From 3a98ba47b8c69220b28d9ea9437bb81ca0bd417a Mon Sep 17 00:00:00 2001
From: Joshua <joshua.chan@connect.polyu.hk>
Date: Wed, 24 Jan 2018 18:22:45 -0500
Subject: [PATCH] Add spec for SteadyCom

---
 MaranasTools.spec | 42 +++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 41 insertions(+), 1 deletion(-)

diff --git a/MaranasTools.spec b/MaranasTools.spec
index 4669219..e8a7eb5 100644
--- a/MaranasTools.spec
+++ b/MaranasTools.spec
@@ -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
@@ -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;
 };