Motivation COPASI is an open source software package for constructing, simulating and
analyzing dynamic models of biochemical networks. COPASI is primarily intended to be …

Motivation Computational systems biology analyses typically make use of multiple software
and their dependencies, which are often run across heterogeneous compute environments …

While scientific disciplines revere reproducibility, many studies–experimental and
computational alike–fall short of this ideal and cannot be reproduced or even repeated when …

A computational technique is described to reduce the model search space and construct an
ensemble of models for systems biology using perturbation data. While doing so, an …

Agent-based modelling (ABM) offers a framework to realistically couple subcellular signaling
pathways to cellular behavior and macroscopic tissue organization. However, these models …