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CITATION.cff
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# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: SBMLToolkit.jl
message: >-
If you use this software, please cite the preferred-citation in this file.
preferred-citation:
type: article
authors:
- given-names: Paul
name-particle: F
family-names: Lang
email: plang@deeporigin.com
affiliation: Deep Origin
orcid: 'https://orcid.org/0000-0002-6388-2405'
- given-names: Anand
family-names: Jain
- given-names: Christopher
family-names: Rackauckas
orcid: 'https://orcid.org/0000-0001-5850-0663'
affiliation: JuliaHub
doi: "10.1515/jib-2024-0003"
journal: "Journal of Integrative Bioinformatics"
month: 5
title: "SBMLToolkit.jl: a Julia package for importing SBML into the SciML ecosystem"
year: 2024
keywords:
- systems biology markup language
- SBML
- Julia
- scientific machine learning
license: CC-BY-4.0
repository-code: >-
https://github.com/JuliaSmoothOptimizers/CaNNOLeS.jl
abstract: >-
Julia is a general purpose programming language that was
designed for simplifying and accelerating numerical
analysis and computational science. In particular the
Scientific Machine Learning (SciML) ecosystem of Julia
packages includes frameworks for high-performance
symbolic-numeric computations. It allows users to
automatically enhance high-level descriptions of their
models with symbolic preprocessing and automatic
sparsification and parallelization of computations. This
enables performant solution of differential equations,
efficient parameter estimation and methodologies for
automated model discovery with neural differential
equations and sparse identification of nonlinear dynamics.
To give the systems biology community easy access to
SciML, we developed SBMLToolkit.jl. SBMLToolkit.jl imports
dynamic SBML models into the SciML ecosystem to accelerate
model simulation and fitting of kinetic parameters. By
providing computational systems biologists with easy
access to the open-source Julia ecosystevnm, we hope to
catalyze the development of further Julia tools in this
domain and the growth of the Julia bioscience community.
SBMLToolkit.jl is freely available under the MIT license.
The source code is available at
https://github.com/SciML/SBMLToolkit.jl.
type: software
authors:
- given-names: Paul
name-particle: F
family-names: Lang
affiliation: Deep Origin
orcid: 'https://orcid.org/0000-0002-6388-2405'
- given-names: Anand
family-names: Jain
- given-names: Christopher
family-names: Rackauckas
orcid: 'https://orcid.org/0000-0001-5850-0663'
affiliation: JuliaHub
- given-names: contributors
repository-code: 'https://github.com/SciML/SBMLToolkit.jl'
license: MIT