/tag/design/DesignWowchemy (https://wowchemy.com)en-usWed, 08 Jun 2022 00:00:00 +0000/images/logo.svg/tag/design//applications/sbolcanvas/Wed, 08 Jun 2022 00:00:00 +0000/applications/sbolcanvas/<p><a href="https://sbolcanvas.org/" target="_blank" rel="noopener">SBOLCanvas</a> is a web application for creation and editing of genetic constructs using the SBOL data and visual standard. SBOLCanvas allows a user to create a genetic design from start to finish, with the option to incorporate existing SBOL data from a SynBioHub repository. SBOLCanvas is created as part of <a href="http://web.synbioks.org" target="_blank" rel="noopener">SynBioKS</a>.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td><a href="https://sbolcanvas.org/about" target="_blank" rel="noopener">Jared Earl, Logan Terry, Samuel Thayer</a></td> </tr> <tr> <td>Organization(s)</td> <td><a href="http://web.synbioks.org" target="_blank" rel="noopener">Synthetic Biology Knowledge System</a></td> </tr> <tr> <td>Programming Language</td> <td>HTML/Java/TypeScript</td> </tr> <tr> <td>OS/Platform</td> <td>Web</td> </tr> <tr> <td>Availability</td> <td>Open-Source</td> </tr> <tr> <td>License</td> <td>Apache 2.0</td> </tr> </tbody> </table>/applications/boost/Tue, 30 Jun 2020 00:00:00 +0000/applications/boost/<p>Build-OptimizatiOn Software Tools (BOOST) is a platform of tools to design DNA sequences for manufacturing. Currently, BOOST consists of three tools: (i) The &ldquo;Juggler&rdquo; reverse translates protein sequences into DNA sequences and codon juggles DNA sequences, (ii) The &ldquo;Polisher&rdquo; verifies DNA sequences against DNA synthesis constraints. In addition, the &ldquo;Polisher&rdquo; can modify the protein coding regions of DNA sequences in order to resolve eventual violations of DNA synthesis constraints. (iii) The &ldquo;Partitioner&rdquo; decomposes large DNA sequences into synthesizable building blocks with assembly-specific overlap sequences.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Ernst Oberortner</td> </tr> <tr> <td>Organization(s)</td> <td>DOE Joint Genome Institute, Lawrence Berkeley National Labs</td> </tr> <tr> <td>Programming Language</td> <td>JAva</td> </tr> <tr> <td>OS/Platform</td> <td>Linux/Mac/Win/Web</td> </tr> <tr> <td>Availability</td> <td>Free for academic users</td> </tr> </tbody> </table>/applications/cello/Tue, 30 Jun 2020 00:00:00 +0000/applications/cello/<p>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.</p> <p>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.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Doug Densmore</td> </tr> <tr> <td>Organization(s)</td> <td>Boston University</td> </tr> <tr> <td>Programming Language</td> <td>Java/HTML/JS/CSS</td> </tr> <tr> <td>OS/Platform</td> <td>Web</td> </tr> <tr> <td>Availability</td> <td>Open-Source</td> </tr> <tr> <td>License</td> <td>BSD 2-Clause</td> </tr> </tbody> </table>/applications/device-editor/Tue, 30 Jun 2020 00:00:00 +0000/applications/device-editor/<table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Nathan Hillson</td> </tr> <tr> <td>Organization(s)</td> <td>Lawrence Berkeley National Lab</td> </tr> <tr> <td>Programming Language</td> <td>JavaScript</td> </tr> <tr> <td>OS/Platform</td> <td>Web</td> </tr> </tbody> </table>/applications/eugene/Tue, 30 Jun 2020 00:00:00 +0000/applications/eugene/<p>Eugene is a textual specification language for the rule-based design of synthetic biological systems, devices, parts, and DNA sequences.</p> <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;"> <iframe src="https://www.youtube.com/embed/KczZskca60g" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; border:0;" allowfullscreen title="YouTube Video"></iframe> </div> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Douglas Densmore</td> </tr> <tr> <td>Organization(s)</td> <td>Boston University</td> </tr> <tr> <td>Programming Language</td> <td>Java</td> </tr> <tr> <td>OS/Platform</td> <td>Linux, Mac, Windows, Web</td> </tr> <tr> <td>Availability</td> <td>Open-Source</td> </tr> <tr> <td>License</td> <td>CC BY-SA 4.0</td> </tr> </tbody> </table>/applications/finch/Tue, 30 Jun 2020 00:00:00 +0000/applications/finch/<table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Swapnil Bhatia</td> </tr> <tr> <td>Organization(s)</td> <td>Boston University</td> </tr> <tr> <td>Programming Language</td> <td>C/Java/Perl</td> </tr> <tr> <td>OS/Platform</td> <td>Web</td> </tr> <tr> <td>Availability</td> <td>Free for academic users</td> </tr> </tbody> </table>/applications/genegenie/Tue, 30 Jun 2020 00:00:00 +0000/applications/genegenie/<p>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.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Neil Swainston</td> </tr> <tr> <td>Organization(s)</td> <td>Manchester Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM)</td> </tr> <tr> <td>Programming Language</td> <td>Java</td> </tr> <tr> <td>OS/Platform</td> <td>Web</td> </tr> <tr> <td>Availability</td> <td>Open-Source</td> </tr> </tbody> </table>/applications/genetech/Tue, 30 Jun 2020 00:00:00 +0000/applications/genetech/<table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Hasan Baig</td> </tr> <tr> <td>Organization(s)</td> <td>Denmark Technical University, Habib University, University of Connecticut</td> </tr> <tr> <td>Programming Language</td> <td>Python, Java</td> </tr> <tr> <td>OS/Platform</td> <td>MacOS, Windows</td> </tr> <tr> <td>Availability</td> <td>Open-source, Free for all users</td> </tr> </tbody> </table>/applications/genocad/Tue, 30 Jun 2020 00:00:00 +0000/applications/genocad/<p>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.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Jean Peccoud</td> </tr> <tr> <td>Organization(s)</td> <td>GenoFAB, LLC</td> </tr> <tr> <td>Programming Language</td> <td>PHP/Java/Prolog/JS</td> </tr> <tr> <td>OS/Platform</td> <td>Web</td> </tr> <tr> <td>Availability</td> <td>Commercial</td> </tr> </tbody> </table>/applications/ibiosim/Tue, 30 Jun 2020 00:00:00 +0000/applications/ibiosim/<p>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.</p> <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;"> <iframe src="https://www.youtube.com/embed/g4xayzlyC2Q" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; border:0;" allowfullscreen title="YouTube Video"></iframe> </div> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Chris Myers</td> </tr> <tr> <td>Organization(s)</td> <td>University of Utah</td> </tr> <tr> <td>Programming Language</td> <td>Java/C++</td> </tr> <tr> <td>OS/Platform</td> <td>Linux, Mac, Windows</td> </tr> <tr> <td>Availability</td> <td>Open-Source</td> </tr> <tr> <td>License</td> <td>MIT</td> </tr> </tbody> </table>/applications/j5/Tue, 30 Jun 2020 00:00:00 +0000/applications/j5/<table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Nathan Hillson</td> </tr> <tr> <td>Organization(s)</td> <td>Lawrence Berkeley National Lab</td> </tr> <tr> <td>Programming Language</td> <td>Perl</td> </tr> <tr> <td>OS/Platform</td> <td>Web</td> </tr> </tbody> </table>/applications/mosec/Tue, 30 Jun 2020 00:00:00 +0000/applications/mosec/<table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Goksel Misirli, Anil Wipat</td> </tr> <tr> <td>Organization(s)</td> <td>Newcastle University</td> </tr> <tr> <td>Programming Language</td> <td>Java</td> </tr> <tr> <td>OS/Platform</td> <td>Linux, Mac, Windows</td> </tr> <tr> <td>Availability</td> <td>Free for all users</td> </tr> </tbody> </table>/applications/partsandpools/Tue, 30 Jun 2020 00:00:00 +0000/applications/partsandpools/<p>Graphical, drag and drop design of synthetic gene circuit with Standard Biological Parts. Eukaryotic parts are modelled via a rule-based approach.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Mario Andrea Marchisio</td> </tr> <tr> <td>Organization(s)</td> <td>Harbin Institute of Technology</td> </tr> <tr> <td>Programming Language</td> <td>Perl/Python</td> </tr> <tr> <td>OS/Platform</td> <td>Linux, Mac, Windows</td> </tr> <tr> <td>Availability</td> <td>Free for all users</td> </tr> </tbody> </table>/applications/pinecone/Tue, 30 Jun 2020 00:00:00 +0000/applications/pinecone/<p>Pinecone is Serotiny’s web-based protein design software aimed at researchers doing R&amp;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.</p> <p>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.</p> <p>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.</p> <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;"> <iframe src="https://www.youtube.com/embed/_6l4KYGeFvQ" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; border:0;" allowfullscreen title="YouTube Video"></iframe> </div> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Justin Farlow</td> </tr> <tr> <td>Organization(s)</td> <td>Serotiny</td> </tr> <tr> <td>Programming Language</td> <td>JavaScript</td> </tr> <tr> <td>OS/Platform</td> <td>Web</td> </tr> <tr> <td>Availability</td> <td>Free for all users</td> </tr> </tbody> </table>/applications/pooldesigner/Tue, 30 Jun 2020 00:00:00 +0000/applications/pooldesigner/<p>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.).</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Nicholas Roehner</td> </tr> <tr> <td>Organization(s)</td> <td>Biological Design Center, Boston University</td> </tr> <tr> <td>Programming Language</td> <td>Java/JavaScript</td> </tr> <tr> <td>OS/Platform</td> <td>Web</td> </tr> <tr> <td>Availability</td> <td>Open-Source</td> </tr> <tr> <td>License</td> <td>BSD 3-Clause</td> </tr> </tbody> </table>/applications/protobiocompiler/Tue, 30 Jun 2020 00:00:00 +0000/applications/protobiocompiler/<p>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.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Jacob Beal</td> </tr> <tr> <td>Organization(s)</td> <td>Raytheon BBN Technologies</td> </tr> <tr> <td>Programming Language</td> <td>C/C++</td> </tr> <tr> <td>OS/Platform</td> <td>Linux/Mac/Win/Web</td> </tr> <tr> <td>Availability</td> <td>Open-Source</td> </tr> <tr> <td>License</td> <td>GPL3 with classpath exception</td> </tr> </tbody> </table>/applications/sboldesigner/Tue, 30 Jun 2020 00:00:00 +0000/applications/sboldesigner/<p>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.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Chris Myers</td> </tr> <tr> <td>Organization(s)</td> <td>University of Colorado, Boulder</td> </tr> <tr> <td>Programming Language</td> <td>Java/HTML/JS/CSS</td> </tr> <tr> <td>OS/Platform</td> <td>Web</td> </tr> <tr> <td>Availability</td> <td>Open-Source</td> </tr> <tr> <td>License</td> <td>BSD 2-Clause</td> </tr> </tbody> </table>/applications/shortbol/Tue, 30 Jun 2020 00:00:00 +0000/applications/shortbol/<table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Matthew Pocock, Anil Wipat</td> </tr> <tr> <td>Organization(s)</td> <td>Newcastle University, Turing Ate My Hamster Ltd</td> </tr> <tr> <td>Programming Language</td> <td>Scala</td> </tr> <tr> <td>OS/Platform</td> <td>Linux/Mac/Win/Web</td> </tr> </tbody> </table>/applications/tellurium/Tue, 30 Jun 2020 00:00:00 +0000/applications/tellurium/<p>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.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Kiri Choi</td> </tr> <tr> <td>Organization(s)</td> <td>University of Washington</td> </tr> <tr> <td>Programming Language</td> <td>C/C++</td> </tr> <tr> <td>OS/Platform</td> <td>Linux, Mac, Windows</td> </tr> <tr> <td>Availability</td> <td>Open-Source</td> </tr> <tr> <td>License</td> <td>BSD</td> </tr> </tbody> </table>/applications/tinkercell/Tue, 30 Jun 2020 00:00:00 +0000/applications/tinkercell/<p>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.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Herbert Sauro</td> </tr> <tr> <td>Organization(s)</td> <td>University of Washington</td> </tr> <tr> <td>Programming Language</td> <td>C/C++</td> </tr> <tr> <td>OS/Platform</td> <td>Linux, Mac, Windows</td> </tr> <tr> <td>Availability</td> <td>Open-Source</td> </tr> <tr> <td>License</td> <td>BSD</td> </tr> </tbody> </table>/applications/vpr/Tue, 30 Jun 2020 00:00:00 +0000/applications/vpr/<p>A repository of modular models of biological components. These models are reusable and composable, and facilitate model-driven design of biological systems.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Goksel Misirli, Anil Wipat</td> </tr> <tr> <td>Organization(s)</td> <td>Newcastle University</td> </tr> <tr> <td>Programming Language</td> <td>Java</td> </tr> <tr> <td>OS/Platform</td> <td>Linux/Web</td> </tr> </tbody> </table>