KarrLab wc_lang issues - Githubissues

KarrLab / wc_lang

Language for describing whole-cell models as reaction networks

MIT License

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Retain comments and changes in merged submodels

#146 artgoldberg opened 3 years ago
0
Support single-use transforms

#145 artgoldberg closed 3 years ago
1
Avoid reaction id collisions in `SplitReversibleReactionsTransform`

#144 artgoldberg opened 3 years ago
2
Problem with wc_lang_io.Reader error formatting

#143 artgoldberg opened 3 years ago
0
Problem with wc_lang_io.Reader unit checking

#142 artgoldberg opened 3 years ago
1
Left and right square brackets reversed

#141 artgoldberg opened 3 years ago
0
Correct the units for DfbaObjectiveSpecies

#140 YinHoon closed 4 years ago
1
get_model_summary should be more comprehensive

#139 artgoldberg opened 4 years ago
0
False positive possible in Model._get_cyclic_deps()

#138 artgoldberg closed 4 years ago
1
Switching off requirement for uniqueness for SpeciesCoefficient

#137 YinHoon closed 4 years ago
7
Change reaction arrow from "==>" to `<=>`

#136 jonrkarr opened 4 years ago
0
Switching off requirement for uniqueness

#135 YinHoon closed 4 years ago
1
Complete support for Data repo metadata

#134 jonrkarr opened 4 years ago
0
Fix to freezing first column

#133 jonrkarr opened 4 years ago
0
Capture additional model metadata

#132 jonrkarr opened 4 years ago
0
Infer units for numeric literals

#131 artgoldberg opened 4 years ago
0
Problem converting to SBML

#130 artgoldberg closed 4 years ago
3
Reduce redundancy in representation of dFBA Reactions

#129 artgoldberg closed 4 years ago
2
Make templates more usable

#128 artgoldberg closed 4 years ago
1
Finish supporting bcforms

#127 jonrkarr opened 4 years ago
0
Simplify and systemize deserialization with grammars

#126 jonrkarr closed 4 years ago
1
Allow error tolerance for checking element and charge balance

#125 YinHoon closed 4 years ago
1
Add reaction type attribute

#124 jonrkarr opened 5 years ago
0
Add optional validation for molecules all defined

#123 jonrkarr opened 5 years ago
0
Writer support for obj_model migration

#122 artgoldberg opened 5 years ago
0
bug in io.Reader().run()

#121 artgoldberg closed 5 years ago
1
delete add_observables branch?

#120 artgoldberg closed 5 years ago
2
Rate law support for lumped reactions

#119 jonrkarr opened 5 years ago
1
Use standard metadata models

#118 artgoldberg opened 5 years ago
0
Support object ids that start with numbers

#117 jonrkarr closed 5 years ago
1
Support complex species

#116 jonrkarr opened 5 years ago
0
Add provenance attributes

#115 jonrkarr opened 5 years ago
0
Integrate provenance with SEPIO

#114 jonrkarr closed 5 years ago
1
Define declarative mapping between WC-Lang and SBML and refactor SBML export/import

#113 jonrkarr opened 5 years ago
0
Raise exceptions if SBML is inconsistent with WC-Lang representation

#112 jonrkarr opened 5 years ago
0
Fix unit compatibility with SBML

#111 jonrkarr closed 5 years ago
1
Integrate BpForms

#110 jonrkarr closed 5 years ago
1
Move ontology to separate repo

#109 jonrkarr closed 5 years ago
1
More metadata for provenance (versions, software, etc.)

#108 jonrkarr closed 5 years ago
1
Add table of contents worksheet

#107 jonrkarr closed 5 years ago
1
pH attribute of compartment

#106 jonrkarr closed 5 years ago
1
Verify protonation state consistent with pH

#105 jonrkarr opened 5 years ago
0
Add transformation that strips out metadata not needed for simulation

#104 jonrkarr closed 5 years ago
1
Export provenance, validation as separate XML file to SBML

#103 jonrkarr opened 5 years ago
0
DatabaseReference.database --> DatabaseReference.namespace

#102 jonrkarr closed 5 years ago
1
Refactor ontology term equality to use utility method

#101 jonrkarr closed 5 years ago
1
Add GitHub id for authors

#100 jonrkarr closed 5 years ago
1
Add SBML import/export to command line

#99 jonrkarr closed 5 years ago
1
Test get_children / stop_conditions

#98 jonrkarr closed 5 years ago
1
Add split submodels to command line

#97 jonrkarr closed 5 years ago
1