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fluentverification / CaseStudies_StochasticModelChecking

Repositories for the collection of models used as case studies for stochastic model checking.
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Update questions for user-input biochemical reaction network #2

Closed zgzn closed 2 years ago

zgzn commented 2 years ago

When running python3 on reactions_v2.py, the script interacts with the user with the questions below:

Which chemical is going to be monitored? Gbg What is the target number for this chemical? 50 Are you interested in seeing when the chemical is above or below the specified number? (type either above or below): above

First, rename "chemical" to "species" in these questions, and all other questions if applicable. Secondly, the statement of the last question listed above can be improved. Do we allow the user to check greater-than-or-equal, less-than-or-equal, and equality relations? The above question's statement seems to allow only strictly greater-than and less than relations. Maybe we can instead provide an itemized list of (in-)equalities for the user to choose? For example, after the user specifies Gbg and 50, the script can list these items below for the user to choose:

1) Gbg = 50 2) Gbg > 50 3) Gbg >= 50 4) Gbg < 50 5) Gbg <= 50

bryantisraelsen commented 2 years ago

I will work fixing the issues and let you know when I have. Thanks!

bryantisraelsen commented 2 years ago

I made the adjustments that you specified, the only difference is that I do not provide the equality option '=' for a guard that can be chosen. So instead it displays the following

Which species is going to be monitored? gbg What is the target number for this species? 50 Which option is your desired guard?

1: gbg >= 50
2: gbg > 50
3: gbg <= 50
4: gbg < 50
zgzn commented 2 years ago

Thank you, Bryant. Do you think we can add the equality option as the goal? Will adding this option affect the reaction priority determination?

bryantisraelsen commented 2 years ago

If we did add the equality option, in order to keep our priority determination the script would have to interpret it as either a '>=' or a '<=' depending on what the target species is initialized to. Is that what you had in mind?

zgzn commented 2 years ago

The interpretation as either '>=' or '<=' will have to depend on the initial and target value difference. We can discuss it at our meeting tomorrow before you make changes in your script.

bryantisraelsen wrote on 7/7/22 12:15 PM:

If we did add the equality option, in order to keep our priority determination the script would have to interpret it as either a '>=' or a '<=' depending on what the target species is initialized to. Is that what you had in mind?

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