Reproducible and flexible simulation experiments with ML-Rules and SESSL

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Abstract

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:

Availability and implementation

ML-Rules git.informatik.uni-rostock.de/mosi/mlrules2

Availability and implementation

ML-Rules Quickstart (Graphical Editor) git.informatik.uni-rostock.de/mosi/mlrules2-quickstart

Availability and implementation

SESSL git.informatik.uni-rostock.de/mosi/sessl and sessl.org

Availability and implementation

SESSL Quickstart (Experiment Template) git.informatik.uni-rostock.de/mosi/sessl-quickstart

Availability and implementation

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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