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.
3DuF – 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
Text-based modular human-readable/writable model definition language with capabilities of easy translation into SMBL.
Analysis and comprehension tool that uses the open-source statistical language, R; AMI and Docker images are available
Analysis and comprehension tool that uses the open-source statistical language, R; AMI and Docker images are available
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
Software for creating genetic circuits, using as input a high-level logic specification written in Verilog.
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.
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.
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.
DAFD is the first microfluidic design automation software that can deliver a user-specified desired performance using machine learning.
A tool for designing combinational libraries of biological systems using response surface methodology.
Eugene – Software Type:
An Ecosystem of Languages tailored for Rule-based Design of Synthetic Biological Systems, Devices, Parts,
and DNA Sequences
GLAMM
Provides maps for metabolic pathways, biosynthesis of secondary metabolites, and macrobial metabolism.
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
Automates the design of microfluidic devices used in synthetic biology by optimizing their layout; specifications are in the text-based MINT language
GeneDesign – Software Type: Design
Web-based synthetic gene designer including various modules such as reverse translator,
codon juggler, etc. for sequence manipulation
gro
Software Type: Test
gro is a language for programming, modeling, specifying and simulating the behavior of cells in growing microcolonies of microorganisms.
GSL
Software Type: 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
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.
Kera
Software Type: Specification
An object-oriented programming language for synthetic biology, which is tempered by the biopart rule library, Samhita.
Mage
Software Type: Design
MAGE is the Java part of MERLIN that allows performance of Merlin Analysis on a package.
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
MoSec
Software Type: 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)
Merlin is a web-based application for genomic reprogramming via a rapid and efficient method known as Multiplex Automated Genome Engineering (MAGE).
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
Phoenix – Software Type: 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.
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
PyHamilton
Software
Type: Assembly
A set of standardized libraries utilized with the Hamilton liquid handling
robots.
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.
RBS Calculator
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.
OWL is a synthetic biology automatic datasheet generator.
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.
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.
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
RoadRunner
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
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.
Sequence
Refiner
Software Type: 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
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
TASBE
Software Type: Test
A variety of synthetic biology automation software tool for tasks from high-level specification to part assignment and assembly
VectorEditor
Software Type: DNA
Web-based DNA sequence-editing and analysis tool with restriction enzyme manager, amino acid translation, and gel digest prediction
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.