Reproducible and flexible simulation experiments with ML-Rules and SESSL
Open accessAbstract
Summary: The modeling language ML-Rules allows specifying and simulating complex systems biology models at multiple levels of organization. The development of such simulation models involves a wide variety of simulation experiments and the replicability of generated simulation results requires suitable means for documenting simulation experiments. Embedded domain-specific languages, such as SESSL, cater to both requirements. With SESSL, the user can integrate diverse simulation experimentation methods and third-party software components into an executable, readable simulation experiment specification. A newly developed SESSL binding for ML-Rules exploits these features of SESSL, opening up new possibilities for executing and documenting simulation experiments with ML-Rules models. Availability and implementation: ML-Rules is implemented in Java, SESSL and its bindings are implemented in Scala. The source code is available under open-source licenses: ML-Rules git.informatik.uni-rostock.de/mosi/mlrules2 ML-Rules Quickstart (Graphical Editor) git.informatik.uni-rostock.de/mosi/mlrules2-quickstart SESSL git.informatik.uni-rostock.de/mosi/sessl and sessl.org SESSL Quickstart (Experiment Template) git.informatik.uni-rostock.de/mosi/sessl-quickstart Furthermore, Maven-compatible compiled packages of ML-Rules, SESSL, and the SESSL bindings are available from the Maven Central Repository at maven.org (org.sessl:* and org.jamesii: mlrules). Supplementary information: Supplementary data are available at Bioinformatics online.
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The reason for the few rule-based models might be partly because support for thorough experimentation with rule-based models including calibration and validation has only become available during the last decade [97-99].
“The reason for this might be partly because support for thorough experimentation with rule-based models including calibration and validation has only become available during the last decade [97–99].”
From Relating simulation studies by provenance—Developing a family of Wnt signaling models (2021) · cites this paper as [97]
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- Authors
- Warnke, T., Helms, T., & Uhrmacher, A. M.
- Affiliations
- University of Rostock (DE)
- Corresponding author
- Warnke, T
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-11-23
- Volume
- 34
- Issue
- 8
- Pages
- 1424-1427
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2770364859
- Cited by
- 9
- References
- 14
- Citations by year
- 2026: 1 · 2024: 1 · 2023: 1 · 2022: 2 · 2021: 2 · 2020: 2
- FWCI
- 0.22
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Deutsche Forschungsgemeinschaft (UH 66/13)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Modeling and Simulation Systems
- Keywords
- simulation experiments, reproducibility, domain-specific languages, systems biology modeling, executable specifications
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