Software: Difference between revisions
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* [https://github.com/calipho-sib/sequence-viewer neXtProt sequence-viewer]: neXtProt protein/DNA sequence viewer (javascript) - From SIB CALIPHO group. ([https://cdn.rawgit.com/calipho-sib/sequence-viewer/master/examples/index.html demo]) | * [https://github.com/calipho-sib/sequence-viewer neXtProt sequence-viewer]: neXtProt protein/DNA sequence viewer (javascript) - From SIB CALIPHO group. ([https://cdn.rawgit.com/calipho-sib/sequence-viewer/master/examples/index.html demo]) | ||
* [https://github.com/calipho-sib/feature-viewer neXtProt feature-viewer]: Library to visualize protein (and DNA, w/ work) sequence features in javascript using D3 - From SIB CALIPHO group; neXtProt project ([https://cdn.rawgit.com/calipho-sib/feature-viewer/v0.1.44/examples/index.html demo]) | * [https://github.com/calipho-sib/feature-viewer neXtProt feature-viewer]: Library to visualize protein (and DNA, w/ work) sequence features in javascript using D3 - From SIB CALIPHO group; neXtProt project ([https://cdn.rawgit.com/calipho-sib/feature-viewer/v0.1.44/examples/index.html demo]) | ||
* [https://github.com/VoigtLab/dnaplotlib dnaplotlib]: DNAplotlib is a library that 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. | |||
* [https://github.com/Synbiota/GENtle2 GENtle2]: In-browser, node.js, no overlapping features support. Annoying to get up and running. | * [https://github.com/Synbiota/GENtle2 GENtle2]: In-browser, node.js, no overlapping features support. Annoying to get up and running. | ||
* [http://wishart.biology.ualberta.ca/PlasMapper/ PlasMapper]: Server side browser-based, java+tomcat, no genbank/sbol support (auto-annotation only) | * [http://wishart.biology.ualberta.ca/PlasMapper/ PlasMapper]: Server side browser-based, java+tomcat, no genbank/sbol support (auto-annotation only) | ||
Revision as of 19:23, 7 October 2016
This is an attempt at list out open source and free to use software and software components for biohackers.
Free as in freedom
Plasmid/sequence viewers/editors
- Giraffe UI: In-browser, js. Depends on Giraffe db for feature metadata. Apparently what AddGene uses?
- AngularPlasmid: In-browser, js (angular), no overlapping features support. Actively developed as of late 2016.
- JBEI Vector Editor: In-browser, very nice but written in flash
- bio-widgets-flex: Modularized version with js integration.
- neXtProt sequence-viewer: neXtProt protein/DNA sequence viewer (javascript) - From SIB CALIPHO group. (demo)
- neXtProt feature-viewer: Library to visualize protein (and DNA, w/ work) sequence features in javascript using D3 - From SIB CALIPHO group; neXtProt project (demo)
- dnaplotlib: DNAplotlib is a library that 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.
- GENtle2: In-browser, node.js, no overlapping features support. Annoying to get up and running.
- PlasMapper: Server side browser-based, java+tomcat, no genbank/sbol support (auto-annotation only)
- DNApy: Non-web integrated desktop app, python
- BioSVG: Perl.
Do we really not have a modern, open source, web-based plasmid viewer without framework dependencies and with overlapping feature support? We just need something like the JBEI Vector Editor but written in js :/ - Marc Juul Christoffersen 18:43, 7 October 2016 (EDT)
