Quick Start

Enter the model in the textbox

• Each equation should be of the form "var=formula"
• Each variable must show up exactly once as a left-hand-side of one of these equationa
• Capitilization matters! Two variables with the same letters but different capitilizations are considered distinct.
• The formula may contain +, -, *, ^, MAX, MIN, and NOT.

Once you have entered the model, click on the submit button. On the backend, we do a quick check to make sure each line is of the form var=formula, but do no other checking.

For this example, we will use a very simple model with two variables, A and B.

Note: You can also upload the model from a text file. File should either be in the above format or be a ternary SBML-qual model. Entered models can downloaded using the button in the lower left.

With the model entered, we are presented with several options

• Each variable (or all variables) may be made "continuous"; meaning that the model will be altered so that no quantity may jump more than 1 level in each time step. Check the corresponding box for any variable you wish to be continuous. The box in the column heading toggles the entire column.
• Each variable may be forced to either be over-expressed (2), at base-line (1), or knocked-out (0) using the dropdown menus in the Forcing column.
• Using the radio-buttons near the bottom, we may select either
  1. Sample fixed points and cycles. In which we generate a uniform random sample of starting points in the configuration space (quantity choosable via dropdown) and let them evolve via the model until they either arrive at a fixed point or cycle. Statistics are generated on number of starting points which are in the basin of attraction for each cycle or fixed point found. We do not guarantee that all cycles or fixed points will be found.
  2. Find all fixed points. In which we use an algorithm to find all fixed points. Here we guarantee that all fixed points will be found. However, this algorithm will not find cycles and does not give any information on the size of the basin of attraction.

The computation will hopefully be quick, but is not instantaneous. Expect a short wait; the next page will be rendered once the server is finished simulating.

Here we show the (bottom part) of the results page for a run where we choose to sample the fixed points and cycles.

• Cycles are labeled by their lengths (fixed points being cycles of length 1) and by their sequence.
• In red, we present the percentage and count of sampled points which are in the basin of attraction for the cycle.
• If you desire to use save the generated data, the button 'Download tsv' will generate a tab separated value called model_results.tsv which contains the displayed data.

If you wish to change model options or the model itself, use the browser's back button to get to the appropriate page.