How to write GeneralODERule to SBML?

[ayush9pandey]

SBML has a rule type called the "rate rule" which can have variables rates be specified (see here: http://sbml.org/Software/libSBML/5.18.0/docs/python-api/classlibsbml_1_1_rate_rule.html). This seems the right kind of rule to write Bioscrape GeneralODERule with. However, SBML needs a rule_variable and a rule_formula object for a rule to be successfully created. I am not sure how to get these for the GeneralODERule. In particular, this line needs a fix :

bioscrape/bioscrape/types.pyx

Line 2336 in 571766a

assert(len(split_eqn) == 2) # Checking rule_dict equation structure.

Uncomment the SBML writing line number 72 in test_rules.py to recreate this error.

[ayush9pandey]

In hindsight, this issue should have been a comment on #107

[WilliamIX]

That looks correct to me. Rule_Variable should be the LHS and rule_formula the RHS of rule_dict['equation'].

One potential difference between SBML and Bioscrape is that rules can be applied to parameters OR species in Bioscrape. Can the SBML Rule Variable be a Species?

[ayush9pandey]

Yes, SBML rule can be species. Can you check the test_rules.py line above, in there you have ode rules with equation keyword and a target keyword but without LHS or RHS. I don't understand how that works.

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On Thu, Jun 24, 2021, 8:44 AM William Poole ***@***.***> wrote: That looks correct to me. Rule_Variable should be the LHS and rule_formula the RHS of rule_dict['equation']. One potential difference between SBML and Bioscrape is that rules can be applied to parameters OR species in Bioscrape. Can the SBML Rule Variable be a Species? — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#110 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB6DDO333CTHKADEDIMRNGDTUKPK5ANCNFSM47G66UPA> .

[WilliamIX]

I see - I misremembered how the ODE rule works. For an ODE dX/dt = f(x), target = 'X' and equation = f(x) is the proper way to do this.

[ayush9pandey]

The issue is fixed now.