered and in the end there was no more time for the biological applications of the methods.
The presentation from the Virtual Cell team was much better and it looks clear that they have nice team of people and are very well funded. They mentioned they want to introduce stochastic methods into Virtual Cell and they want to make the whole code free (eventually and by steps).
Look forward for the next three days to here some nice talks.
Comments
Questions
Sounds great. Could you explain a little about what Petri nets is? It's not very clear from their website. And how advanced is Virtual Cell - are we getting closer to actually being able to model a whole cell, e.g. E. coli?
and my final silly question, is Heidelberg as pretty as everyone says?
About Petri nets I could not
About Petri nets I could not explain a lot. At the tutorial they focused more on the mathematical part of it. It basically seemed to be of some use to analyze the properties of networks when considering the static picture. No rates, just connections between components. I guess it might be a good first approximation to the analysis.
The virtual cell is going nicely. I think being able to do a simulation of cells right now is more a question of knowing the parameters. There are lots of simulation tools but not enough parameters. There is still missing some high throughput biochemistry.
Heidelberg is exactly like Chris explained. I guess it is a nice place for a PhD but maybe to small to live in, anyway, I like it here. If anybody comes for a conference let me know :)
Heidelberg
wrt your last question: yes. Heidelberg is a very picturesque middle-ages small german town, dominated by a brooding castle on the hill. It's a university town (the oldest Uni in Europe), so the old centre is predominantly gothic/neo-gothic public buildings (the original library and cathedral stand out). The old part of town is mostly cobbled walkways, so you can mosy around at your leisure, and enjoy a drink or seven at the microbreweries on each corner. It nestles in coniferous forests which give it a calm if slightly gloomy atmosphere.
It was considered culturally important enough to be spared bombing during WWII, although Frankfurt, about 150km down the road, was pulverised.