BLACKSBURG, Va., June 18, 2014 – Pedro Mendes at the University of Connecticut Health Center and Stefan Hoops at the Virginia Bioinformatics Institute will offer two workshops this Summer and Fall to help systems biologists build better computational models.
Systems biology takes a holistic approach to the internal workings of organisms, encompassing biochemical interactions that operate at different scales: molecular, cellular, on up to organs. The models typically represent changing amounts and effects of species and their regulatory processes by listing their varied biochemical pathways with sets of ordinary or partial differential equations.
One difficulty, however, is to tell whether a model is functioning as it should. The organizers have spent years developing a user-friendly software tool COPASI (Complex Pathway Simulator) to help scientists define and evaluate how close their ideas about a system align with reality. In models that track 20 or more species, when a mismatch occurs, it’s not easy to decipher where the problem lay. COPASI was built to help interdisciplinary teams expose weaknesses in models in order to prioritize the next set of experiments, which will in turn, lead to a better predictive model. The first workshop is geared to early career scientists curious about the many facets of COPASI in general, while the second will focus on modeling cell dynamics specific to cancer.
“COPASI was built to enable life scientists to use sophisticated numerical algorithms for simulating and analyzing biological processes. It offers a Swiss army knife of routines that address the various kinds of mismatches that occur between experimental data and the model’s predictions.” Pedro Mendes said. “Not everyone needs to program in order to do Systems Biology but understanding the right questions to ask is key.”
The first workshop will be held July 8 to 10 at Virginia Tech’s National Capitol Region center in Arlington, Virginia.
Both beginners and advanced users of COPASI will find the workshop useful. Topics like basic modeling and simulation, stochastic simulation sensitivity analysis, and optimization, among many others, will be covered.
The second workshop will take place at the Math Biosciences Institute in Columbus, Ohio from September 29 to October 1. Users will be given an introduction to COPASI and how it might aid them in their models of cancer.
“We intend to march early career biologists through their paces. We’ve planned three intensive days of hands on experience with lots of sample data taken from experiments,” Stefan Hoops said. “We hope the participants will bring their own models too.”
June 18, 2014