SBMLtoOdin and Menelmacar: Interactive visualisation of systems biology models for expert and non-expert audiences
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arXiv
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| Autores principales: | , , , , , , |
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| Formato: | Preprint |
| Publicado: |
2025
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| _version_ | 1866909596959899648 |
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| author | Lorenz, Leonie J. Andréoletti, Antoine Nguyen, Tung V. N. Hermjakob, Henning FitzJohn, Richard G. Sheriff, Rahuman S. Malik Lees, John A. |
| author_facet | Lorenz, Leonie J. Andréoletti, Antoine Nguyen, Tung V. N. Hermjakob, Henning FitzJohn, Richard G. Sheriff, Rahuman S. Malik Lees, John A. |
| contents | Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often restricted to experts in programming and mathematics. This is due to the need to implement entire models and solvers from the mathematical notation models are normally presented as. Implementation: Here, we present SBMLtoOdin, an R package that translates differential equation models in SBML format from the BioModels database into executable R code using the R package odin, allowing researchers to easily reuse models. We also present Menelmacar, a a web-based application that provides interactive visualisations of these models by solving their differential equations in the browser. This platform allows non-experts to simulate and investigate models using an easy-to-use web interface. Availability: SBMLtoOdin is published under open source Apache 2.0 licence at https://github.com/bacpop/SBMLtoOdin and can be installed as an R package. The code for the Menelmacar website is published under MIT License at https://github.com/bacpop/odinviewer, and the website can be found at https://biomodels.bacpop.org/. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2504_20710 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | SBMLtoOdin and Menelmacar: Interactive visualisation of systems biology models for expert and non-expert audiences Lorenz, Leonie J. Andréoletti, Antoine Nguyen, Tung V. N. Hermjakob, Henning FitzJohn, Richard G. Sheriff, Rahuman S. Malik Lees, John A. Quantitative Methods Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often restricted to experts in programming and mathematics. This is due to the need to implement entire models and solvers from the mathematical notation models are normally presented as. Implementation: Here, we present SBMLtoOdin, an R package that translates differential equation models in SBML format from the BioModels database into executable R code using the R package odin, allowing researchers to easily reuse models. We also present Menelmacar, a a web-based application that provides interactive visualisations of these models by solving their differential equations in the browser. This platform allows non-experts to simulate and investigate models using an easy-to-use web interface. Availability: SBMLtoOdin is published under open source Apache 2.0 licence at https://github.com/bacpop/SBMLtoOdin and can be installed as an R package. The code for the Menelmacar website is published under MIT License at https://github.com/bacpop/odinviewer, and the website can be found at https://biomodels.bacpop.org/. |
| title | SBMLtoOdin and Menelmacar: Interactive visualisation of systems biology models for expert and non-expert audiences |
| topic | Quantitative Methods |
| url | https://arxiv.org/abs/2504.20710 |