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Aquarium

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

Assembly

BioPSy

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

Test

Cello

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

Specification

Double Dutch

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

Design

Fluigi

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

Assembly

GeneDesign

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

Design

MAGE

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

Design

OWL

OWL is a synthetic biology automatic datasheet generator.

Data Management

ProMot

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

Specification

Raven

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.

Design

Sequence Refiner

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

Protein

TinkerCell

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

Test

iBioSim

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.

Design

3DuF

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

Assembly

Asmparts

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

Specification

Bioconductor

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

Test

Clotho

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.

Data Management

Eugene

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

Specification

GLAMM

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

Design

Geneious Plugin

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MoSeC

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)

Specification

Pigeon

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.

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PySCeS

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

Test

RoadRunner

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

Test

SynBioHub

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.

Design

VectorEditor

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

DNA

Antimony

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

Specification

BioJADE

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

Design

COPASI

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.

Test

DNALD

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

Assembly

FlowCal

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

Test

GSL

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

Specification

Kera

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

Specification

Morpheus

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

Test

Primer3

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

Assembly

RBS Calculator

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

SBOL Designer

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.

SBOL

TASBE

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

Test

gro

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

Test