SynBioSS: the synthetic biology modeling suite

UNLABELLED SynBioSS (Synthetic Biology Software Suite) is a suite of software for the modeling and simulation of synthetic genetic constructs. SynBioSS utilizes the registry of standard biological parts, a database of kinetic parameters, and both graphical and command-line interfaces to multiscale simulation algorithms. AVAILABILITY SynBioSS is available under the GNU General Public License at http://synbioss.sourceforge.net.

[1]  Linda R. Petzold,et al.  Stochastic modelling of gene regulatory networks , 2005 .

[2]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[3]  Yiannis N. Kaznessis,et al.  Models for synthetic biology , 2007, BMC Systems Biology.

[4]  Yiannis N Kaznessis,et al.  Model-driven designs of an oscillating gene network. , 2005, Biophysical journal.

[5]  Russ Rew,et al.  NetCDF: an interface for scientific data access , 1990, IEEE Computer Graphics and Applications.

[6]  Vassilios Sotiropoulos,et al.  Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes , 2007, BMC Systems Biology.

[7]  Vassilios Sotiropoulos,et al.  Multiscale Hy3S: Hybrid stochastic simulation for supercomputers , 2006, BMC Bioinformatics.

[8]  Yiannis N Kaznessis,et al.  Optimization of a stochastically simulated gene network model via simulated annealing. , 2006, Biophysical journal.

[9]  Linda R. Petzold,et al.  Stochastic Modeling of Gene Regulatory Networks y , 2005 .

[10]  A. Arkin,et al.  Simulation of prokaryotic genetic circuits. , 1998, Annual review of biophysics and biomolecular structure.

[11]  Rudiyanto Gunawan,et al.  Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network , 2008, IEEE Transactions on Automatic Control.

[12]  D. Gillespie.  A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .

[13]  Hitesh Mistry,et al.  Stochastic Modeling of Gene Regulatory Networks , 2007 .

[14]  Michael Hucka,et al.  LibSBML: an API Library for SBML , 2008, Bioinform..

[15]  D. Endy,et al.  Refinement and standardization of synthetic biological parts and devices , 2008, Nature Biotechnology.

[16]  Donald A. McQuarrie,et al.  Kinetics of Small Systems. I , 1963 .

[17]  Mads Kaern,et al.  The engineering of gene regulatory networks. , 2003, Annual review of biomedical engineering.

[18]  D. Gillespie,et al.  Stochastic Modeling of Gene Regulatory Networks † , 2005 .

[19]  Bo Leuf,et al.  The Wiki Way: Quick Collaboration on the Web , 2001 .

[20]  R. Watson,et al.  Data Management , 1980, Bone Marrow Transplantation.

[21]  A. Arkin,et al.  It's a noisy business! Genetic regulation at the nanomolar scale. , 1999, Trends in genetics : TIG.