Reproducible and flexible simulation experiments with ML-Rules and SESSL.
basic_science · Level V
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- Record sourced from PubMed, PMID 29186288.
- Also identified by DOI 10.1093/bioinformatics/btx741.
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Abstract
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 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. ML-Rules is implemented in Java, SESSL and its bindings are implemented in Scala. The source code is available under open-source licenses: ML-Rulesgit.informatik.uni-rostock.de/mosi/mlrules2ML-Rules Quickstart (Graphical Editor)git.informatik.uni-rostock.de/mosi/mlrules2-quickstartSESSLgit.informatik.uni-rostock.de/mosi/sessl and sessl.orgSESSL 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). The supplementary material contains a more complex case study that exemplifies the usage of the SESSL binding for ML-Rules. tom.warnke@uni-rostock.de.