Software

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This is an attempt at listing open source and free to use software and software components for biohackers.

Free as in freedom

Circular DNA (plasmid) viewers/editors

  • Open Vector Editor: In-browser. JS. Renders in SVG. Depends on React. Not quite ready for production but actively developed - October 2016
  • 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.
  • Coral plasmid viewer In-browser. JS + d3. Single-file. Does not handle overlapping features well.
  • JBEI Vector Editor: In-browser. Very nice but written in flash
  • 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, unmaintained.
  • 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)

Linear DNA viewers/editors

For viewing linearized DNA in a zoomed out view where the individual bases are not shown but annotations are visible.

  • GENtle2: In-browser, node.js, scrollable vertical layout, seems sluggish, unmaintained.


DNA/RNA/AA sequence viewers/editors

For directly editing the sequence on a single nt/aa basis. Like a text editor but for DNA/RNA/AA.

Free as in beer

Plasmid/sequence viewers/editors