Ian Holmes

http://holmeslab.org/

UC Berkeley SF Bay Area time to larn those machines a thing or two about human nature

Results 69 issues of


Ian Holmes

Timers and clocks

1

comment

- Regular interval timer - One-off timeout - Time spent on last page

Implement search & replace

Should be applied separately to each defined symbol. It will be easy to break the parser with this, so re-parse the entire graph afterwards.

Try harder NOT to encode co-ordinates in implicit links

They should dangle at a fixed position relative to the parent (determined by include rank), unless they've been moved.

Automatically promote implicit nodes to defined nodes

Connecting an edge to an implicit node should trigger its promotion to a separately defined node.

Implement undo for playthrough

Remove internal links & reveals from tweets

http -> https redirect for bracery.org

Experiment with CloudFront...

Add UI for user to upload own GAF file for their species

enhancement

Allow positive & negative counts in geneSet

1

comment

Implement HMMER's handling of X's (for protein) and N's (for DNA)

HMMER weights IUPAC degenerate emissions using the reciprocal of the perplexity of the underlying match state (see `esl_abc_FExpectScore` function in HMMER3 source) This has the effect that the "score" for...

enhancement