StochKitSimulator, an interface to the stochastic simulator StochKit. See
InitialsSensitivity, a tool to perform pairwise sensitivity analysis of initial conditions. See
- Import models directly from BioModels from just their ID (BIOMDxxx... or MODELxxx...) with
- Faster simulation runs for models with many expressions (~60x speedup for a 200-expression model).
- Improved accuracy and better error reporting when parsing SBML expressions in
- The Kappa interface has been upgraded to support Kappa version 4. This also means Kappa v3 is no longer supported.
CupSodaSimulatornow works on Python 3.
- Simulators now fully respect parameter value overrides for initial condition parameters (#252).
- Simulators now allow overriding a non-zero initial condition to zero (#251).
- Simulators no longer have problems with parameter names that are unicode objects (still only ASCII characters are allowed, though) (#278).
- Model components with the same name as a top-level sympy object (anything you would see in
from sympy import *) no longer cause errors when simulating (#259).
- Applying a compartment condition to a MonomerPattern that already has one now correctly raises an exception (#258).
PysbFlatExporternow works with compartments using inline size declarations (#210).
ComplexPattern.is_equivalent_tonow correctly handles certain combinations of compartments that were previously mishandled (#257).