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.
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
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.
DAFD is the first microfluidic design automation software that can deliver a user-specified desired performance using machine learning.
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
Kera
Software Type: Specification
An object-oriented programming language for synthetic biology, which is tempered by the biopart rule library, Samhita.
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)
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
Text-based modular human-readable/writable model definition language with capabilities of easy translation into SMBL.
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.
Automates the design of microfluidic devices used in synthetic biology by optimizing their layout; specifications are in the text-based MINT language
Mage
Software Type: Design
MAGE is the Java part of MERLIN that allows performance of Merlin Analysis on a package.
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
PyHamilton
Software Type: Assembly
A set of standardized libraries utilized with the Hamilton liquid handling robots.
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
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
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.
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.
Provides maps for metabolic pathways, biosynthesis of secondary metabolites, and macrobial metabolism.
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
Merlin is a web-based application for genomic reprogramming via a rapid and efficient method known as Multiplex Automated Genome Engineering (MAGE).
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
