Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / KarrLab/wc_sim issues and pull requests
#115 - Test RunResults using a model with a dFBA submodel, and check on dfba_reaction_fluxes
Issue -
State: open - Opened by artgoldberg almost 4 years ago
#114 - refactor rate law and enabled reaction calculations in DynamicSubmodel so eval_dynamic_rate_laws can use them
Issue -
State: open - Opened by artgoldberg almost 4 years ago
#113 - Double-check coefficient scaling in unscale_conv_opt_solution() in wc_sim/submodels/dfba.py
Issue -
State: closed - Opened by artgoldberg almost 4 years ago
- 1 comment
Labels: bug, question
#112 - Remove use of typing module in message_types.py when earliest supported Python version >= 3.9
Issue -
State: open - Opened by artgoldberg almost 4 years ago
#111 - Handle ambient species, which are used in reactions but have "infinite" supply
Issue -
State: open - Opened by artgoldberg about 4 years ago
Labels: enhancement
#110 - Support simulation of large models in modest amounts of RAM
Issue -
State: open - Opened by artgoldberg about 4 years ago
Labels: enhancement
#109 - WC Sim container for BioSimulators
Issue -
State: open - Opened by artgoldberg about 4 years ago
Labels: enhancement
#108 - Report invalid positive reaction rates in ODE submodels
Issue -
State: open - Opened by artgoldberg about 4 years ago
Labels: enhancement
#107 - Dynamically reduce the time steps of dFBA submodels
Issue -
State: open - Opened by artgoldberg about 4 years ago
Labels: enhancement
#106 - Bound dFBA reactions to avoid negative populations
Issue -
State: closed - Opened by artgoldberg about 4 years ago
- 1 comment
Labels: enhancement
#105 - Avoid positive propensities for reactions in discrete submodels that lack adequate reactants
Issue -
State: closed - Opened by artgoldberg about 4 years ago
- 1 comment
Labels: enhancement
#104 - Support access to a LocalSpeciesPopulation species by multiple continuous submodels
Issue -
State: closed - Opened by artgoldberg about 4 years ago
- 1 comment
Labels: enhancement
#103 - Warn about potential negative species
Issue -
State: closed - Opened by artgoldberg about 4 years ago
- 3 comments
Labels: enhancement
#102 - Improve performance of WC expression evaluation
Issue -
State: open - Opened by artgoldberg about 4 years ago
#101 - Optimization for reaction network dependency analysis
Issue -
State: open - Opened by artgoldberg about 4 years ago
Labels: enhancement
#100 - Investigate possible problem with SsaTestCase 00003
Issue -
State: open - Opened by artgoldberg about 4 years ago
Labels: bug
#99 - Properly handle RandomStates
Issue -
State: open - Opened by artgoldberg over 4 years ago
Labels: enhancement
#98 - RunResults visualization
Issue -
State: open - Opened by artgoldberg over 4 years ago
Labels: enhancement
#97 - Make NRM a simulation method in the onto, instead of a framework
Issue -
State: open - Opened by artgoldberg over 4 years ago
- 1 comment
Labels: enhancement
#96 - Double-check NRM dependencies analysis
Issue -
State: closed - Opened by artgoldberg over 4 years ago
- 1 comment
Labels: bug
#95 - Run-time error checking of caching
Issue -
State: open - Opened by artgoldberg over 4 years ago
Labels: enhancement
#94 - To improve performance suspend default run-time error checking more broadly
Issue -
State: open - Opened by artgoldberg over 4 years ago
#93 - Add logging in propensity calculations and a method that takes a model and evaluates its performance at time 0
Issue -
State: open - Opened by artgoldberg over 4 years ago
- 1 comment
#92 - Add options to 'wc-sim sim' CLI interface
Issue -
State: open - Opened by artgoldberg over 4 years ago
Labels: enhancement
#91 - test SSA & NRM with many more runs
Issue -
State: open - Opened by artgoldberg over 4 years ago
#90 - Generalize validation with SBML test suite
Issue -
State: open - Opened by artgoldberg over 4 years ago
Labels: enhancement
#89 - Decide what to do about propensities < 0
Issue -
State: open - Opened by artgoldberg over 4 years ago
Labels: bug
#88 - Evaluate NRM performance
Issue -
State: closed - Opened by artgoldberg over 4 years ago
#87 - compare performance of SSA and NRM
Issue -
State: open - Opened by artgoldberg over 4 years ago
#86 - Improve NRM submodel
Issue -
State: open - Opened by artgoldberg over 4 years ago
- 1 comment
Labels: enhancement
#85 - Clean-up ssa.py and test_ssa.py
Issue -
State: closed - Opened by artgoldberg over 4 years ago
- 1 comment
#84 - Clean up wc_sim/message_types.py
Issue -
State: open - Opened by artgoldberg over 4 years ago
#83 - Enhance RunResults
Issue -
State: open - Opened by artgoldberg over 4 years ago
Labels: enhancement
#82 - Support performance profiling
Issue -
State: closed - Opened by artgoldberg over 4 years ago
- 1 comment
Labels: enhancement
#81 - Clean up debugging code in ODEsubmodel
Issue -
State: closed - Opened by artgoldberg over 4 years ago
#80 - Add Next Reaction Method as alternative to Direct Method for SSA
Issue -
State: closed - Opened by artgoldberg over 4 years ago
Labels: enhancement
#79 - Improve validation with SBML test suite
Issue -
State: closed - Opened by artgoldberg over 4 years ago
- 1 comment
#78 - Investigate warnings
Issue -
State: open - Opened by artgoldberg over 4 years ago
#77 - Improve error handling in Simulation.run()
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 2 comments
#76 - Make progress bar available through simulate.run()
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 1 comment
#75 - Give abstract compartments fixed volume & document that behavior
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 1 comment
#74 - More comprehensively integrate SimulationConfig
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 2 comments
#73 - Refine multi-algorithmic synchronization
Issue -
State: open - Opened by artgoldberg almost 5 years ago
- 1 comment
#72 - Optional argument to Simulate.run(): list of submodels to simulate or not
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 2 comments
#71 - Finish implementing `RunResults.get_concentrations()`
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 1 comment
#70 - Enhance RunResults
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 4 comments
#69 - Have checkpoints execute after all simultaneous events
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 1 comment
#68 - Better test coverage
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 4 comments
#67 - Properly integrate DynamicSpecies with LocalSpeciesPopulation
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 1 comment
#66 - Implement Monte Carlo simulations
Issue -
State: open - Opened by artgoldberg almost 5 years ago
- 1 comment
Labels: enhancement
#65 - dFBA submodels
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 1 comment
#64 - Misc
Issue -
State: open - Opened by artgoldberg almost 5 years ago
#63 - Improve dynamic tests
Issue -
State: open - Opened by artgoldberg almost 5 years ago
- 5 comments
#62 - Give abstract compartments control over their volumes
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 1 comment
#61 - Select Stop Condition(s) to execute
Issue -
State: open - Opened by artgoldberg almost 5 years ago
Labels: enhancement
#60 - Integrate ODEs, SBML test suite, and other code from fall 2018 wc_sim branch
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 4 comments
#59 - Combine `DynamicSpecies` with the local species population
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 1 comment
#58 - Dynamic dFBA expressions
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 1 comment
Labels: enhancement
#57 - Replace normal with single-tailed distribution(s) for initializing non-negative values
Issue -
State: open - Opened by artgoldberg almost 5 years ago
- 1 comment
#56 - Separate the initialization of simulation state from the construction of simulation objects
Issue -
State: closed - Opened by artgoldberg almost 5 years ago
- 1 comment
#55 - Properly initialize the multi-algorithmic simulator
Issue -
State: closed - Opened by artgoldberg about 5 years ago
Labels: enhancement
#54 - move phold.py to de_sim
Issue -
State: closed - Opened by artgoldberg about 5 years ago
- 2 comments
Labels: refactor
#53 - capture output generated by testing
Issue -
State: closed - Opened by artgoldberg about 5 years ago
- 1 comment
#52 - Speed up wc_sim tests
Issue -
State: closed - Opened by artgoldberg about 5 years ago
- 2 comments
#51 - Failure to validate reading of examples/translation_metabolism_hybrid_model/model.xlsx
Issue -
State: closed - Opened by artgoldberg about 5 years ago
- 3 comments
Labels: bug
#50 - Error if model has no sub-models
Issue -
State: closed - Opened by artgoldberg over 5 years ago
- 2 comments
Labels: enhancement
#49 - Add integration tests for different mass dynamics schemes
Issue -
State: closed - Opened by jonrkarr almost 6 years ago
- 1 comment
Labels: enhancement
#48 - Simulation results should be logged to the specified directory rather than a subdirectory whose name is the date
Issue -
State: closed - Opened by jonrkarr over 5 years ago
- 1 comment
#47 - Remove `wc_sim.log` which is redundant with `RunResults`
Issue -
State: closed - Opened by jonrkarr over 5 years ago
- 1 comment
#46 - Consider merging `dynamic_component` and `dynamic_expression` modules
Issue -
State: closed - Opened by jonrkarr over 5 years ago
#45 - Move `get_species_and_compartment_from_name` to wc_lang.Species
Issue -
State: closed - Opened by jonrkarr over 5 years ago
- 1 comment
Labels: refactor
#43 - Consider merging `wc_sim.multialgorithm.dynamic_expressions.DynamicExpression.prepare` with expression parsing in `obj_model.expression`
Issue -
State: closed - Opened by jonrkarr over 5 years ago
- 4 comments
Labels: enhancement, refactor
#42 - Separate all code for testing into a separate test module
Issue -
State: closed - Opened by jonrkarr almost 6 years ago
- 1 comment
Labels: enhancement
#41 - Sample from new distributions of initial conditions
Issue -
State: closed - Opened by jonrkarr almost 6 years ago
- 3 comments
Labels: enhancement
#40 - Address issues noted in wc_lang.expression_utils
Issue -
State: closed - Opened by jonrkarr almost 6 years ago
- 2 comments
#39 - stop recording history in LocalSpeciesPopulation; checkpointing is a better approach
Issue -
State: closed - Opened by artgoldberg almost 6 years ago
- 1 comment
#38 - Improve ODE submodels
Issue -
State: open - Opened by artgoldberg almost 6 years ago
#37 - re-enable Mass Action in DynamicRateLaw.eval()
Issue -
State: closed - Opened by artgoldberg almost 6 years ago
- 1 comment
#36 - loosen 'time of previous _record_history() ({}) not less than current time ({})'
Issue -
State: closed - Opened by artgoldberg almost 6 years ago
#35 - Handle rate laws with k_cat but no k_M
Issue -
State: closed - Opened by artgoldberg almost 6 years ago
- 1 comment
#34 - Support dynamic compartment volumes
Issue -
State: closed - Opened by jonrkarr almost 6 years ago
- 5 comments
Labels: enhancement
#33 - Remove compartment attribute from submodels
Issue -
State: closed - Opened by jonrkarr almost 6 years ago
- 1 comment
Labels: invalid
#32 - Implement sampling of initial conditions
Issue -
State: closed - Opened by jonrkarr almost 6 years ago
- 1 comment
Labels: duplicate, enhancement
#31 - Speed up RunResults
Issue -
State: closed - Opened by jonrkarr almost 6 years ago
- 2 comments
Labels: enhancement
#30 - Store computed volumes and masses for all compartments
Issue -
State: closed - Opened by jonrkarr almost 6 years ago
- 1 comment
Labels: enhancement
#29 - Submodels with no reactions or no propensity generate a large number of events
Issue -
State: closed - Opened by jonrkarr almost 6 years ago
- 1 comment
Labels: bug
#28 - Propensities to run_results
Issue -
State: closed - Opened by szb37 about 6 years ago
- 3 comments
Labels: enhancement
#26 - Compute reaction rates in abundance space
Issue -
State: closed - Opened by artgoldberg about 6 years ago
- 2 comments
#25 - Make MW>0 check optional
Issue -
State: closed - Opened by artgoldberg about 6 years ago
- 2 comments
Labels: enhancement
#24 - Add perturbation events
Issue -
State: open - Opened by artgoldberg about 6 years ago
Labels: enhancement
#21 - sim results should be stored in the specified directory rather than a subdirectory with a timestep
Issue -
State: closed - Opened by jonrkarr over 6 years ago
- 1 comment
Labels: enhancement
#20 - Enable restart of a simulation from a checkpoint or RunResults
Issue -
State: open - Opened by artgoldberg over 6 years ago
- 1 comment
Labels: enhancement
#19 - record metadata about all the code used
Issue -
State: closed - Opened by artgoldberg over 6 years ago
- 1 comment
#15 - downstream dependence + relation to old_wc_sim
Issue -
State: closed - Opened by szb37 over 6 years ago
- 4 comments
Labels: question
#12 - Simulate a reduced size model, & then scale the predictions
Issue -
State: open - Opened by artgoldberg over 6 years ago
#10 - Support function observables
Issue -
State: closed - Opened by jonrkarr over 6 years ago
- 1 comment
Labels: enhancement
#9 - stop condition
Issue -
State: closed - Opened by artgoldberg over 6 years ago
- 2 comments
#8 - observable with weighted sum of species concentrations
Issue -
State: closed - Opened by artgoldberg over 6 years ago
- 2 comments
#6 - Rework and simplify config code; follow usage style from datanator or another repo
Issue -
State: closed - Opened by artgoldberg over 6 years ago
- 1 comment
#3 - Separate core into distinct, public repo
Issue -
State: closed - Opened by artgoldberg over 6 years ago
- 6 comments