May 24 – 27, 2021
America/Chicago timezone

Running COPASI biochemical simulations with HTCondor

May 25, 2021, 11:40 AM



Pedro Mendes (UConn Health)


COPASI is a widely used simulator for chemical and
biochemical reaction networks based on ordinary differential equations
or stochastic methods. It includes various analysis methods such as
optimization, parameter estimation, sensitivity analysis, and several
others. While COPASI is mostly used in a standalone GUI-based mode,
several compute-intesive tasks benefit from parallelization. We created
a web-based system which facilitates transforming such tasks into
smaller sub-tasks that can be run independently. This system then allows
the user to submit these tasks to HTCondor from the web interface, and
assembles the numerical results in their expected order. Thus the end
user never has to interact directly with HTCondor.

Primary author

Pedro Mendes (UConn Health)

Presentation materials