TY - JOUR
T1 - Computational methods in synthetic biology
AU - Kaznessis, Yiannis N.
PY - 2009/10/1
Y1 - 2009/10/1
N2 - We discuss how a theoretical synthetic biology research programme may liberate empiricism in biological sciences beyond the unaided human brain. Because synthetic biological systems are relatively small and largely independent of evolutionary contexts, they can be represented with mathematical models strongly founded on first principles of molecular biology and laws of statistical thermodynamics. A universal mathematical formalism for describing synthetic constructs may then be plausibly used to explain in unambiguous, quantitative terms how biological phenotypic complexity emerges as a result of well-defined biomolecular interactions. SynBioSS, a publicly available software package, is described that implements this mathematical formalism.
AB - We discuss how a theoretical synthetic biology research programme may liberate empiricism in biological sciences beyond the unaided human brain. Because synthetic biological systems are relatively small and largely independent of evolutionary contexts, they can be represented with mathematical models strongly founded on first principles of molecular biology and laws of statistical thermodynamics. A universal mathematical formalism for describing synthetic constructs may then be plausibly used to explain in unambiguous, quantitative terms how biological phenotypic complexity emerges as a result of well-defined biomolecular interactions. SynBioSS, a publicly available software package, is described that implements this mathematical formalism.
KW - Biochemical networks
KW - Hybrid stochastic simulation
KW - Markov processes
KW - Stochastic chemical kinetics
KW - SynbioSS
UR - http://www.scopus.com/inward/record.url?scp=70449575870&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=70449575870&partnerID=8YFLogxK
U2 - 10.1002/biot.200900163
DO - 10.1002/biot.200900163
M3 - Review article
C2 - 19830714
AN - SCOPUS:70449575870
VL - 4
SP - 1392
EP - 1405
JO - Biotechnology Journal
JF - Biotechnology Journal
SN - 1860-6768
IS - 10
ER -