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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…
SYNBADm
Desktop

SYNBADm

A Matlab-based toolbox for the automatic design of biological circuits with…

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…

CADLIVE
Desktop

CADLIVE Computer-Aided Design of LIVing systEms

A comprehensive computational tool that analyzes and rationally designs…

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…

VisBOL
Web

VisBOL

An open source project providing visualization of synthetic biology designs…

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…

D-VASim
Desktop

D-VASim Dynamic Virtual Analyzer and Simulator

Provides a virtual laboratory environment to simulate and analyze the behavior…

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…

BioJADE
Desktop

BioJADE

A design and simulation tool for synthetic biological systems. BioJADE is…

A design and simulation tool for synthetic biological systems. BioJADE is written in Java, and utilizes the BioBricks repositories. It supports Oracle, MySQL and XML based repositories based on the…

BioSCRAPE
Desktop
CellDesigner
Desktop

CellDesigner

A structured diagram editor for drawing gene-regulatory and biochemical…

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…

BioFNet
Web

BioFNet

A biological functional network database which can cover the whole cell at the…

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…

SynBioSS
Desktop
Web

SynBioSS Synthetic Biology Software Suite

A suite of software for the modeling and simulation of synthetic genetic…

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…

DNAplotlib
Desktop

DNAplotlib

A computational toolkit for the programmable visualization of highly…

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…

GB
Web

GB GoldenBraid

A comprehensive technological framework that aims to foster the exchange of…

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…

DACCAD
Desktop

DACCAD DNA Artificial Circuit Computer Assisted Design

A computer-assisted design software that supports the construction of systems…

A computer-assisted design software that supports the construction of systems for the DNA toolbox. DACCAD is ultimately aimed to design actual in vitro implementations, which is made possible by…

AutoBioCAD
Desktop

AutoBioCAD

A tool aimed at the automated design of gene regulatory circuits. AutoBioCAD…

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…

SynBioLGDB
Dataset

SynBioLGDB

A synthetic biology database of experimentally genetic validated logic gates.…

A synthetic biology database of experimentally genetic validated logic gates. LGDB documents more than 189 genetic logic gates with experimental evidence involving 80 AND gates and 16 NOR gates in…

TinkerCell
Desktop
Web

TinkerCell

A computer-aided design software tool for synthetic biology. It combines visual…

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…

PEDI
Desktop

PEDI Parameter Estimation by Decomposition and Integration

A framework for efficient and scalable parameter estimation that focuses…

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…

RoVerGeNe
Desktop

RoVerGeNe

A tool for the analysis of genetic regulatory networks under parameter…

A tool for the analysis of genetic regulatory networks under parameter uncertainty. This modeling framework is well adapted to the experimental data currently available. Moreover, these models…

BioNetCAD
Desktop

BioNetCAD

A methodology for the construction of synthetic biochemical networks based on…

A methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. BioNetCAD, a CellDesigner plug-in, helps users to go…

PROMOT
Desktop

PROMOT Process Modeling Tool

A software tool for the construction and manipulation of complex technical and…

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…

iBioSim
Desktop

iBioSim

Supports learning of genetic circuit models, efficient abstraction-based…

Supports learning of genetic circuit models, efficient abstraction-based analysis of these models and the design of synthetic genetic circuits. iBioSim includes project management features and a…

MoSeC
Desktop

MoSeC

A Java application for synthetic biology design that takes a model annotated…

A Java application for synthetic biology design that takes a model annotated with the DNA sequence information of genetic elements and converts it into a DNA sequence. Both CellML and SBML models…

GEC
Desktop

GEC Genetic Engineering of living Cells

Allows logical interactions between potentially undetermined proteins and genes…

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…

Proto…
Desktop

Proto BioCompiler

Generates optimized genetic regulatory network designs from specifications…

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…

SBML2SMW
Desktop

SBML2SMW

Allows extraction and storage of Celldesigner model information in a Semantic…

Allows extraction and storage of Celldesigner model information in a Semantic Mediawiki server as well as integration of this information in a Celldesigner model.

Clotho
Desktop
Web

Clotho

Provides a data model for representing biological objects, a common API for…

Provides a data model for representing biological objects, a common API for manipulating these objects, and a common platform for developing Apps for designing synthetic biological systems. The Core…

GenoCAD
Web

GenoCAD

An environment to design expression vectors, genetic constructs, artificial…

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…

Asmparts
Desktop

Asmparts

A computational tool to produce models of biological systems by assembling…

A computational tool to produce models of biological systems by assembling models from biological parts. Asmparts not only takes advantage of modularity, but it also enforces standardisation in part…

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