Tutorial

Basics

transsys provides a concise and powerful language for describing gene regulatory networks (GRNs). Networks are described in units that correspond to the key biological objects: genes and gene products, called "factors" in transsys parlance. A transsys program enables simulating the dynamics of gene expression, and thus to study the dynamical properties of GRNs. transsys uses object oriented concepts, and this enables the use of transsys models as components for integrated, "multi-scale" models. The object oriented structure also provides a basis for developing tools for validating transsys against molecular data, as well as its use as a source of realistic simulated gene expression data.

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.

Minimal and Useless Example

A minimal, empty transsys program is

 transsys emptyexample
 {
 }

Here, the program's name is "emptyexample". As you may correctly expect, this program is entirely incapable of doing anything interesting, as it is devoid of any content. It's just technically a complete transsys program, somewhat like an empty wallet is still techically a complete wallet. So let's look at what we can use to fill our transsys program.

Factor Declarations

Factors are transsys's representations of gene products. During a transsys simulation, each factor is characterised by its expression level, i.e. its amount or concentration. Factors are characterised by a decay rate. They also have a diffusibility, which is provided as a facility for constructing models with (possibly complex) spatial structures but not used by the core simulator. The declaration of a factor myfirstfactor with a decay rate of 0.1 and a diffusibility of 0.4711 would for example look like this:

 factor myfirstfactor
 {
   decay: 0.1;
   diffusibility: 0.04711;
 }

You could stick this factor declaration into the empty transsys program shell shown above and obtain another valid transsys program. This program would enable you to simulate the temporal dynamics of myfirstfactor. But because there is no gene that encodes myfirstfactor, it's expression level will always be 0, and the "dynamics" will thus be a flat line. Obviously, that's not particularly interesting but you can have a look at that here:

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