This documentation provides a comprehensive overview of various software tools useful for synthetic biology applications. These tools cover a range of purposes including modular model definition, flow cytometry data analysis, genetic circuit creation, metabolic pathway mapping, genomic reprogramming, and DNA sequence generation.
A text-based modular human-readable/writable model definition language with capabilities of easy translation into SMBL.
A library for reading, analyzing, and calibrating flow cytometry data; accepts FCS files as input and is compatible with different calibration particles, fluorescent probes, and cell types.
An object-oriented programming language for synthetic biology, tempered by the biopart rule library, Samhita.
Software for creating genetic circuits, using as input a high-level logic specification written in Verilog.
Provides maps for metabolic pathways, biosynthesis of secondary metabolites, and microbial metabolism.
A web-based application for genomic reprogramming via a rapid and efficient method known as Multiplex Automated Genome Engineering (MAGE).
An ecosystem of languages tailored for rule-based design of synthetic biological systems, devices, parts, and DNA sequences.
A language that facilitates the design of large and complex DNA constructs used to engineer genomes; incorporates a set of low-level DNA manipulation primitives.
Java application capable of generating DNA sequences, and exporting formats such as FASTA, GenBank, EMBL, and SBOL from SBML and CellML models.
This document provides a brief overview and resource links for synthetic biology tools to aid in various applications. For further information, visit the respective project websites and source code repositories.