namespaces.md

Namespaces

This example demonstrate the usage of "namespaces" in Heta and how it can be used for creating of different models.

Shared files

The following two files are heta modules. They will be used to create different models.

/* cell-dynamics.heta file */

blood @Compartment .= 5.3;
cell_count @Species { compartment: blood } .= 1;
v_prol @Reaction { actors: => cell_count } 
    := k_prol * cell_count;

k_prol @Const = 1e-3;

/* intracell.heta file */

cell_vol @Compartment := 1e-6 * cell_count;
m1 @Species { compartment: cell_vol } .= 0;
m2 @Species { compartment: cell_vol } .= 0;

vsyn_m1 @Reaction { actors: => m1 } 
    := ksyn * cell_vol;
v_m1_m2 @Reaction { actors: m1 => m2 } 
    := kcat_m1 * m1 / (Km1 + m1) * cell_vol;
vtr_m2 @Reaction { actors: m2 => } 
    := P * S * m2;

ksyn @Const = 1e-2;
kcat_m1 @Const = 1e-1;
Km1 @Const = 12;
P @Const = 1.2;
S @Const = 1e-8;

/* index.heta file */

#include { source: intracell.heta };
#include { source: cell-dynamics.heta };

Creating two models in one platform

/* index.heta */

#include { source: intracell.heta };
#include { source: cell-dynamics.heta };

// add new species in blood
m3 @Species { compartment: blood } .= 0;
// update transport
vtr_m2 { actors: m2 => m3 }
  := P * S * (m2- m3);

namespace intracell begin
  #include { source: intracell.heta };
  cell_count @Const = 1;
end

Cloning models with import

/* index.heta */
#include { source: intracell.heta };
#include { source: cell-dynamics.heta };

// add new species in blood
m3 @Species { compartment: blood } .= 0;
// update transport
vtr_m2 { actors: m2 => m3 }
  := P * S * (m2- m3);

#setNS {space: modified};
#importNS { space: modified, fromSpace: nameless };
modified::vcl_m3 @Reaction { actors: m3 => }
  := kcl_m3 * m3 * blood;
modified::kcl_m3 @Const = 1e-2;

Cloning models with renaming components

/* index.heta */
#include { source: intracell.heta };
#include { source: cell-dynamics.heta };

// add new species in blood
m3 @Species { compartment: blood } .= 0;
// update transport
vtr_m2 { actors: m2 => m3 }
  := P * S * (m2 - m3);

#setNS {space: modified};
#importNS {
  space: modified, fromSpace: nameless,
  suffix: _1, rename: {m3: m3}
};
#importNS {
  space: modified, fromSpace: nameless,
  suffix: _2, rename: {m3: m3}
};
#importNS {
  space: modified, fromSpace: nameless,
  suffix: _3, rename: {m3: m3}
};

modified::ksyn_3 = 1e-8;