Locating and loading a model

All models stored on JWS Online are assigned a unique slug for easy identification, and all models are stored under:

For example, the yeast glycolytic model published by Teusink et al. (Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.) is referred to on JWS online with the simple teusink slug, and thus can be accessed directly at:

The Model Database link in the navigation bar will take you to a table of all the models available on JWS Online.


Models can be located using the search criteria in the filter box on the righthand side. In this example the model list is constrained to show the models matching teusink in the name criterion:


Each listed model has a set of action buttons model_buttons. These buttons allow the model to be downloaded in SBML, Mathematica notebook, JWS, and PySCeS format respectively. The play_button loads the model in the Model Simulation page. From this page all the simulation and analysis features of JWS Online can be explored.


Uploading a model

Models may be uploaded to JWS Online in SBML or JWS format by clicking on the Upload model link in the navigation bar, and selecting a file, then clicking Upload. Additionally, it may be specified that JWS Online attempts to Regenerate IDs from element names if generic IDs have been used (e.g. species1, reaction1). Finally, if the model should be treated as a constraint-based model (regardless of whether it actually IS a constraint-based model), this too may be specified: