This is your work, valued

SF Bay Area

Ian Holmes

Elite
@ihh

time to larn those machines a thing or two about human nature

holmeslab.org/

graphgram. Graph grammar library

52

dart. DNA, Amino Acid and RNA Tests

33

bracery. Procedural text generator, somewhat compatible with Tracery

23

gfftools. Perl scripts for working with the GFF format

16

bilby. Jax code for functional genomics ML

14

trajectory-likelihood. Calculate indel trajectory likelihoods using methods of Miklós, Lunter & Holmes (2004), De Maio (2020), and Holmes (2020)

14

dnastore. Software for error-tolerant coding of information into DNA sequences using finite-state transducers.

12

abrowse. Multiple sequence alignment browser

11

bbcmicrobot-codec. A wrapper for dasm and @bbcmicrobot

10

zoogas. Z00 G45. A simple entropy-maximizing game on a Lotka-Volterra cellular automaton

8

quaff. FASTA/FASTQ alignment

5

tree-align-view. A multiple alignment viewer with integrated phylogeny and structure browsing.

4

pixelzoo. C

4

carder. Lightweight wrapper to Gajus Kuizinas' Swing for building card-swiping interactive fiction on the web.

3

stockholm-js. Parser for Stockholm format

2

boswell. IDE for multiplayer choice-based fiction

2

brokentelephone. Phylogenetic alignment parlor game

2

gertie. Perl

2

bioe241. Materials for UC Berkeley class BioE241

2

rnastatalign-paper. Paper: "Evolutionary Triplet Models of Structured RNA", PLoS Comp Biol 2009

2

hg19-perl. Perl scripts for munging UCSC hg19 table dumps

2

EvolPairHMM. Evolutionary Pair HMM

1

phylogenetic-likelihood. JavaScript implementation of phylogenetic likelihood calculations

1

ihh.github.io. Holmes lab website

1

jukes-cantor. Jukes-Cantor formula and distance matrix

1

spongelife. JavaScript

1

wikimess. Wiki Messenger

1

latex-tutorial. TeX

1

funkscene. A series of interesting choices.

1

nanopair. C

1

schooz. Scheme hypertext framework

1

transducer-tutorial. TeX

1

tag-parser. Algorithms to parse biological tree-adjoining grammars

1