Assembly

Visual CAD tool for the design of microfluidic devices; outputs STL for CNC milling and SVG for lithography, as well as a textual JSON representation

Specification

Text-based modular human-readable/writable model definition language with capabilities of easy translation into SMBL.

Assembly

An assembly design tool for generating scalable, reproducible, and transferable molecular biology workflows

Specification

A deprecated tool for modular specification of biological devices; Asmparts takes advantage of standardization by considering a model for each part in the design.

Design

A java-based design and simulation tool for synthetic biological systems with interactive use of BioBrick repositories.

Test

Performs guaranteed parameter set synthesis for ODE biological models expressed in SBML given a desired behavior expressed by time-series data

Test

Analysis and comprehension tool that uses the open-source statistical language, R; AMI and Docker images are available

Test

COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations.

Specification

Software for creating genetic circuits, using as input a high-level logic specification written in Verilog.

Data Management

Clotho is a framework for engineering synthetic biological systems and managing the data used to create them. You can author data schemas, run functions and algorithms, and tie Clotho into existing applications.

Design

Constellation can parse a rich set of operators as defined by GOLDBAR and enumerate genetic designs that satisfy user defined specifications through graphs that are mathematically rigorous and
provably correct.

Design

DAFD is the first microfluidic design automation software that can deliver a user-specified desired performance using machine learning.

Assembly

DNA assembly planning tool for binary assembly; improves on algorithm performance of prior binary algorithms

Design

A tool for designing combinational libraries of biological systems using response surface methodology.

Specification

An Ecosystem of Languages tailored for Rule-based Design of Synthetic Biological Systems, Devices, Parts, and DNA Sequences

Test

A library for reading, analyzing, and calibrating flow cytometry data; it accepts FCS files as input and is compatible with different calibration particles, fluorescent probes, and cell types

Assembly

Automates the design of microfluidic devices used in synthetic biology by optimizing their layout; specifications are in the text-based MINT language

Design

Provides maps for metabolic pathways, biosynthesis of secondary metabolites, and macrobial metabolism.

Specification

A language that facilitates design of large and complex DNA constructs used to engineer genomes; it also incorporates a set of low-level DNA manipulation primitives

Design

Web-based synthetic gene designer including various modules such as reverse translator, codon juggler, etc. for sequence manipulation

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Specification

An object-oriented programming language for synthetic biology, which is tempered by the biopart rule library, Samhita.

Design

MAGE is the Java part of MERLIN that allows performance of Merlin Analysis on a package.

Design

Merlin is a web-based application for genomic reprogramming via a rapid and efficient method known as Multiplex Automated Genome Engineering (MAGE).

Specification

Java application capable of generating DNA sequences. MoSeC has the ability to generate FASTA, GenBank,
EMBL, and SBOL formats from SBML and CellML models (ico2s.org/software/mosec.html)

Test

A modeling environment for simulating cell-based models with ordinary differential equations and reaction–diffusion systems; multiscale biological models can be defined in biological terms and mathematical expressions

Design

Neptune is a complete, end-to-end microfluidic design suite for synthetic biologists. With Neptune, researchers and microfluidic designers have all the tools needed to design, fabricate, and control microfluidic devices.

Data Management

OWL is a synthetic biology automatic datasheet generator.

Design, Test

The Phoenix project describes a framework to design complex genetic systems where the focus is on how the system behaves over time instead of its behavior at steady-state.

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Pigeon is a Web-based tool that translates a textual description of a synthetic biology design into an image. It allows programmatic generation of design visualizations, is easy to learn, is easily extensible to new glyphs and notation, and can be connected to other software tools for visualizing their output.

Assembly

A tool used to design and analyze primers for PCR reactions with the ability to select primers for sequencing reactions and hybridization probes

Specification

A tool for construction and manipulation of biological dynamic models based on differential-algebraic equations ProMot is matched with the simulation environment Diana

Test

Provides a variety of tools for the analysis of cellular systems; these include a human readable model description language, a structural, and a bifurcation analysis module—PySCeS supports SBML and SED-ML

Design

Allows for predicting and controlling translation initiation and protein expression in bacteria; can also be used for optimizing synthetic RBS sequences to achieve a targeted translation initiation rate.

Design

Raven uses a sophisticated dynamic programming algorithm to design high-quality DNA assembly plans. Raven produces SBOL compliant images that visualize your assembly plan as well as human readable instructions.

Test

A portable simulation engine for systems and synthetic biology models in SBML format; RoadRunner is written in C# and incorporates C, Cþþ, and Python APIs

SBOL

SBOLDesigner is a simple, biologist-friendly CAD software tool for creating and manipulating the sequences of genetic constructs using the Synthetic Biology Open Language (SBOL) 2.2 data model.

Protein

Sequence alignment tool that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core model of a protein family

Design

SynBioHub is a design repository for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them.

Test

A variety of synthetic biology automation software tool for tasks from high-level specification to part assignment and assembly

Test

Incorporates a diagram that is detailed enough so that it can be mapped to models or experimental results; various mathematical analyses can then be run on those models

DNA

Web-based DNA sequence-editing and analysis tool with restriction enzyme manager, amino acid translation, and gel digest prediction

Test

gro is a language for programming, modeling, specifying and simulating the behavior of cells in growing microcolonies of microorganisms.

Design

iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed.