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Add spec for SteadyCom #1

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Add spec for SteadyCom #1

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42 changes: 41 additions & 1 deletion MaranasTools.spec
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,17 @@ module MaranasTools {
/* The id of a compound that exists either in the model or in the biochemistry.
*/
typedef string compound_id;


/* A string representing a reaction id.
*/
typedef string reaction_id;

/* A string representing a Media id.
*/
typedef string media_id;



/*
model - the FBA model to use as a basis for modification
start_compound - the initial compound to be used as a source for the pathway
Expand Down Expand Up @@ -44,6 +54,36 @@ module MaranasTools {
string report_ref;
} OptStoicOutput;

/*
model - the community FBA model

*/
typedef structure {
model_upa model;
media_id medium;

list<reaction_id> reaction_fva;
float gr_tol; /* tolerance for convergence of max growth rate */
list<float> opt_gr_percent; /* % of max growth rate at which FVA is performed */

boolean use_random_uptake_bounds;
float total_carb_uptake; /* total specific uptake rate of carbon in C-mmol/gDW/hr, used only if use_random_uptake_bounds is true */
list<string> custom_bound_list;
list<compound_id> media_supplement_list;
boolean return_min_sum_flux;
/* Need: additional constraints on fluxes and organism abundances,
e.g., for implementing maximum total carbon uptake rate, molecular crowding constraints. */
} SteadyComParams;

typedef structure {
string report_name;
string report_ref;
/* Need: maximum growth rate, flux distribution, organism abundance,
FVA ranges (at different % of maximum growth rate) */
} SteadyComOutput;


funcdef run_optstoic(OptStoicParams params) returns (OptStoicOutput output) authentication required;

funcdef run_steadycom(SteadyComParams params) returns (SteadyComOutput output) authentication required;
};