/tag/repository/RepositoryWowchemy (https://wowchemy.com)en-usWed, 08 Jun 2022 00:00:00 +0000/images/logo.svg/tag/repository//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/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/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/flapjack/Tue, 30 Jun 2020 00:00:00 +0000/applications/flapjack/<p>Flapjack is a data management and analysis app for genetic circuit characterization to store, share, mix, analyze and plot your SynBio data.It has a database backend, a webapp as frontend and a Python API, this allows you to access your data remotely using an intuitive user interface and be able to integrate it easily in Python workflows for automation.</p> <table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Gonzalo Vidal</td> </tr> <tr> <td>Organization(s)</td> <td>Newcastle University</td> </tr> <tr> <td>Programming Language</td> <td>Python, JavaScript</td> </tr> <tr> <td>OS/Platform</td> <td>Linux, MacOS, Windows, Web</td> </tr> <tr> <td>Availability</td> <td>Open-Source</td> </tr> <tr> <td>License</td> <td>MIT License</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/ice/Tue, 30 Jun 2020 00:00:00 +0000/applications/ice/<table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Hector Plahar</td> </tr> <tr> <td>Organization(s)</td> <td>Lawrence Berkeley National Lab</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> <tr> <td>License</td> <td>BSD</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/sbolvalidator/Tue, 30 Jun 2020 00:00:00 +0000/applications/sbolvalidator/<p>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.</p> <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;"> <iframe src="https://www.youtube.com/embed/tQ28wj4fmW8" 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>Zach Zundel</td> </tr> <tr> <td>Organization(s)</td> <td>University of Utah</td> </tr> <tr> <td>Programming Language</td> <td>Python/Java</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/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/sbolme/Tue, 30 Jun 2020 00:00:00 +0000/applications/sbolme/<table> <thead> <tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Contact Person</td> <td>Hiroyuki Kuwahara</td> </tr> <tr> <td>Organization(s)</td> <td>KAUST</td> </tr> <tr> <td>Programming Language</td> <td>HTML/PHP/Python/SQL</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/synbiohub/Tue, 30 Jun 2020 00:00:00 +0000/applications/synbiohub/<p>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.</p> <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;"> <iframe src="https://www.youtube.com/embed/9C96PwM0jQQ" 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>Anil Wipat</td> </tr> <tr> <td>Organization(s)</td> <td>Newcastle University</td> </tr> <tr> <td>Programming Language</td> <td>JavaScript</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>BSD 2-Clause</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>