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KarrLab
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wc_sim
A multi-algorithmic simulator for whole-cell models
MIT License
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Test RunResults using a model with a dFBA submodel, and check on dfba_reaction_fluxes
#115
artgoldberg
opened
3 years ago
0
refactor rate law and enabled reaction calculations in DynamicSubmodel so eval_dynamic_rate_laws can use them
#114
artgoldberg
opened
3 years ago
0
Double-check coefficient scaling in unscale_conv_opt_solution() in wc_sim/submodels/dfba.py
#113
artgoldberg
closed
3 years ago
1
Remove use of typing module in message_types.py when earliest supported Python version >= 3.9
#112
artgoldberg
opened
3 years ago
0
Handle ambient species, which are used in reactions but have "infinite" supply
#111
artgoldberg
opened
3 years ago
0
Support simulation of large models in modest amounts of RAM
#110
artgoldberg
opened
3 years ago
0
WC Sim container for BioSimulators
#109
artgoldberg
opened
3 years ago
0
Report invalid positive reaction rates in ODE submodels
#108
artgoldberg
opened
3 years ago
0
Dynamically reduce the time steps of dFBA submodels
#107
artgoldberg
opened
3 years ago
0
Bound dFBA reactions to avoid negative populations
#106
artgoldberg
closed
3 years ago
1
Avoid positive propensities for reactions in discrete submodels that lack adequate reactants
#105
artgoldberg
closed
3 years ago
1
Support access to a LocalSpeciesPopulation species by multiple continuous submodels
#104
artgoldberg
closed
3 years ago
1
Warn about potential negative species
#103
artgoldberg
closed
4 years ago
3
Improve performance of WC expression evaluation
#102
artgoldberg
opened
4 years ago
0
Optimization for reaction network dependency analysis
#101
artgoldberg
opened
4 years ago
0
Investigate possible problem with SsaTestCase 00003
#100
artgoldberg
opened
4 years ago
0
Properly handle RandomStates
#99
artgoldberg
opened
4 years ago
0
RunResults visualization
#98
artgoldberg
opened
4 years ago
0
Make NRM a simulation method in the onto, instead of a framework
#97
artgoldberg
opened
4 years ago
1
Double-check NRM dependencies analysis
#96
artgoldberg
closed
4 years ago
1
Run-time error checking of caching
#95
artgoldberg
opened
4 years ago
0
To improve performance suspend default run-time error checking more broadly
#94
artgoldberg
opened
4 years ago
0
Add logging in propensity calculations and a method that takes a model and evaluates its performance at time 0
#93
artgoldberg
opened
4 years ago
1
Add options to 'wc-sim sim' CLI interface
#92
artgoldberg
opened
4 years ago
0
test SSA & NRM with many more runs
#91
artgoldberg
opened
4 years ago
0
Generalize validation with SBML test suite
#90
artgoldberg
opened
4 years ago
0
Decide what to do about propensities < 0
#89
artgoldberg
opened
4 years ago
0
Evaluate NRM performance
#88
artgoldberg
closed
3 years ago
0
compare performance of SSA and NRM
#87
artgoldberg
opened
4 years ago
0
Improve NRM submodel
#86
artgoldberg
opened
4 years ago
1
Clean-up ssa.py and test_ssa.py
#85
artgoldberg
closed
4 years ago
1
Clean up wc_sim/message_types.py
#84
artgoldberg
opened
4 years ago
0
Enhance RunResults
#83
artgoldberg
opened
4 years ago
0
Support performance profiling
#82
artgoldberg
closed
4 years ago
1
Clean up debugging code in ODEsubmodel
#81
artgoldberg
closed
4 years ago
0
Add Next Reaction Method as alternative to Direct Method for SSA
#80
artgoldberg
closed
4 years ago
0
Improve validation with SBML test suite
#79
artgoldberg
closed
4 years ago
1
Investigate warnings
#78
artgoldberg
opened
4 years ago
0
Improve error handling in Simulation.run()
#77
artgoldberg
closed
4 years ago
2
Make progress bar available through simulate.run()
#76
artgoldberg
closed
4 years ago
1
Give abstract compartments fixed volume & document that behavior
#75
artgoldberg
closed
4 years ago
1
More comprehensively integrate SimulationConfig
#74
artgoldberg
closed
4 years ago
2
Refine multi-algorithmic synchronization
#73
artgoldberg
opened
4 years ago
1
Optional argument to Simulate.run(): list of submodels to simulate or not
#72
artgoldberg
closed
4 years ago
2
Finish implementing `RunResults.get_concentrations()`
#71
artgoldberg
closed
4 years ago
1
Enhance RunResults
#70
artgoldberg
closed
4 years ago
4
Have checkpoints execute after all simultaneous events
#69
artgoldberg
closed
4 years ago
1
Better test coverage
#68
artgoldberg
closed
4 years ago
4
Properly integrate DynamicSpecies with LocalSpeciesPopulation
#67
artgoldberg
closed
4 years ago
1
Implement Monte Carlo simulations
#66
artgoldberg
opened
4 years ago
1
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