KarrLab wc_sim issues - Githubissues

KarrLab / 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 3 years ago
3
Improve performance of WC expression evaluation

#102 artgoldberg opened 3 years ago
0
Optimization for reaction network dependency analysis

#101 artgoldberg opened 3 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 3 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 3 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