top of page

Synthetic Biology Programs

Nona supports over 40 applications in the synthetic biology community and plenty on our Github. Search through Nona’s curated software repository to see if someone else has already solved your problems for you. Nona hopes to empower all community members to be makers and creators rather than passive recipients. Everyone is encouraged to contribute, no matter what skill level. Code in Nona’s archive needs testing, bug reports, user documentation, and code examples.

Abstract Lines

Sort by Program Type

3duf.png

3DμF

Software Type: 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

Project Website
Source Code
Demo
3duf.png

BioConductor

Software Type: Test

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

Project Website
Source Code
3duf.png

Clotho

Software Type: 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.

Source Code
Demo
3duf.png

DAFD

Software Type: Design

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

Project Website
Source Code
3duf.png

FloCal

Software Type: Specify

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

Project Website
Source Code
3duf.png

GSL

Software Type: Specify

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

Source Code
3duf.png

Knox

Software Type: Data Management

Knox is a web-enabled repository for storing, modifying, and tracking changes to genetic design spaces encoding thousands of genetic design variants as directed graphs. Knox can be accessed at any domain for <insertname>.knoxcad.org

Project Website
Source Code
3duf.png

MoSec

Software Type: Specify

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)

Source Code
3duf.png

Phoenix

Software Type: Design

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.

Project Website
Source Code
Demo
3duf.png

Puppeteer

Software Type: Design

Puppeteer is a web-based planning and instruction generation tool which automates the task of DNA assembly by tracking, managing, and controlling laboratory tasks, reagents, and equipment. It is designed to translate protocols into sets of human- and machine-readable instructions, reducing the labor cost of building genetic devices.

Project Website
3duf.png

RBS Calcualtor

Software Type: 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.

Project Website
Demo
3duf.png

SBOL Designer

Software Type: 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.

Project Website
Demo
3duf.png

TASBE

Software Type: Design

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

Project Website
Source Code
Demo
3duf.png

gro

Software Type: Test

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

Project Website
Source Code
3duf.png

Antimony

Software Type: Specify

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

Project Website
Source Code
3duf.png

BioPSy

Software Type: Test

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

Source Code
3duf.png

Constellation

Software Type: 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 probably correct.

Project Website
Source Code
Demo
3duf.png

Double Dutch

Software Type: Design

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

Demo
3duf.png

Fluigi

Software Type: Assembly

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

Project Website
Source Code
Demo
3duf.png

GeneDesign

Software Type: Design

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

Project Website
Source Code
3duf.png

Mage

Software Type: Design

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

Source Code
3duf.png

Morpheus

Software Type: 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

Project Website
Source Code
3duf.png

Pigeon

Software Type: Design

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.

Project Website
3duf.png

PyHamilton

Software Type: Assembly

A set of standardized libraries utilized with the Hamilton liquid handling
robots.

Source Code
3duf.png

Raven

Software Type: 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.

Project Website
Source Code
Demo
3duf.png

Sequence Refiner

Software Type: Design

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

Project Website
3duf.png

Tinkercell

Software Type: 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

Project Website
Demo
3duf.png

iBioSim

Software Type: 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.

Project Website
Source Code
Demo
3duf.png

Aquarium

Software Type: Test

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

Project Website
Source Code
3duf.png

CELLO

Software Type: Specify

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

Project Website
Source Code
Demo
3duf.png

Copasi

Software Type: 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.

Project Website
Source Code
Demo
3duf.png

Eugene

Software Type: Specify

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

Project Website
Source Code
Demo
3duf.png

GLAMM

Software Type: Specify

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

Project Website
Source Code
3duf.png

Kera

Software Type: Specify

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

Source Code
3duf.png

Merlin

Software Type: Specify

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

Project Website
Source Code
3duf.png

OWL

Software Type: Data Management

OWL is a synthetic biology automatic datasheet generator.

Source Code
3duf.png

Primer3

Software Type: Assembly

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

Project Website
Source Code
Demo
3duf.png

Pysces

Software Type: 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

Project Website
Source Code
3duf.png

Road Runner

Software Type: 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

Project Website
Source Code
3duf.png

SynBioHub

Software Type: 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.

Project Website
3duf.png

Vector Editor

Software Type: Design

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

Project Website
Source Code
Demo
bottom of page