Biological software developped in Serrano's laboratory

Versions of SmartCell

Version 4.3 beta3

In this new beta version, we have included the active transport as an alternative to classic diffusion in the command line version.The functionality should be available in the GUI version of the final v4.3.
The simulator software includes now a hybrid method combining the fast aspect of the ODE with the stochasticity of Gillespie algorithm.

Version 4.3 beta2

In this new version 4.3, we have improved the GUI in order to be able to easily define your model and connect SmartCell with other simulation tool.
The simulator software includes now a hybrid method combining the fast aspect of the ODE with the stochasticity of Gillespie algorithm.

Version 4.2

In this new version V4.2, we distribute SmartCell as a package containing a simulator software in C++ and a GUI in Java.
The simulator software integrates now the flux balance analysis. A new kind of reaction: Metabolic reaction has been integrated. The GUI has been improved with a better separation between single voxel project and multi voxel project.

Version 3.0 beta3

In the version V3.0, we distribute SmartCell as a package containing a simulator software in C++ and a GUI in Java.
The simulator software integrates 4 different methods to solve the same problem, 3 stochastic algorithms and 1 deterministic algorithm:

  • the next event method based on Gillespie algorithm (1976)
  • the next subvolume method based on Elf algorithm (SystBiol, 2004)
  • the tau leap method based on Gillespie algorithm (2001)
  • the ODE solver with 5 differents algorithms

SmartCell simulator give in output the evolution of number of particles of different spieces in each voxel of the cell.
The graphic user interface (GUI) was also really improved with the addition of an output analyzer and a link to several databases.
The network can now be defined in 4 different steps:

  • the definition of all reactions
  • the definition of compartments and the localisation of species and reactions in these different compartments
  • the localisation of these compartments in the cell by the assocation between voxels and compartment
  • the definition of several simulation parameters

Each 4 different steps could be created by the user or loaded from an old simulation or from a database. For the geometry, the user need to choose between creating it by himself or using predefined geometry, realised with 3D tomogram pictures representing E. coli and C. crescentus cells with different types of voxelisation.
The GUI allow also the possibility to deal with the SmartCell outputs. It allows you to make graphs with only species, compartments you are interested in and also to analyze multiple simulations (to calculate the mean, standard deviation...etc...).
In order to use all the capacities of the 3D viewer, it is strongly recommended that your computer has at least the following features: Pentium IV, 2 GHz processor with 512 MB RAM (recommended: 1 GB RAM).