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.
Silicon
Cell ready to use.: the website with silicon cells that can be run over the
web. Please contact us
when interested in joining this international consortium.
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)
page