qbio 2015, August 5, 2015 Wednesday
=> rule based modeling http://bionetgen.org/index.php/Q-bio-14
bionetgen use matlab for parameter estimation. The .m files can be converted to .c file for faster computing needs. Some kind of simulated annealing approach seems to be used.
Currently, rule-based modeling has not been applied to spatial modeling. "Everything is coded to ODEs".
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