Ian Holmes

Login: ihh

Company: UC Berkeley

Location: SF Bay Area

Bio: null

Blog: http://biowiki.org/IanHolmes

Blog: http://biowiki.org/IanHolmes

Member of

1. Evolutionary Software Foundation
2. Generic Model Organism Database Project

Repositories

bioe241

Materials for UC Berkeley class BioE241

biomake

Make-like build system based on prolog

biomake-appnote

Applications Note for Biomake

bossmachine

Bioinformatics Open Source Sequence machine

boswell

IDE for multiplayer choice-based fiction

bracery

Procedural text generator, somewhat compatible with Tracery

brokentelephone

Phylogenetic alignment parlor game

choicescript

ChoiceScript is a language for developing multiple-choice games.

compromise

modest natural-language processing in javascript

d3

A JavaScript visualization library for HTML and SVG.

darkroomjs

Extensible image editing tool in your browser

dart

DNA, Amino Acid and RNA Tests

dnastore

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

dracula

JavaScript browser based layout and representation of connected graphs.

facesjs

A JavaScript library for generating vector-based cartoon faces

fast5

A C++ header-only library for reading Oxford Nanopore Fast5 files

figlet-js

JavaScript parser for FIGlet fonts

funkscene

A series of interesting choices.

gertie

null

gfftools

Perl scripts for working with the GFF format

gp120sim

Indel Historian simulation benchmark

grained

Generate animated noise texture with grained.js

graphgram

Graph grammar library

guile-json

A basic JSON parser written in Guile scheme

hdf5.node

A node module for reading/writing the HDF5 file format.

hg19-perl

Perl scripts for munging UCSC hg19 table dumps

indel-review

null

jbrowse

AJAX Genome Browser

klib

A standalone and lightweight C library

latex-tutorial

null

naivechain

A blockchain implementation in 200 lines of code

nanocall

An Oxford Nanopore Basecaller

nanopair

null

nanopair-data

null

quaff

FASTA/FASTQ alignment

quaff-appnote

Applications Note for quaff

rnastatalign-paper

Paper: "Evolutionary Triplet Models of Structured RNA", PLoS Comp Biol 2009

rotunda

null

schooz

Scheme hypertext framework

shotgunpoet

null

sigma.js

an open-source lightweight JavaScript graph drawing library

swing

A swipeable cards interface. The swipe-left/swipe-right for yes/no input. As seen in apps like Jelly and Tinder.

tag-parser

Algorithms to parse biological tree-adjoining grammars

transducer-tutorial

null

Twiki-to-Mediawiki

Converts twiki .txt files to the mediawiki format.

VivaGraphJS

Graph drawing library for JavaScript

wiki-messenger

A messenger client with predictive, procedurally generated text using a communally-edited context free grammar

wtfgenes-paper

null

zoogas

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

Commits To