Applications

If you are a synthetic biologist, you may not be aware that there are already many software tools available that support different aspects of the synthetic biology workflow, such as optimizing DNA assembly or simulating gene networks.  Each of the software tools listed here supports exchange of genetic designs in the SBOL file format (SBOL core) or supports display of genetic designs using standard SBOL Visual glyphs.

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ApplicationKnowledge ManagementSequence Design
Circuit DesignModelingVisualizationSBOL VisualImport
SBOL1
Import
SBOL2
Export
SBOL1
Export
SBOL2
Pigeon Visualizer


A simple chart, cheat sheet, and short accessible document describing the latest SBOL data model. A faster adoption process for SBOL Visual glyphs



Contact Person: Swapnil Bhatia

Organization(s): Bhatia Lab at Boston University

Programming Language : Perl


OS/Platform: Web


Availability: Free


DNAplotlib


DNAplotlib enables highly customizable visualization of individual genetic constructs and libraries of design variants. It can be thought of in many ways as matplotlib for genetic diagrams.



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Contact Person: Thomas Gorochowski

Organization(s): University of Bristol, UK (originally Voigt Lab, MIT)

Programming Language: Python


OS/Platform: Linux, Mac, Windows


Availability: Open-Source


License: MIT






SBOLDesigner

SBOLDesigner 2.1 is a simple, biologist-friendly CAD software tool for creating and manipulating the sequences of genetic constructs using the Synthetic Biology Open Language (SBOL) 2.0 data model. Throughout the design process, SBOL Visual symbols, a system of schematic glyphs, provide standardized visualizations of individual parts. SBOLDesigner 2.1 completes a workflow for users of genetic design automation tools. It combines a simple user interface with the power of the SBOL standard and serves as a launchpad for more detailed designs involving simulations and experiments. Some new features in SBOLDesigner 2.1 are SBOL Stack integration, local repositories, importing of parts/sequences from existing files, import and export of GenBank and FASTA files, extended role ontology support, the ability to partially open designs with multiple root ComponentDefinitions, backward compatibility with SBOL 1.1, and versioning. SBOLDesigner is made freely available under the Apache 2.0 license.



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Contact Person: Michael Zhang


Organization(s): University of Utah


Programming Language: Java


OS/Platform : Linux/Mac/Win


Availability: Open-Source


License: Apache 2.0








ICE

Physical and Informatic repository and associated tools for plant seeds, microbial strains, DNA and protein sequences.



Contact Person: Hector Plahar

Organization(s): Lawrence Berkeley National Lab

Programming Language: Java


OS/Platform: Web


Availability: Open-Source


License: BSD






j5

DNA assembly design automation



Contact Person: Nathan Hillson

Organization(s): Lawrence Berkeley National Lab

Programming Language: Perl


OS/Platform: Web






DeviceEditor


Visual biocad canvas for specifying combinatorial DNA constructs for fabrication



Contact Person: Nathan Hillson

Organization(s): Lawrence Berkeley National Lab

Programming Language: JavaScript


OS/Platform: Web







Finch


Rule-based generation of constructs



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Demo



Contact Person: Swapnil Bhatia

Organization(s): Boston University


Programming Language: C/Java/Perl


OS/Platform: Web


Availability: Free for academic users








Pool Designer

The Pool Designer application is capable of analyzing a library of genetic construct variants encoded in SBOL and breaking this library down into pools of genetic parts that can be assembled into any library variant using multiplex assembly methods (see L. Woodruff et al., “Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration,” Nucl. Acids Res., 2016.).



Contact Person: Nicholas Roehner

Organization(s): Biological Design Center, Boston University

Programming Language: Java/JavaScript


OS/Platform: Web


Availability: Open-Source


License: BSD 3-Clause


Virtual Parts Repository

A repository of modular models of biological components. These models are reusable and composable, and facilitate model-driven design of biological systems.



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Contact Person: Goksel Misirli, Anil Wipat

Organization(s): Newcastle University

Programming Language: Java


OS/Platform: Linux/Web







MoSeC

Automated derivation of genetic circuit designs from computational models.



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Contact Person: Goksel Misirli, Anil Wipat

Organization(s): Newcastle University

Programming Language: Java


OS/Platform: Linux/Mac/Win


Availability: Free for all users




Shortbol


A shorthand language for SBOL



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Contact Person: Matthew Pocock, Anil Wipat

Organization(s): Newcastle University, Turing Ate My Hamster Ltd

Programming Language: Scala


OS/Platform: Linux/Mac/Win/Web



Pinecone

Pinecone is Serotiny’s web-based protein design software aimed at researchers doing R&D for therapeutics, materials, as well as those in basic research. Serotiny optimized Pinecone for designing protein constructs by focusing on functional protein domains as the basic unit of design.


Pinecone’s high-level approach allows plain language design, analysis and transmission of complex genetic construct sets. Researchers can design single proteins, or they can benefit from the economies of scale in designing combinatorial sets or mutation libraries. Pinecone then matches the design with CROs or DNA Synthesizers to produce and deliver the desired material, such as dsDNA, plasmid or purified protein.


Serotiny aims to democratize protein engineering with Pinecone - bringing nano-scale genetic-tools to disparate disciplines that aren’t necessarily experts in genetics or molecular cloning, while also freeing geneticists and protein engineers to focus on experimental approach and execution rather than on the tedious design and construction of their starting material.



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Contact Person: Justin Farlow

Organization(s): Serotiny


Programming Language: JavaScript


OS/Platform: Web


Availability: Free for all users





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. iBioSim also includes modeling and visualization support for multi-cellular and spatial models as well. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). It can import all levels and versions of SBML and is able to export Level 3 Version 1. It supports all core SBML modeling constructs except some types of fast reactions, and also has support for the hierarchical model composition, layout, flux balance constraints, and arrays packages. It was the first tool to produce correct results for all examples in the SBML benchmark suite. It has also been tested successfully on the stochastic benchmark suite and the curated models in the BioModels database. Finally, it is one of the first tools to also support the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology.



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Contact Person: Chris Myers

Organization(s): University of Utah

Programming Language: Java/C++


OS/Platform: Linux/Mac/Win


Availability: Open-Source


License: MIT








SBOL<->Genbank Converter

Loss-less interconversion of SBOL v1.1 and GenBank



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Contact Person: Nathan Hillson

Organization(s): Berkeley Lab

Programming Language: Perl


OS/Platform: Web


Availability: Free for all users



GenoCAD


GenoCAD is a rule-based DNA design tool. It includes an extensive library of genetic parts derived from the annotation of common plasmids. It allows users to define domain specific languages to design expression systems for particular applications.



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Contact Person: Jean Peccoud

Organization(s): GenoFAB, LLC

Programming Language: PHP/Java/Prolog/JS


OS/Platform: Web


Availability: Commercial







SBOLme

SBOLme is an open-access repository of SBOL 2-compliant biochemical parts for a wide range of metabolic engineering applications.



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Contact Person: Hiroyuki Kuwahara

Organization(s): KAUST

Programming Language: HTML/PHP/Python/SQL


OS/Platform: Web


Availability: Free for all users


SynBioHub


SynBioHub is a registry for storing and sharing genetic circuit designs using the SBOL2 standard. Designs can be uploaded in SBOL or GenBank format, assigned a public link to share with collaborators and for publications, and searched using rich querying functionality.



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Contact Person: Anil Wipat

Organization(s): Newcastle University

Programming Language: JavaScript


OS/Platform: Linux/Mac/Win/Web


Availability: Open-Source


License: BSD 2-Clause






VisBOL


VisBOL is a JavaScript software library to visualize DNA features from SBOL2 documents using the SBOL Visual standard. A Web interface is also provided to enable end-user access to generate diagrams for presentations and publications.



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Contact Person: Anil Wipat

Organization(s) : Newcastle University

Programming Language: JavaScript


OS/Platform: Lin/Mac/Win/Web


Availability: Open-Source


License: BSD 2-Clause



GeneGenie

GeneGenie supports the design and self-assembly of synthetic genes and constructs. GeneGenie allows for the design of oligonucleotide cohorts encoding the gene sequence optimized for expression in any suitable host through
an intuitive, easy-to-use web interface. The tool ensures
consistent oligomer overlapping melting temperatures,
minimizes the likelihood of misannealing,
optimizes codon usage for expression in a selected
host, allows for specification of forward and reverse
cloning sequences and
also provides support for mutagenesis or directed
evolution studies. Directed evolution studies are enabled
through the construction of variant libraries via
the optional specification of ‘variant codons’, containing
mixtures of bases, at any position. For example,
specifying the variant codon TNT (where N is any
nucleotide) will encode
a mixture of the amino acids Tyr, Ser, Cys and
Phe.




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Contact Person: Neil Swainston

Organization(s): Manchester Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM)

Programming Language: Java


OS/Platform: Web


Availability: Open-Source


Tellurium



Tellurium is a Python environment based on spyder2 IDE, designed for systems and synthetic biology simulations. It combines a number of existing libraries, including libRoadRunner, libAntimony, and phraSED-ML, alongside with standards support through libSBML, libSEDML, and pySBOL. Additionally, other Python packages such as matplotlib and NumPy are used to provide extra analysis, optimization, and plotting capabilities.



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Contact Person: Kiri Choi

Organization(s): University of Washington

Programming Language: Python


OS/Platform: Linux/Mac/Win


Availability: Open-Source


License: Apache 2.0






Eugene

Eugene is a textual specification language for the rule-based design of
synthetic biological systems, devices, parts, and DNA sequences.



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Demo



Contact Person: Douglas Densmore

Organization(s): Boston University

Programming Language: Java


OS/Platform: Linux/Mac/Win/Web


Availability: Open-Source


License: CC BY-SA 4.0





BOOST


Build-OptimizatiOn Software Tools (BOOST) is a platform of tools to design DNA sequences for manufacturing. Currently, BOOST consists of three tools: (i) The "Juggler" reverse translates protein sequences into DNA sequences and codon juggles DNA sequences, (ii) The "Polisher" verifies DNA sequences against DNA synthesis constraints. In addition, the "Polisher" can modify the protein coding regions of DNA sequences in order to resolve eventual violations of DNA synthesis constraints. (iii) The "Partitioner" decomposes large DNA sequences into synthesizable building blocks with assembly-specific overlap sequences.



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Contact Person: Ernst Oberortner

Organization(s): DOE Joint Genome Institute, Lawrence Berkeley National Labs

Programming Language: Java


OS/Platform: Linux/Mac/Win/Web


Availability: Free for academic users





Tinkercell

TinkerCell is a widely used open source network design and simulation application tool for synthetic biology (tinkercell.org). The software allows synthetic biologists to design new synthetic circuits and simulate them. TinkerCell is written in C++ and runs on Windows, Mac and Linux. It uses Qt as the GUI framework. Currently TinkerCell only has very limited support for SBOL.



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Demo



Contact Person: Herbert Sauro

Organization(s): University of Washington

Programming Language: C/C++


OS/Platform: Linux/Mac/Win


Availability: Open-Source


License: BSD






Graphviz

Graphviz (short for Graph Visualization Software) is a package of open-source tools initiated by AT&T Labs Research for drawing graphs specified in DOT language scripts. It also provides libraries for software applications to use the tools. Graphviz is free software licensed under the Eclipse Public License. Graphviz includes SBOL visual symbols in its set of node shapes, and has edge shapes compatible with proposed regulatory arc shapes.



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Contact Person: Graphviz Community

Organization(s): Graphviz Community

Programming Language: C


OS/Platform: Linux/Mac/Win


Availability: Open-Source


License: Eclipse Public License - v 1.0


Proto BioCompiler


Proto BioCompiler generates optimized genetic regulatory network designs from specifications written in a high-level programming language, producing both SBOL specifications, visualization, and ODE models.



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Contact Person: Jacob Beal

Organization(s): Raytheon BBN Technologies

Programming Language: C/C++


OS/Platform: Linux/Mac/Win/
Web


Availability: Open-Source


License: GPL3 with classpath exception





Cello


Cello is a framework that describes what is essentially a programming language to design computational circuits in living cells. The circuits generated on plasmids expressed in Escherichia coli required careful insulation from their genetic context, but primarily functioned as specified. The circuits could, for example, regulate cellular functions in response to multiple environmental signals. Such a strategy can facilitate the development of more complex circuits by genetic engineering.



Cello converts electronic design specifications of combinational logic to complete DNA sequences encoding transcriptional logic circuits that can be executed in bacterial cells. A database of transcriptional repressors characterized in the Voigt lab provide genetic NOT gates and NOR gates that can be composed into any Boolean logic function specified in Verilog.



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Contact Person: Prashant Vaidyanathan

Organization(s): Boston University

Programming Language: Java/HTML/JS/CSS


OS/Platform: Web


Availability: Open-Source


License: BSD 2-Clause




SBOL Validator/Converter


SBOL Validator/Converter is a simple, easy-to-use software tool that allows for conversion between SBOL/GenBank/FASTA files using the Synthetic Biology Open Language (SBOL) 2.0 data model. The motivation behind the SBOL Validator/Converter is to provide a universally-accepted tool with the capability to check the validity of files. This tool serves as a platform for developers to verify correct implementation of the SBOL data standard, authors to ensure that data is represented properly, and editors to verify SBOL compliance of all software tools and libraries. Some key features of the Validator/Converter include its ability to convert between SBOL, FASTA, and GenBank files and that the tool is web-based which promotes ease of access and allows for central maintenance of validation methods. SBOL Validator/Converter is made freely available under the Apache 2.0 license.



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Contact Person: Zach Zundel

Organization(s): University of Utah

Programming Language: Python/Java


OS/Platform: Web


Availability: Open-Source


License: Apache 2.0





Parts&Pools



Graphical, drag and drop design of synthetic gene circuit with Standard Biological Parts. Eukaryotic parts are modelled via a rule-based approach.



Contact Person: Mario Andrea Marchisio

Organization(s): Harbin Institute of Technology

Programming Language: Perl/Python


OS/Platform: Linux/Mac/Win


Availability: Free for all users