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Circuit modeling software tools | Synthetic biology

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.

Source text:
(Slusarczyk et al., 2012) Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genet.

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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).
SynBioSS / Synthetic Biology Software Suite
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. SynBioSS is a complete software suite for each step in the construction of a synthetic network model: creating a kinetic model, locating kinetic information and simulating that model accurately and efficiently.
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 Matlab-based toolbox for the automatic design of biological circuits with targeted functions from libraries of components. SYNBADm allows single and multi-objective optimal design of biological circuits from a set of parts and a set of specifications. This tool makes use of global optimization to simultaneously search the space of structures and kinetic parameters. SYNBADm handles efficiently high levels of circuit complexity, incorporates multiple design criteria through multiobjective optimization. Further, it provides flexible design capabilities, i.e. the user can define the modeling framework, library of components and target performance function(s).
GB / GoldenBraid
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.
PEDI / Parameter Estimation by Decomposition and Integration
A framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, PEDI decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure.
D-VASim / Dynamic Virtual Analyzer and Simulator
Provides a virtual laboratory environment to simulate and analyze the behavior of genetic logic circuit models represented in an SBML (Systems Biology Markup Language). Hence, SBML models developed in other software environments can be analyzed and simulated in D-VASim. D-VASim offers deterministic as well as stochastic simulation; and differs from other software tools by being able to extract and validate the Boolean logic from the SBML model. D-VASim is also capable of analyzing the threshold value and propagation delay of a genetic circuit model.
A tool aimed at the automated design of gene regulatory circuits. AutoBioCAD loads a library of models of genetic elements and implements evolutionary design strategies to produce (i) nucleotide sequences encoding circuits with targeted dynamics that can then be tested experimentally and (ii) circuit models for testing regulation principles in natural systems, providing a new tool for synthetic biology. AutoBioCAD can be used to model and design genetic circuits with dynamic behavior, thanks to the incorporation of stochastic effects, robustness, qualitative dynamics, multiobjective optimization, or degenerate nucleotide sequences, all facilitating the link with biological part/circuit engineering.
An open source project providing visualization of synthetic biology designs using the SBOL Visual glyph set. VisBOL designs can be exported to formats including PNG and SVG images to be embedded in Web pages, presentations and publications. The VisBOL tool enables the automated generation of visualizations from designs specified using the Synthetic Biology Open Language (SBOL) version 2.0, as well as a range of well-known bioinformatics formats including GenBank and Pigeoncad notation. VisBOL is provided both as a user accessible Web site and as an open-source (BSD) JavaScript library that can be used to embed diagrams within other content and software.
A biological functional network database which can cover the whole cell at the level of molecular interactions. BioFNet takes an advantage in implementing the simulation program for the mathematical models of the functional networks, visualizing the simulated results. It presents a sound basis for rational design of biochemical networks and for understanding how functional networks are assembled to create complex high-level functions, which would reveal design principles underlying molecular architectures.
GEC / Genetic Engineering of living Cells
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.
Proto BioCompiler
Generates optimized genetic regulatory network designs from specifications written in a high-level programming language. Proto BioCompiler provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. This platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.
A computational toolkit for the programmable visualization of highly customizable, standards-compliant genetic designs. DNAplotlib provides functions to aid with both visualization tasks and to extract and overlay associated experimental data. High-quality output is produced in the form of vector-based PDFs, rasterized images, and animated movies. All aspects of the rendering process can be easily customized or extended by the user to cover new forms of genetic part or regulation. DNAplotlib supports improved communication of genetic design information and offers new avenues for static, interactive and dynamic visualizations that map and explore the links between the structure and function of genetic parts, devices and systems; including metabolic pathways and genetic circuits.
BioSCRAPE / Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation
Allows fast and flexible modeling and simulation for biological circuits. BioSCRAPE is useful in deterministic or stochastic simulations and incorporates delayed reactions, cell growth, and cell division. It aims to provide tools for doing parameter estimation for synthetic and systems biology. The tool can perform parameter estimation for both simulated and experimental data for integrase recombination dynamics in the TX-TL cell free in vitro system.
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