InteractiveModels

Models and simulator for Interactive modeling site: https://sites.google.com/view/interactive-modeling/home

Adding a model to the Interactive Modeling webpage (on Google Sites)

1. Add the SBML model to the ../models/ dir
2. Go to the Google sites page where you want the simulation to run.
3. Embeded the template code into the page:

• Template is in ../templates/sysbioTemplate.html.

• Fill out the following part of the template with model simulation details:

  `// **** Simulation info to fill out: ********

  const modelURL = 'https://sys-bio.github.io/InteractiveModels/models/modelFileName.xml'; // Location of sbml model file on github.

  const newRT = '10'; // Length of run in model time units

  const newSS = '0.10'; // integrator step size, total pts = newRt/newSS, 100 points: (10/0.10)

  const staticRun = 'true'; // Display after all calculations are done.

  const sliders = 'k1, p_3, comp1';// Sliders 12 max, exact id match, '' for first 8 params and first 4 species of model.

  const spPlot = 'S1, deS2, Oxy2'; // Species to plot, exact id match, '' for first up to 8 species.

  const yLabel = 'conc (uM)'; // Plot label, displayed at bottom as: yLabel vs. xLabel

  const xLabel = 'sec';

  // *** END of Simulation info to fill out *** `

• Insert the whole template, including the load button and iframe information into the page.

4. Save and publish page. Check page out to confirm model loads and runs as expected.

Updating Simulator

1. Add new simulator files to ../simulator
2. Make sure ../simulator/index.html exists, this is the launch point for the simulator.