First steps · Browser Workbench

Your first SBML simulation

Use a small synthetic model to learn the workflow before bringing your own file. It describes material moving from S1 to S2 through one reaction, with a parameter named k controlling the rate.

Open and inspect the example

1. Choose Open teaching example. Workbench opens transfer.xml. Nothing runs automatically.
2. Inspect the Model outline. Select S1, S2, k or the reaction to see the source information.
3. Open the transfer.xml source tab if you want to read the XML beside the model overview.

Run a time course

1. Open Simulate & edit and use Single run with the standard reaction-model profile.
2. Keep the default end time of 10 and 101 output points. This model declares time in seconds.
3. Select S1 amount and S2 amount. Read Review this run, including the server disclosure and numerical settings.
4. Choose Run simulation. Inspect the trajectories under Completed time course.

S1 starts at 10 mole and S2 at zero. For this transfer model, S1 falls as S2 rises. The example teaches a workflow; it is not a validated biological system.

Keep your work and recover from errors

Use Download current model to keep the source. For supported investigation work, use the explicit save and export controls; an open browser tab is not permanent storage.

If a run fails, read the displayed error and check the selected outputs and supported model profile. After server expiry, preserve your current source and reload before starting a new run. Do not repeatedly submit a failed run without checking the error.

Bring your own model

Start a fresh workspace and choose one SBML XML file. Opening a file keeps its contents on your device. Choosing a hosted scientific action such as Run sends the model to the server, as disclosed beside that action. Supported profiles have explicit limits; importing a file does not mean every SBML feature can be simulated.

For the first trial, use the included example or a public model you are comfortable sending to the hosted service. Optional assistant questions have their own context and provider disclosures.