Modeling Course at Indiana University

Not that kind of modeling, but the kind that involves building computational models of biochemical networks and multicellular systems.

James Glazier, the Director of the Biocomplexity Institute at Indiana University is the lead organizer behind a series of workshops that are held every year in the charming University Town of Bloomington. The workshop goes on for two weeks (August 8th-19th, 2011), the first week being devoted to subcellular modeling and the second week to multicellular modeling. This means it is possible to do just one of the weeks or both weeks if you have the time. This was my second year where I teach subcellular modeling in the first week. This year I included far more hands on modeling exercises which I believe the students appreciated. The tools we used where Jarnac, JDesigner and the SBW General Simulation Tools. All three tools are part of the SBW suite (download at the sourceforge site) .  At the end of the week the most students gravitated towards Jarnac for model entry and simulation and the general simulation tool for further graphical analysis, particularly the use of the sliders.In all there were about 20 to 25 enthusiastic US and international students. Details of the first week of the course can be found here. As a result of feedback from the students at the course there will be new versions of Jarnac and JDesigner coming up in the next month or so. Some of the changes include a brand new graphing module for Jarnac that is produces much nicer output. Not more jaggies on the graphing curves, 🙂

In the second week the studentsl focus on the use of CompuCell3D which is an open source multicellular simulator that uses the extended Glazier and Graner model which in turn is based on the Cellular Potts model. By combining the Glazier and Graner model and subcellular modeling we have a comprehensive system for modeling the developmental processes in tissues, organs and disease states such as cancer. Details of the second week of the course can be found here.

The images below show examples of simulations carried out using Jarnac and then the general simulation tool. The images shows a simulation of the Jana Wolf glycolytic model.

Jarnac showing scripting window and console

Jarnac showing results from a simulation

Model passed to the general simulation tool illustrating slider control

The SBW project has in the past three years being funded by generous support from the NIGMS at the NIH.

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