COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations.
Clotho is a framework for engineering synthetic biological systems and managing the data used to create them. You can author data schemas, run functions and algorithms, and tie Clotho into existing applications.
Constellation can parse a rich set of operators as defined by GOLDBAR and enumerate genetic designs that satisfy user defined specifications through graphs that are mathematically rigorous and provably correct.
A modeling environment for simulating cell-based models with ordinary differential equations and reaction–diffusion systems; multiscale biological models can be defined in biological terms and mathematical expressions
Neptune is a complete, end-to-end microfluidic design suite for synthetic biologists. With Neptune, researchers and microfluidic designers have all the tools needed to design, fabricate, and control microfluidic devices.
Pigeon is a Web-based tool that translates a textual description of a synthetic biology design into an image. It allows programmatic generation of design visualizations, is easy to learn, is easily extensible to new glyphs and notation, and can be connected to other software tools for visualizing their output.
Provides a variety of tools for the analysis of cellular systems; these include a human readable model description language, a structural, and a bifurcation analysis module—PySCeS supports SBML and SED-ML
Allows for predicting and controlling translation initiation and protein expression in bacteria; can also be used for optimizing synthetic RBS sequences to achieve a targeted translation initiation rate.
Raven uses a sophisticated dynamic programming algorithm to design high-quality DNA assembly plans. Raven produces SBOL compliant images that visualize your assembly plan as well as human readable instructions.
iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed.