Biochemical modeling tools are designed to help modelers build models with a specific set of parameter values.
However a common scenario involves different parametrization of the same model to account for mutation of the initial model (e.g. gene knock-out, overexpressions). This scenario is not well supported by existing biochemical modeling editors, forcing the user to manually generate, store and maintain big sets of variation of the same model.
We developed an extension of our modeling editor (MSMB) (
Palmisano, A., Hoops, S., Watson, L. T., Jones Jr, T. C., Tyson, J. J., and Shaffer, C. A.(2014). Multistate model builder (MSMB): a flexible editor for compact biochemical models. BMC Systems Biology, 8(1), 42.) called
JigCell Run Manager (JC-RM).
This extension allows the modeler to define a hierarchy of parameter values, simulation and plot settings and to save them together with the initial model. MSMB-RM allows the generation of simulation plots within the tool, as well as export to COPASI and SBML for further analysis.
JC-RM offers many innovative features:
- graphical interface to define parameter configurations of a single model in a hierarchical way. The different configurations are displayed in a graph and each node typically differs from the others in only minor ways. This makes it easy to define and maintain big sets of small parameter changes;
- for each node, specific values can be changed either to new numerical values or to complex expressions involving values from ancestor nodes: in this way the propagation of changes from parent nodes to all the descendants is carried seamlessly by the tool;
- hierarchical graphs can be defined for model's values, simulation runs and plot settings. The different graphs are linked but independent one another;
- the ensemble of parameter lists, simulation and plotting information can be run inside the tool or exported to a single COPASI file;
- support in detecting and communicating errors/conflicts that can raise during the definition of configurations (multiple inheritance).
JC-RM Publications:
- (journal paper) under review
JC-RM Documentation:
This documentation applies to MSMB - version 2.0 (which includes RM) released on September 2014.
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