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lib Scopes
#summary SBML simulation using libScopes
Many a times it so happens that a Boolean Network is not available for a particular set of biochemical reactions. libScopes provides a method of simulating reaction pathways defined in the SBML format.
This library assigns a state to each chemical, the ones which are relevant to our simulator are present and depleted, some of the additional states like blocking are not yet supported.
Currently only a subset of features of the libScopes library are supported in the simulator.
- Importing SBML files
- Applying a Guess Seed
- Step Simulation
- Attractor search
Only simple simulations of SBML files are supported, there is no inhibition/activation support, nor any time series insertions/deletions.
The libScopes library has been written in C/C++, hence it had to be run on a server. The interfacing in web2py was done using SWIG for Python. Hence while developing this particular feature there was a side benefit to the libScopes library of getting a Python wrapper.