Add BioPreDyn-bench B1, B2, B4, B5 benchmarks#1496
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ChrisRackauckas-Claude wants to merge 5 commits intoSciML:masterfrom
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Add BioPreDyn-bench B1, B2, B4, B5 benchmarks#1496ChrisRackauckas-Claude wants to merge 5 commits intoSciML:masterfrom
ChrisRackauckas-Claude wants to merge 5 commits intoSciML:masterfrom
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Build Artifact ReviewReviewed the CI build artifacts for B4 and B5 benchmarks: B4 (BioPreDynB4.jmd) - All Good
B5 (BioPreDynB5.jmd) - Fixed one issue
Julia Tests CI failure - Not related to this PRThe "Julia Tests" check failed with Fix pushedCommit |
Add four benchmarks from the BioPreDyn-bench suite for systems biology ODE solver comparison: - B1: S. cerevisiae genome-wide kinetics (285 ODEs, 1759 parameters) - B2: E. coli central carbon metabolism (18 ODEs, 116 parameters) - B4: CHO cell metabolism (35 ODEs, 117 parameters, log-linear kinetics) - B5: EGF/TNFa signal transduction logic network (26 ODEs, 124 parameters) B1 and B2 use SBMLImporter to load SBML models with parameter values extracted from the original BioPreDyn-bench Matlab files. B4 and B5 are manually translated from Matlab/C sources since their SBML representations use rate rules and SBML-qual respectively. B3 (E. coli gene regulation, 47 ODEs with events) is deferred due to SBMLImporter callback compatibility issues. Closes SciML#555 Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Ser (serine) and inh (inhibitor) are standard abbreviations in systems biology models, not typos. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
rodas() and radau() from ODEInterfaceDiffEq require compiled Fortran libraries that may not be available in CI. Replace with Rodas5() and RadauIIA5() from OrdinaryDiffEq. Also remove ODEInterfaceDiffEq import from B2, B4, B5 since it's no longer used. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…rade B1 and B2 require SBMLImporter v3 which needs Catalyst v15+, but the existing Bio benchmarks (BCR, Bidkhori2012, etc.) are written for Catalyst v14. Widening compat caused CI to resolve Catalyst v15 and break existing benchmarks. Revert Project.toml and Manifest.toml to master's versions. B4 and B5 are self-contained (manually coded ODE functions) and don't need SBMLImporter or Catalyst. B1/B2 will be added in a follow-up PR once SBMLImporter compatibility is resolved. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The default ODE plot recipe creates subplots with uneven grid layout (10, 10, 6) for 26 variables, causing a DimensionMismatch. Plot the solution matrix directly instead to render all variables on one axis. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
_to_floatbug and parameter mapping issuesEach benchmark includes: model loading, solution visualization, reference solution generation, and work-precision diagrams at high/low tolerances with SDIRK methods and a summary comparison.
Closes #555
Test plan
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