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Windows, macOS: GPL: Collaborative project GenoCAD: A computer-assisted design (CAD) tool for synthetic biology, used to design genetic constructs based on grammar rules. Linux, macOS, Windows: Apache License 2.0 GenoCAD Team (Virginia Bioinformatics Institute) Genomespace
Genetic regulatory circuits (also referred to as transcriptional regulatory circuits) is a concept that evolved from the Operon Model discovered by François Jacob and Jacques Monod. [ 1 ] [ 2 ] [ 3 ] They are functional clusters of genes that impact each other's expression through inducible transcription factors and cis-regulatory elements .
COPASI [1] (COmplex PAthway SImulator) is an open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others.
iBioSim [5] [6] is a computer-aided design (CAD) tool for the modeling, analysis, and design of genetic circuits. multiplatform (Java/C++) Apache License: Yes CompuCell3D: GUI/Scripting tool [7] for building and simulating multicellular models. multiplatform (C++/Python) MIT: Yes, but only for reactions. COPASI
Autodesk Genetic Constructor (suspended) BIOFAB Clotho BIOFAB Edition; BIOFAB BIOFAB Studio; EGF Codons and EGF CUBA (Collection of Useful Biological Apps) by the Edinburgh Genome Foundry; Integrative Genomics Viewer (part of Google Genomics) Mengqvist's DNApy
Category:Molecular dynamics software; Structural alignment software; Other. Compression of genomic sequencing data; Bioinformatics workflow management system; List of genetic engineering software; List of systems biology visualization software; List of systems biology modelling software; 2D gel analysis software; List of mass spectrometry software
Gene Designer is a computer software package for bioinformatics. [1] [2] It is used by molecular biologists from academia, government, and the pharmaceutical, chemical, agricultural, and biotechnology industries to design, [3] clone, and validate genetic sequences. It is proprietary software, released as freeware needing registration.
The RNAiFold software provides two algorithms to solve the inverse folding problem: i) RNA-CPdesign explores the complete search space and ii) RNA-LNSdesign based on the large neighborhood search metaheuristic is suitable to design large structures. The software can also design interacting RNA molecules using RNAcofold of the ViennaRNA Package.