JWS Online is a web-based repository for curated mathematical models of biological systems. The database currently holds over 600 models, that can be simulated in a web-browser and are downloadable in several different formats, such as SBML and Mathematica. The simulation functionality is limited to time course integration, steady state analyses, including metabolic control analysis and flux balance analysis. By using standard model formats, model exchange between programs is relatively straightforward. The idea is to run some quick basic tests on a model in JWS, to which you were directed via a link in a journal, before downloading and working in dedicated stand alone simulators such as Copasi, or work in a coding environment such as Mathematica.

In addition to a model repository, JWS Online also stores simulation experiments in SED-ML format, now over 200 model simulations linked to figures in scientific publications are available. The SED-ML scripts can be linked to models in JWS Online and to data in the FAIRDOMHub, a model and data management platform, that fully integrates JWS Online. The SED-ML functionality makes it possible to reproduce figures in manuscripts with a single mouse click, which we use in our collaboration with journals such as Molecular Systems Biology.

I will illustrate JWS Online with examples from active research projects with workflows for model construction, validation, and publication, stressing the importance of transparency, and reproducibility.