Bio-chemical Modeling Tools

Nowadays, biologists of the world use computers for efficient and fast simulation of chemical reactions. Concerning the human immune system, lots of complex interactions exist, including those between cells, proteins and other kind of molecules that have to be taken into account.

Before using the power of actual computers, we need to have simple and uniform representation models of these problems. Many models exist, but they may not be intuitive for biologists or do not provide clear documentation. One would need a simple model, which could reproduce the desired operations without presenting technical difficulties such as compatibility, long computation time or complex syntax.

The proposed programming language, TSed, enables fast chemical formulas writing, and compiling into the scientific SBML format file for further purposes. The main objectives of this software is to reduce as much as possible the complexity of a programming language, while allowing it to describe a large set of biological models.

A simple commented TSed file:

// TSED program example

// Declarations Block for constants and functions
declare:

  // 3 constants a, b and c
  a = 1.0;
  b = a * 2;
  c = (a+b)/2;

end declare;

// Body Block for chemical reactions
body:

  // Birth of species "A" with rate "a"
  BIRTH -> A | a;
  
  // Death of species "B" with rate "0.75"
  B -> DEATH | 0.75;

  // Specie "X" produces specie "Y" with rate "c"
  X -> Y | c;

end body;