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whole-cell-tutors / whole-cell-reduced

the reduced model developed in salt lake city
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[Integration][All] Format of initial amounts input #19

Open den2042 opened 9 years ago

den2042 commented 9 years ago

In Translation module we have SBMLmodelgenrator python script which contains 

## create species
    for One_Species_ID in Translation_Species_List:
       ## TODO parse initial amount
        initialAmount=1 
        create_species(model,One_Species_ID,initialAmount)

What we need is a format of the input with initial amounts. eg csv file with 2 columns with one line header: ID, amount; or SBML file; or something else Actual values are not important at the moment, but the format is.

den2042 commented 9 years ago

Probably it would be better to discuss it a bit more. Initial amounts should be generated from 'copy_number' with some random noise

binfalse commented 9 years ago

In general I'd say we shouldn't actually care about initial amounts, as that is the typically the simulation setup and should be initialised by e.g. an SED-ML script (and the software executing the simulation should take care of..). The initial amounts in SBML are in my eyes just a hint.

Later on, the integration guys will probably nevertheless need to overwrite every initial value before simulating the next time step, won't they?