iBioSim is a computer-aided design (CAD) tool aimed for the modeling, analysis, and design of genetic circuits. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). iBioSim also supports the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology.
Considering that synthetic gene circuits are mainly being built and tested =
in model organisms, it may be helpful in the future to have template iBioSi=
m models with typical compartment sizes, mRNA and protein degradation rates=
, etc. for E. coli and S. cerevisiae. Another nice future functionality cou=
ld be if the effects of cell growth (binomial partitioning and dilution of =
molecules) could be automatically incorporated into models in organism-depe=
ndent manner.=
buggsley
commented
8 years ago
Considering that synthetic gene circuits are mainly being built and tested = in model organisms, it may be helpful in the future to have template iBioSi= m models with typical compartment sizes, mRNA and protein degradation rates= , etc. for E. coli and S. cerevisiae. Another nice future functionality cou= ld be if the effects of cell growth (binomial partitioning and dilution of = molecules) could be automatically incorporated into models in organism-depe= ndent manner.=