Paul Lang paulflang
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| /* | |
| THIS IS A GENERATED/BUNDLED FILE BY ESBUILD | |
| if you want to view the source, please visit the github repository of this plugin | |
| */ | |
| var __create = Object.create; | |
| var __defProp = Object.defineProperty; | |
| var __getOwnPropDesc = Object.getOwnPropertyDescriptor; | |
| var __getOwnPropNames = Object.getOwnPropertyNames; | |
| var __getProtoOf = Object.getPrototypeOf; |
paulflang
/ case23_structural_simplify_issue.jl
Created
June 6, 2022 22:06
structural_simplify complains about extra variables despite ODEProblem does just fine, even when checkl_length_true
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| using Downloads, SBMLToolkit#pl-refactor_v0.1.13 | |
| using OrdinaryDiffEq, ModelingToolkit | |
| case = "00023" | |
| sbml_url = "https://raw.githubusercontent.com/sbmlteam/sbml-test-suite/master/cases/semantic/$case/$case"*"-sbml-l3v2.xml" | |
| sbml = String(take!(Downloads.download(sbml_url, IOBuffer()))) | |
| ml = readSBMLFromString(sbml, doc -> begin | |
| set_level_and_version(3, 2)(doc) | |
| convert_simplify_math(doc) |
paulflang
/ mwe_fix_unassigned_nonconstant_par_to_init.jl
Created
June 1, 2022 22:18
MWE to illustrate the requirement for fix_unassigned_nonconstant_par_to_init (without it I get: ERROR: ExtraVariablesSystemException: The system is unbalanced. There are 4 highest order derivative variables and 3 equations.)
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| using SBMLToolkit | |
| using SBML | |
| using Catalyst | |
| using Downloads | |
| case = "00170" | |
| function read_case(case) | |
| base_url = "https://raw.githubusercontent.com/sbmlteam/sbml-test-suite/master/cases/semantic/$case/$case" | |
| sbml_url = base_url*"-sbml-l3v2.xml" |
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| ################################################ | |
| # Critical dependencies from Manifest.toml: | |
| # [[SBML]] | |
| # deps = ["DocStringExtensions", "IfElse", "Libdl", "SBML_jll", "SparseArrays", "Symbolics", "Unitful"] | |
| # git-tree-sha1 = "79cff18661b3a649ba852e23d70c8e9415f933f3" | |
| # repo-rev = "pl-extensivemath_compID" | |
| # repo-url = "https://github.com/paulflang/SBML.jl.git" | |
| # uuid = "e5567a89-2604-4b09-9718-f5f78e97c3bb" | |
| # version = "0.10.1" |
paulflang
/ states_neq_eqs.xml
Created
May 14, 2022 18:05
Two enzyme catalysed reactions. Enzymes E1 and E2 appear on both sides of reaction and are boundaryCondition=false, constant=false. E2 is determined by an asssignmentRule
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| <?xml version="1.0" encoding="UTF-8"?> | |
| <!-- Created by COPASI version 4.27 (Build 217) on 2022-05-14 11:57 with libSBML version 5.18.0. --> | |
| <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1" level="3" version="1" layout:required="false" render:required="false"> | |
| <model metaid="COPASI0" id="New_Model" name="New Model" substanceUnits="substance" timeUnits="time" volumeUnits="volume" areaUnits="area" lengthUnits="length" extentUnits="substance"> | |
| <annotation> | |
| <COPASI xmlns="http://www.copasi.org/static/sbml"> | |
| <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> | |
| <rdf:Description rdf:about="#COPASI0"> | |
| <dcterms:created> | |
| <rdf:Description> |
paulflang
/ species_gt_eqs.xml
Created
May 8, 2022 21:55
Valid SBML failing in convert(ODESystem, rs)
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| <?xml version="1.0" encoding="UTF-8"?> | |
| <!-- Created by COPASI version 4.27 (Build 217) on 2022-05-08 22:12 with libSBML version 5.18.0. --> | |
| <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4"> | |
| <model metaid="COPASI0" id="New_Model" name="New Model"> | |
| <annotation> | |
| <COPASI xmlns="http://www.copasi.org/static/sbml"> | |
| <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> | |
| <rdf:Description rdf:about="#COPASI0"> | |
| <dcterms:created> | |
| <rdf:Description> |