Ecosyste.ms: Issues

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GitHub / KarrLab/wc_sim issues and pull requests

#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

#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

#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

#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

#47 - Remove `wc_sim.log` which is redundant with `RunResults`

Issue - State: closed - Opened by jonrkarr over 5 years ago - 1 comment

#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

#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

#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

#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

#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

#3 - Separate core into distinct, public repo

Issue - State: closed - Opened by artgoldberg over 6 years ago - 6 comments