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Another Genetic Circuit Transcriber
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Error type: undefined. Note: this is a nested preset so please contact the preset author if you are unable to fix it yourself.
We should standardize the way we import dependencies
This prevents the definition of a degradation rate or other relevant properties.
It would be nice to be able to set the type of the product, but in this case I would need it to be a protein.
e.g.:
chemical reactions{
"CREB_I +Ca2+_cAMP" to "CREB"
}
"CREB" {
has a degradation.rate of 0.5
}
It is not signalled as error but it produces one at runtime:
Exception in thread "main" java.lang.IllegalStateException: "CREB" is a molecule so it cannot degrade.
Create circuit "Genetic Toggle Switch" containing {
the gene promoter1 that codes {
the protein "repressor2"
regulated by {
the protein "repressor1"
with a regulating.rate of 0.1
with a degradation.rate of 2
}
}
} with {
a default initial.concentration of 0
a default degradation.rate of 0.1
}
gives error
The floating-point literal does not conform to the expected type Int
"if it's not on CI, it's not working"
chemical reactions {
"repressor1 + inducer1" to "repressor1_inducer1"
"repressor1_inducer1" to "repressor1 + inducer1"
}
"repressor1_inducer1"{
has a binding.rate of 1.4
has an unbinding.rate of 0.2
}
gives error
``
Type mismatch.
Required:
agct.degradation.Rate
Found:
agct.binding.Rate
``
Possible solution: allow dashes, but in the generator translate them, e.g., as a double underscore (ad forbid double underscores from the name set)
Create circuit "Genetic Toggle Switch" containing {
the gene promoter1 that codes {
the protein "repressor2"
regulated by {
the protein "repressor1"
with a regulating.rate of 0.1
with a basal.rate of 0.2
}
}
}
gives the error:
None of the following functions can be called with the arguments supplied. a(agct.binding.Rate) defined in agct.RegulationLevel.With a(agct.regulating.Rate) defined in agct.RegulationLevel.With
The readme should give a clear description and quickstart for the project
On windows the java commands gets too long and fails.
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