Software: Difference between revisions
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This is an attempt at | This is an attempt at listing open source and free to use software and software components for biohackers. | ||
= Free as in freedom = | = Free as in freedom = | ||
Revision as of 12:34, 10 October 2016
This is an attempt at listing 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, seems sluggish, 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)
