Question

What is the simulation engine/algorithm of the CI tool: What is the algorithm of choosing the next reaction/transition to execute?

Answer

In order to keep the fairness of firing, the transition is selected randomly.

Question

How can Genomic Object Net (GON) version 1.0 read my .pn file that was modeled on version 0.919? Should I build my model again?

Answer

No, you do not need to rebuild from a scratch. If you send us the HFPN file of the pn format, we can convert the file in GON1.0 format and send it to you.

Question

Is it possible to "clone" a pathway a number of times and run all of the clones, and collect the results? Would all of the "clones" produce exactly the same results? Or would there be some variance in the results (or is it possible to make sure there is some variance in the results).

Answer

Cell Illustrator can produce some variance in the above results.

Question

The idea is to simulate a collection of cells and simulate the production of microarray data which could then be used to test some learning algorithms... If it is possible how would you do it?

Answer

You can generate test data and use it for learning algorithms.

Question

There was a mention of restrictions on the model that could be used on GenomicObjectNet. What is/are the restrictions? How big can a model be?

Answer

the restriction of publicly available GenomicObjectNet is, you can not edit and run a model that exceed five thousand components on the GenomicObjectNet. Here, components mean places and arcs and transitions of Petri net that we used for the core architecture in GenomicObjectNet.
There are no limitation to size of models. But large models take a long time to simulate and therefore need to be trated with care.