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doc/amici_refs.bib

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@@ -1495,6 +1495,21 @@ @Article{JostWei2025
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url = {https://www.biorxiv.org/content/early/2025/04/17/2025.04.11.648323},
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}
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@Article{PerssonFro2025,
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author = {Persson, Sebastian and Frohlich, Fabian and Grein, Stephan and Lomna, Torkel and Ognissanti, Damiano and Hassselgren, Viktor and Hasenauer, Jan and Cvijovic, Marija},
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journal = {bioRxiv},
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title = {PEtab.jl: Advancing the Efficiency and Utility of Dynamic Modelling},
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year = {2025},
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abstract = {Dynamic models are useful to study processes ranging from cell signalling to cell differentiation. Common modelling workflows, such as model exploration and parameter estimation, are computationally demanding. The Julia programming language is a promising tool to address these computational challenges. To evaluate it, we developed SBMLImporter.jl and PEtab.jl, a package for model fitting. SBMLImporter.jl was used to evaluate different stochastic simulators against PySB and RoadRunner, overall Julia simulators proved fastest. For Ordinary Differential Equations (ODE) models solvers, gradient methods, and parameter estimation performance were evaluated using PEtab benchmark problems. For the latter two tasks PEtab.jl was compared against pyPESTO, which employs the high-performance AMICI library. Guidelines for choosing ODE solver were produced by evaluating 31 ODE solvers for 29 models. Further, by leveraging automatic differentiation PEtab.jl proved efficient and, for up to medium-sized models, was often at least twice faster than pyPESTO, showcasing how Julia{\textquoteright}s ecosystem can accelerate modelling workflows.Competing Interest Statement.F consults for DeepOrigin, no impact on study.Swedish Research CouncilSwedish Research Council, , VR2023-04319, VR2017-05117Swedish Foundation for Strategic ResearchSwedish Foundation for Strategic Research, , FFL15-0238},
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creationdate = {2025-05-05T09:44:36},
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doi = {10.1101/2025.04.30.651378},
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elocation-id = {2025.04.30.651378},
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eprint = {https://www.biorxiv.org/content/early/2025/05/04/2025.04.30.651378.full.pdf},
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modificationdate = {2025-05-05T09:44:36},
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publisher = {Cold Spring Harbor Laboratory},
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url = {https://www.biorxiv.org/content/early/2025/05/04/2025.04.30.651378},
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}
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@Comment{jabref-meta: databaseType:bibtex;}
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doc/references.md

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# References
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List of publications using AMICI. Total number is 98.
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List of publications using AMICI. Total number is 99.
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If you applied AMICI in your work and your publication is missing, please let us know via a new
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[GitHub issue](https://github.com/AMICI-dev/AMICI/issues/new?labels=documentation&title=Add+publication&body=AMICI+was+used+in+this+manuscript:+DOI).
@@ -34,6 +34,13 @@ Noordijk, Ben, Marcel Reinders, Aalt D. J. van Dijk, and Dick de Ridder.
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Gene Module Expression.”</span> <em>bioRxiv</em>. <a
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href="https://doi.org/10.1101/2025.02.18.638670">https://doi.org/10.1101/2025.02.18.638670</a>.
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</div>
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<div id="ref-PerssonFro2025" class="csl-entry" role="listitem">
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Persson, Sebastian, Fabian Frohlich, Stephan Grein, Torkel Lomna,
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Damiano Ognissanti, Viktor Hassselgren, Jan Hasenauer, and Marija
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Cvijovic. 2025. <span>“PEtab.jl: Advancing the Efficiency and Utility of
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Dynamic Modelling.”</span> <em>bioRxiv</em>. <a
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href="https://doi.org/10.1101/2025.04.30.651378">https://doi.org/10.1101/2025.04.30.651378</a>.
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</div>
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<div id="ref-SmithMal2025" class="csl-entry" role="listitem">
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Smith, Lucian, Rahuman S. Malik-Sheriff, Tung V. N. Nguyen, Henning
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Hermjakob, Jonathan Karr, Bilal Shaikh, Logan Drescher, et al. 2025.

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