Synthetic gene circuits are designed to program new biological behaviour, dynamics and logic control. For all but the simplest synthetic phenotypes, this requires a structured approach to map the desired functionality to available molecular and cellular parts and processes.
A structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver, SBML Simulation Core and Copasi. By using CellDesigner, you can browse and modify existing SBML models with references to existing databases, simulate and view the dynamics through an intuitive graphical interface.
A software tool for the construction and manipulation of complex technical and biological systems. Since its last major publication in 2003, PROMOT has gained new functionality in particular support of logical models, efficient editing, visual exploration, model validation and support for SBML.
A comprehensive technological framework that aims to foster the exchange of standard DNA parts for plant synthetic biology. GoldenBraid relies on the use of type IIS restriction enzymes for DNA assembly and proposes a modular cloning schema with positional notation that resembles the grammar of natural languages. Apart from providing an optimized cloning strategy that generates fully exchangeable genetic elements for multigene engineering, the GoldenBraid toolkit offers an evergrowing open collection of DNA parts, including a group of functionally tested, premade genetic modules to build frequently used modules like constitutive and inducible expression cassettes, endogenous gene silencing and protein-protein interaction tools, etc.
A comprehensive computational tool that analyzes and rationally designs large-scale biochemical networks at the molecular interaction level. CADLIVE consists of a GUI network constructor, database, a pathway search module for knockout mutants, a network layout module, and the dynamic simulator that automatically converts biochemical network maps into mathematical models.
An environment to design expression vectors, genetic constructs, artificial gene networks, and any other synthetic DNA you can think of. GenoCAD is built on the idea that DNA is a language to program biological systems. GenoCAD includes large libraries of annotated genetic parts, which serve as the words of the genetic language. GenoCAD also includes design rules describing how parts should be combined to form functional genetic constructs. You can customize your workspace by importing your favorite genetic parts and editing the design rules to make them match the specifics of your project. The design rules and parts libraries underpin a construction wizard that guides you through the process of designing complex genetic constructs. When you are satisfied with a design you can export its sequence using standard formats (FASTA, GenBank, and tab-delimited text).
A computer-aided design software tool for synthetic biology. It combines visual interface with programming API (Python, Octave, C, Ruby) and allows users to share their code with each other via a central repository.
Allows logical interactions between potentially undetermined proteins and genes to be expressed in a modular manner. Programs can be translated by a compiler into sequences of biological parts, a process which relies on logic programming and prototype databases containing known biological parts and protein interactions. Programs can also be translated to reactions, allowing simulations to be carried out. The language is a first step towards the automatic translation of high-level behavioural designs to low-level DNA code.