SiC!: The Silicon Cells
A silicon cell is a precise replica of (part of) a living cell. It is based on experimentally determined rate laws and parameter values, i.e. only on data, not on fitted values or assumptions. It merely calculates the system biology implications of the molecular properties that are already known. Silicon cell is not a package of software for simulations. The international silicon cell program thereby differs (i) from the Virtual Cell (www.nrcam.uchc.edu ), which offer web-based complete modeling environment for cell biology that can be used to calculate what happens in cells (and is more powerful for spatial aspects) and has some actual models for the purpose of demonstrating the procedure), (ii) and from the E-Cell which also offers such an environment but only for down-loading to one’s own computer and E-cell (http://www.e-cell.org/ ), (iii) from Sympheny of Genomatica (http://www.genomatica.com/index.shtml , which is not freeware but also has organism and pathway specific information) in that it calculates kinetics, rather than analyzing which pathways are possible or actually used.
At present silicon cells exist for glycolysis in yeast, trypanosomes, E. coli, erythrocytes, EGF induced signal transduction, for histone-gene expression in early development. Most of these can be found on the ready-to-use website (also ideal for teaching purposes) pioneered by Jacky Snoep.
Extended examples and instructions for using the Silicon Cells (i.e. the website; contains questions with answers; may be used for teaching biochemistry and integrative bioinformatics courses)