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Merge pull request #261 from sebapersson/update_readme
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Add SBMLImporter to the README
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exaexa authored Nov 22, 2024
2 parents b9a9f34 + 7d6519f commit ea7fee2
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50 changes: 0 additions & 50 deletions .github/workflows/downstream.yml

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21 changes: 13 additions & 8 deletions README.md
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# SBML.jl

| Build status | Documentation | Stats |
|:---:|:---:|:---:|
| ![CI status](https://github.com/LCSB-BioCore/SBML.jl/workflows/CI/badge.svg?branch=master) [![codecov](https://codecov.io/gh/LCSB-BioCore/SBML.jl/branch/master/graph/badge.svg?token=eJehiv1yWs)](https://codecov.io/gh/LCSB-BioCore/SBML.jl) | [![stable documentation](https://img.shields.io/badge/docs-stable-blue)](https://lcsb-biocore.github.io/SBML.jl/stable) [![dev documentation](https://img.shields.io/badge/docs-dev-cyan)](https://lcsb-biocore.github.io/SBML.jl/dev) | [![SBML Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/SBML)](https://pkgs.genieframework.com?packages=SBML) |
| Build status | Documentation |
|:---:|:---:|
| ![CI status](https://github.com/LCSB-BioCore/SBML.jl/workflows/CI/badge.svg?branch=master) [![codecov](https://codecov.io/gh/LCSB-BioCore/SBML.jl/branch/master/graph/badge.svg?token=eJehiv1yWs)](https://codecov.io/gh/LCSB-BioCore/SBML.jl) | [![stable documentation](https://img.shields.io/badge/docs-stable-blue)](https://lcsb-biocore.github.io/SBML.jl/stable) [![dev documentation](https://img.shields.io/badge/docs-dev-cyan)](https://lcsb-biocore.github.io/SBML.jl/dev) |


This is a simple wrap of some of the libSBML functionality, mainly the model loading for purposes of COBRA analysis methods and exploration of ODE system and reaction dynamics.
Expand All @@ -12,17 +12,22 @@ You might like to try the packages that use SBML.jl; these now include:
- [COBREXA.jl](https://github.com/LCSB-BioCore/COBREXA.jl), the exascale-ready
constraint-based analysis and reconstruction toolkit for finding and modeling
steady metabolic fluxes with the models
- [SBMLToolkit.jl](https://github.com/SciML/SBMLToolkit.jl), for working with
the reaction dynamics of the models as ODE systems, well connected to the
[SciML](https://github.com/SciML)
[ModelingToolkit](https://github.com/SciML/ModelingToolkit.jl) ecosystem.
- Connections to the [SciML](https://github.com/SciML)
[ModelingToolkit](https://github.com/SciML/ModelingToolkit.jl) ecosystem:
- [SBMLToolkit.jl](https://github.com/SciML/SBMLToolkit.jl), for working with
the models' reaction dynamics as ODE systems.
- [SBMLImporter.jl](https://github.com/sebapersson/SBMLImporter.jl) for
importing the SBML models into
[Catalyst.jl](https://github.com/SciML/Catalyst.jl), allowing simulations
via Catalyst's `JumpProblem`, `SDEProblem`, or `ODEProblem` and fitting
models to data via [PEtab.jl](https://github.com/sebapersson/PEtab.jl).

Other functionality will be added as needed. Feel free to submit a PR that increases the loading "coverage".

#### Acknowledgements

`SBML.jl` was developed at the Luxembourg Centre for Systems Biomedicine of the
University of Luxembourg ([uni.lu/lcsb](https://www.uni.lu/lcsb)), and the UCL
University of Luxembourg ([lcsb.uni.lu](https://lcsb.uni.lu/)), and the UCL
Research Software Development Group
([ucl.ac.uk/arc](https://www.ucl.ac.uk/arc)). The development was supported by
European Union's Horizon 2020 Programme under PerMedCoE project
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2 changes: 1 addition & 1 deletion src/unitful.jl
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Expand Up @@ -57,7 +57,7 @@ $(TYPEDSIGNATURES)
Converts a [`UnitPart`](@ref) to a corresponding Unitful unit.
The conversion is done according to the formula from
[SBML L3v2 core manual release 2](http://sbml.org/Special/specifications/sbml-level-3/version-2/core/release-2/sbml-level-3-version-2-release-2-core.pdf)(section 4.4.2).
[SBML L3v2 core manual release 2](https://sbml.org/specifications/sbml-level-3/version-2/core/release-2/sbml-level-3-version-2-release-2-core.pdf)(section 4.4.2).
"""
unitful(u::UnitPart) =
(u.multiplier * UNITFUL_KIND_STRING[u.kind] * exp10(u.scale))^u.exponent
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