The JWS online simulation database

Johann J. Eicher · David D. van Niekerk · Dagmar Waltemath · Jacky L. Snoep

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Scientific Computing and Data Management Simulation Techniques and Applications Gene Regulatory Network Analysis

Abstract

SUMMARY: JWS Online is a web-based platform for construction, simulation and exchange of models in standard formats. We have extended the platform with a database for curated simulation experiments that can be accessed directly via a URL, allowing one-click reproduction of published results. Users can modify the simulation experiments and export them in standard formats. The Simulation database thus lowers the bar on exploring computational models, helps users create valid simulation descriptions and improves the reproducibility of published simulation experiments. AVAILABILITY AND IMPLEMENTATION: The Simulation Database is available on line at https://jjj.bio.vu.nl/models/experiments/ . CONTACT: jls@sun.ac.za .

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2011Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language 2014COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

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2022BioSimulators : a central registry of simulation engines and services for recommending specific tools 2021RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats 2020Publishing reproducible dynamic kinetic models 2026From FAIR to CURE: guidelines for computational models of biological systems

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