Biological software developped in Serrano's laboratory

SmartCell Simulation Description

SmartCell allows the modelisation and simulation of some biological network.The description of the biological network is composed by 3 parts, the geometry, the species and the reaction network.

Geometry Description

The network is simulated in a cell of part of the cell. This space is represented in SmartCell as a group of voxel. A voxel is the smallest division of the cell and is caracterised by its size: the lattice unit and its coordinates. 3 types of voxel are possible: the voxel, the half-voxel and the corner.

Species Description

The main goal of SmartCell is the evaluation of the behavior of all species during a time interval. By default, SmartCell will consider the number of copy of every species instead of the concentration. In case you prefer to work with concentration, you need to manually specify it in the input file.
In addition to define a name and the initial concentration/copy number in every compartment, you can specify the diffusion and the active transport. Without defining anything, the species will be consider as fixe in the cell and won't move between voxels and compartments. You can define 3 kinds of species movements in the cell:

  • the diffusion inside a compartment, ie between 2 neighbours voxels belonging to the same compartment.
  • the diffusion between 2 compartments, ie between 2 neighbours voxels belonging to 2 different compartments.
  • the active transport between 2 compartments, ie followig the shortest way to go from one compartment to another one.

 

Network Description

The network description will be the list of reaction that may happen in your simulation. SmartCell accepts 2 kinds of reaction: the simple reaction (production, degradation, binding...), defined by a rate, a reverse rate, a localisation and the catalysis reaction defined by a catalysis rate.