KarrLab/wc_lang issues and pull requests

#146 - Retain comments and changes in merged submodels

Issue - State: open - Opened by artgoldberg over 3 years ago
Labels: bug

#145 - Support single-use transforms

Issue - State: closed - Opened by artgoldberg almost 4 years ago - 1 comment
Labels: enhancement

#144 - Avoid reaction id collisions in `SplitReversibleReactionsTransform`

Issue - State: open - Opened by artgoldberg almost 4 years ago - 2 comments
Labels: bug

#143 - Problem with wc_lang_io.Reader error formatting

Issue - State: open - Opened by artgoldberg almost 4 years ago
Labels: bug

#142 - Problem with wc_lang_io.Reader unit checking

Issue - State: open - Opened by artgoldberg almost 4 years ago - 1 comment
Labels: bug, help wanted

#141 - Left and right square brackets reversed

Issue - State: open - Opened by artgoldberg about 4 years ago

#140 - Correct the units for DfbaObjectiveSpecies

Issue - State: closed - Opened by YinHoon about 4 years ago - 1 comment

#139 - get_model_summary should be more comprehensive

Issue - State: open - Opened by artgoldberg about 4 years ago
Labels: enhancement

#138 - False positive possible in Model._get_cyclic_deps()

Issue - State: closed - Opened by artgoldberg over 4 years ago - 1 comment
Labels: bug

#137 - Switching off requirement for uniqueness for SpeciesCoefficient

Issue - State: closed - Opened by YinHoon over 4 years ago - 7 comments

#136 - Change reaction arrow from "==>" to `<=>`

Issue - State: open - Opened by jonrkarr over 4 years ago

#135 - Switching off requirement for uniqueness

Issue - State: closed - Opened by YinHoon over 4 years ago - 1 comment

#134 - Complete support for Data repo metadata

Issue - State: open - Opened by jonrkarr over 4 years ago
Labels: bug

#133 - Fix to freezing first column

Issue - State: open - Opened by jonrkarr over 4 years ago
Labels: bug

#132 - Capture additional model metadata

Issue - State: open - Opened by jonrkarr over 4 years ago

#131 - Infer units for numeric literals

Issue - State: open - Opened by artgoldberg almost 5 years ago
Labels: enhancement

#130 - Problem converting to SBML

Issue - State: closed - Opened by artgoldberg almost 5 years ago - 3 comments
Labels: bug

#129 - Reduce redundancy in representation of dFBA Reactions

Issue - State: closed - Opened by artgoldberg almost 5 years ago - 2 comments
Labels: discussion

#128 - Make templates more usable

Issue - State: closed - Opened by artgoldberg almost 5 years ago - 1 comment
Labels: enhancement

#127 - Finish supporting bcforms

Issue - State: open - Opened by jonrkarr about 5 years ago
Labels: enhancement

#126 - Simplify and systemize deserialization with grammars

Issue - State: closed - Opened by jonrkarr about 5 years ago - 1 comment
Labels: enhancement

#125 - Allow error tolerance for checking element and charge balance

Issue - State: closed - Opened by YinHoon about 5 years ago - 1 comment

#124 - Add reaction type attribute

Issue - State: open - Opened by jonrkarr about 5 years ago
Labels: enhancement

#123 - Add optional validation for molecules all defined

Issue - State: open - Opened by jonrkarr about 5 years ago
Labels: enhancement

#122 - Writer support for obj_model migration

Issue - State: open - Opened by artgoldberg about 5 years ago
Labels: enhancement, future

#121 - bug in io.Reader().run()

Issue - State: closed - Opened by artgoldberg about 5 years ago - 1 comment
Labels: bug

#120 - delete add_observables branch?

Issue - State: closed - Opened by artgoldberg about 5 years ago - 2 comments
Labels: enhancement

#119 - Rate law support for lumped reactions

Issue - State: open - Opened by jonrkarr over 5 years ago - 1 comment
Labels: enhancement

#118 - Use standard metadata models

Issue - State: open - Opened by artgoldberg over 5 years ago
Labels: enhancement

#117 - Support object ids that start with numbers

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

#116 - Support complex species

Issue - State: open - Opened by jonrkarr over 5 years ago

#115 - Add provenance attributes

Issue - State: open - Opened by jonrkarr over 5 years ago
Labels: enhancement

#114 - Integrate provenance with SEPIO

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

#113 - Define declarative mapping between WC-Lang and SBML and refactor SBML export/import

Issue - State: open - Opened by jonrkarr over 5 years ago
Labels: enhancement, future

#112 - Raise exceptions if SBML is inconsistent with WC-Lang representation

Issue - State: open - Opened by jonrkarr over 5 years ago
Labels: enhancement, future

#111 - Fix unit compatibility with SBML

Issue - State: closed - Opened by jonrkarr over 5 years ago - 1 comment
Labels: enhancement, future

#110 - Integrate BpForms

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

#109 - Move ontology to separate repo

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

#108 - More metadata for provenance (versions, software, etc.)

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

#107 - Add table of contents worksheet

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

#106 - pH attribute of compartment

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

#105 - Verify protonation state consistent with pH

Issue - State: open - Opened by jonrkarr over 5 years ago
Labels: enhancement

#104 - Add transformation that strips out metadata not needed for simulation

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

#103 - Export provenance, validation as separate XML file to SBML

Issue - State: open - Opened by jonrkarr over 5 years ago
Labels: enhancement, future

#102 - DatabaseReference.database --> DatabaseReference.namespace

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

#101 - Refactor ontology term equality to use utility method

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

#100 - Add GitHub id for authors

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

#99 - Add SBML import/export to command line

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

#98 - Test get_children / stop_conditions

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

#97 - Add split submodels to command line

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

#96 - Class for DNA, RNA, protein structure

Issue - State: closed - Opened by jonrkarr over 5 years ago - 2 comments
Labels: enhancement

#95 - Add model classes to ontology

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

#94 - Add class to represent verifications

Issue - State: open - Opened by jonrkarr over 5 years ago - 1 comment
Labels: enhancement

#93 - Implement UnitsAttribute

Issue - State: closed - Opened by jonrkarr over 5 years ago - 2 comments
Labels: refactoring

#92 - Add author, change classes to track who made decisions

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

#91 - Rename Submodel.algorithm --> Submodel.framework

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

#90 - Create base class for units

Issue - State: closed - Opened by jonrkarr over 5 years ago - 1 comment
Labels: enhancement, refactoring

#89 - Replace type enumerations with ontologies

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

#88 - Add attributes for asssumptions, design decisions

Issue - State: closed - Opened by jonrkarr over 5 years ago - 2 comments
Labels: enhancement

#87 - add pH units

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

#86 - Better error messages for failing validation

Issue - State: closed - Opened by szb37 over 5 years ago - 1 comment
Labels: enhancement

#85 - Rename DfbaNetReaction --> DfbaObjectiveReaction

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

#84 - Refactor io to facilitate migration

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

#83 - Merge model from multiple files

Issue - State: closed - Opened by jonrkarr over 5 years ago - 2 comments
Labels: enhancement

#82 - Add option not to validate model after reading from file

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#81 - Add pH, temperature attributes

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#80 - refactor expression module to obj_model

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 2 comments
Labels: enhancement, refactoring

#79 - Factor out references to specific parameters in wc-sim

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#78 - Sample new initial conditions in wc_sim

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#76 - Create empirical formula attribute

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#74 - Eliminate M s^-1 reaction rate units

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#73 - Compile expressions to byte code for performance

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 2 comments
Labels: enhancement

#71 - Clarify mass, density, and volume calculations

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#70 - Add CompartmentType attribute

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#69 - Add ability to validate models without element/charge balance from CLI

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#68 - Update submodel merging for changes and test that all related objects are merged

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#67 - Clarify initial conditions

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#66 - Add standard error to Parameter

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#65 - Add density to Compartment

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#64 - Add schema migration to command line program

Issue - State: open - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#63 - Extend Expression.eval to take compartment volumes

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#62 - Copy units to intro_to_wc_modeling

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#61 - Update documentation

Issue - State: open - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#60 - Enhance test coverage of new features

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#59 - Add units for dFBA net components

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#58 - Fix application of "default" dFBA flux bounds (don't override specified bounds)

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: bug

#57 - Add implicit dFBA exchange reactions for metabolic byproducts of other submodels

Issue - State: open - Opened by jonrkarr almost 6 years ago
Labels: enhancement, future

#56 - add id constraint on biomass components

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: refactoring

#52 - Validate reaction element, charge balance

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#49 - Refactor wc_lang.prepare.PrepareModel with transforms

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: refactoring

#47 - Make DatabaseReferences inline

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 2 comments
Labels: enhancement, refactoring

#42 - Update wc_sim and other packages

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 2 comments
Labels: refactoring

#41 - Add column labels for default values, units

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 2 comments
Labels: enhancement

#36 - Implement reading from SBML to enable round trip testing

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 3 comments
Labels: enhancement

#35 - Support area volumes (e.g. mol dm^-2)

Issue - State: open - Opened by jonrkarr almost 6 years ago
Labels: enhancement, future

#32 - Structure evidence

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#31 - Rename BiomassReaction to MetabolismNetReaction

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement, refactoring

#30 - Validate units of rate laws

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 3 comments
Labels: enhancement

#26 - Build representation of model of distribution of initial conditions

Issue - State: closed - Opened by jonrkarr almost 6 years ago - 1 comment
Labels: enhancement

#5 - express optional sub-model function that determines volume

Issue - State: closed - Opened by artgoldberg over 6 years ago - 2 comments
Labels: enhancement

GitHub / KarrLab/wc_lang issues and pull requests