Tutorial

Basics

transsys Programs

Gene regulatory networks (GRNs) are specified by transsys programs. A transsys program consists of the keyword transsys, followed by a name and a block containing the actual GRN specification. The block contains factor declarations and gene declarations, as described below. The block may be empty. A minimal, empty transsys program is

 transsys containsnothing
 {
 }

Here, the program's name is "containsnothing".

Introductory Example

The following is a transsys program comprised of one factor, firstfactor and one gene, called firstgene, which encodes that factor:

 transsys firstexample
 {
   factor firstfactor
   {
     decay: 0.1;
     diffusibility: 1.0;
   }
 
   gene firstgene
   {
     promoter
     {
       constitutive: 0.2;
     }
     product
     {
       default: firstfactor;
     }
   }
 }

You can see a demo of this here