CD2H gitForager

Richard Smith-Unna

Login: blahah

Company: @fathomlabs

Location: Tigoni, Kenya

Bio: All my contributions on github issue trackers are placed in the public domain using the CC-Zero v1.0 (https://goo.gl/vUqlmV) dedication.

Blog: rik.smith-unna.com

Member of

Repositories

2014_chlamy_ccm: Chlamydomonas CCM perturbation RNAseq experiment
adventure-time: a web based environment for doing nodeschool adventures
AMI-diagrams-demo-paper: AMI-diagrams demo paper for WOSP 2014
ami-plugin: null
anki: Anki for desktop computers
append-tree: Model a tree structure on top off an append-only log.
array-split-stream: a nodeJS transform stream that splits arrays
assemblotron: Automated optimisation of de-novo transcriptome assembly
assemblotron-paper: Paper for Assemblotron
awesome-choo: :steam_locomotive: Awesome things related with choo framework
beau-selector: Run XPath or CSS selectors on arbitrary X(HT)ML documents in the command-line
bel: :dragon: A simple library for composable DOM elements using tagged template strings.
better-blast: An evolving prototype experimenting with some ways to improve on BLAST. If it works, we'll engineer an industrial-strength suite.
bettersam: Extended SAM file parsing in ruby
bindeps: Binary dependency management for Ruby
bioinformatics: Tools for bioinformatics
Bio.jl: Bioinformatics and Computational Biology Infrastructure for Julia
biopsy: Biopsy - the Bioinformatic Optimisation System
bioruby-blast: A wrapper for BLAST+ to make it an easy dependency for gems
bioruby-blat: TODO: one-line summary of your gem
bioruby-faster: A fast and simple parser for Fasta / FastQ files
blahah.github.io: my personal site
boxplots-paper: null
bullseye: :dart: Attach elements onto their target
cache-component: Cached bel components
cakefile-template: This is a cakefile template for coffeescript, docco and mocha
carpel: Bayesian segmentation Ruby gem
chain: bioinformatic pipelines with minimal effort
choo: :steam_locomotive::train::train::train: - sturdy 4kb frontend framework
choo-asyncify: make choo's events non-blocking ... :train: ...
choo-kanye: kanye (w)rapper for choo - easily add keyboard shortcuts to your choo app :steam_locomotive::train::train: + :train::notes::microphone:
choo-log: Development logger for choo
command_line_bootcamp: :computer: command-line bootcamp adventure in your browser
contrast-syntax: null
crb-blast: Condition Reciprocal Best Blast
csvconf-2016-reusing-science-output: Talk at CSVconf 2016 - massive-scale reuse of scientific outputs
d3-bootstrap-plugins: Porting some of bootstrap's plugins over to d3
dactyl-keyboard: Parameterized ergonomic keyboard
data: Repository for crowd-sourced data from genomics analysis of the UK ash dieback (Chalara fraxinea) outbreak 2012
datastructures: A collection of data structures in Ruby for my data structures challenge
datmon: cli tool for monitoring dats
dat-next-next: Experimental quick-n-dirty file sharing tool on top of dat
dexperimentr: Differential expression experiment workflows
dib-lab: Issue tracker and Web site for the Lab for Data Intensive Biology at UC Davis.
discovery-swarm: A network swarm that uses discovery-channel to find peers
docker-browser-server: Spawn and expose docker containers over http and websockets
docker-nightmare: Nightmare JS Headless image
dotfiles: dotfiles
dreamcatcher: use nightmare.js to automate tricky download / scraping scenarios
EBSeq: clone of EBSeq from bioconductor - beware experimental features
electron-builder: A complete solution to package and build a ready for distribution Electron app with ?auto update? support out of the box
electron-dat-test: testing dat in node and electron with sciencefair feeds
electron-debug: Adds useful debug features to your Electron app
electronify-server: electronify-server is a lightweight tool which starts a local web server and opens a url in an Electron shell
electron-rebuild: Package to rebuild native Node.js modules against the currently installed Electron version
electron-renderify: Browserify transform to allow bundling for Electron renderer processes
electron-sane-cachepath: set the electron cache path to a sane default for the current OS
elife-fathomlabs-statement-of-work: statement of work for development of scienceFair to create compelling offline-lens experience.
elife-sciencefair-metadata: eLife sciencefair datasource metadata
etherpad-archive: Archive your etherpads!
exploring_openness: OpenPlant March 2016
eXpress: Streaming fragment assignment and quantification for high-throughput sequencing.
facs: Fast and Accurate Classification of Sequences using Bloom filters
fellows-class-2015: The go-to place for materials, contributions and work for the 2015 Mozilla Fellows for Science.
fellows-onboarding-talk: null
fig1: null
flaveria_pipeline: null
folder-walker: Get a stream of files walking recursively through a folder
fs-readstream-progress: fs.createReadStream wrapper that emits progress events. Also works with hyperdrive.
get-package-readme: Get the GitHub readme for an npm package
ggplot2: An implementation of the Grammar of Graphics in R
graphsample: Subsample FASTQ by sampling connected components of a de-Bruijn graph
hint: Awesome tooltips at your fingertips
homebrew-science: :microscope: Scientific formulae for the Homebrew package manager
how_to_open: A collection of resources for doing work openly, creating open spaces and communities, and pushing for openness as a default
hyperdrive-binary-search: Binary search for entries in a hyperdrive archive by name
ice: Web based Registry platform for managing synthetic biological parts
idba_tran: Mirror of IDBA tran to provide a stable location for binary distribution
inquirer-autocomplete-prompt: Autocomplete prompt for inquirer
installing-node-tools: Cross-platform node tool installation instructions to be linked from READMEs/documentation
intro_to_open_science: A introductory course on open science
iOS-DiffMatchPatch: DiffMatchPatch iOS universal frameworks
isolator: Rapid and robust analysis of RNA-Seq experiments.
java-download: Node module to download a particular Java package (JVM / JDK) from Oracle
jekyll-midnight: Github Pages midnight theme ported to Jekyll
journal-scrapers: Journal scraper definitions for the ContentMine framework
JSoC2015: Proposal for Julia Summer of Code 2015
juju: A version manager for Julia
julia: The Julia Language: A fresh approach to technical computing.
kaia: kaia is our Working Golden Retriever puppy - this is her training management repo
kanye: Smash your keyboards with ease
KAT: The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
Kiko: :apple: Kiko, a Jekyll Theme
lens: A novel way of seeing content
lens-1: A Substance Writer for scientists.
lens-starter: Minimal Lens integration, use as a starting point for development
Lexicon.jl: Julia package documentation generator.
lorem-ipsum-dom: Returns a div containing the full 4500 words of Lorem Ipsum, in paragraphs
m-cli: ? Swiss Army Knife for Mac OS X
meteor-autocompletion: Autocompletion using data from MeteorJS collections
meteor-pagedown-bootstrap: Meteor smart package for pagedown-bootstrap
mirror-maker: Make mirrors of major bioinformatics repositories to serve the local science community
mocha-chai-coffee: Minimal Node.js module example with production code written in pure JavaScript and unit tests written in CoffeeScript. Tests written against the Mocha and Chai libraries. Continuous integration via Travis.
mozilla_science_fellowship: Keeping track of my work during my Mozilla Science Lab Fellowship
mozilla_science_fellowship_application: My application to the Mozilla Science Fellowship, 2015
nala-stream: WIP - very simple opinionated streaming natural language processing
natural: general natural language facilities for node
NoCaSS: Norwich-Cambridge Student Symposium website
node-browserify: browser-side require() the node.js way
node-config: Node.js Application Configuration
norma: Convert XML/SVG/PDF into normalised, sectioned, scholarly HTML
npm-dedupe-symlinks: Dedupes a package even if it contains symbolic links
npmlog: The logger that npm uses
nv: Always-on-top version of nvAlt
nvm: Node Version Manager - Simple bash script to manage multiple active node.js versions
oai-pmh: OAI-PMH 2.0 harvester module for nodejs
oarr-compendium: Compendium of the "state of the art" in the philosophy and practice of Open Access and Reproducible Research
opencon_2015_talk: Opening ourselves up: my talk at OpenCon Cambridge 2015
open-data-primers: [project] collection of exercises to educate people in open data use/reuse
openresearch-talk-2014: Slides for my talk at OpenResearchCambridge 2014
orb14_bestpractice: Sketch of a community site for best-practise data processing and reporting in bioinformatics
pdf-narcissist: Hide a PDF inside a thumbnail of its own first page
pdf-to-png: render a PDF to a PNG with electron
peercast: torrent-stream + chromecast
penguegg: Rockhopper Penguin Egg project
phd: My phd thesis (WIP)
Phylogenetics.jl: The Julia package for analysis of evolution and phylogeny
planets: Planning our escape from Earth
pouchdb: :koala: - PouchDB is a pocket-sized database.
prompt: a beautiful command-line prompt for node.js
pubpeer-pubmed: Chrome plugin to integrate PubPeer comments with PubMed articles
ralink_RT5370_linux_driver: ralink RT5370 linux driver fixed to compile with v3+ kernel
rb-libsvm: Ruby language bindings for LIBSVM
RecipSnpFinder: null
related-reading: Queries several open online medical/scientific resources and returns some agregated/organised results.
remark: A simple, in-browser, markdown-driven slideshow tool.
rest-api-doc: Documentation for CrossRef's REST API
rnaseq_tools: miscellaneous tools for analysis of RNA-seq data
rnaseq_training: WIP
r-novice-gapminder: Introduction to R for non-programmers using gapminder data.
root: a lightweight prototypical middleware web framework
round-robin: Multiple sequence annotation
rpi-3g-wifi-hub: null
rubocop: A robust Ruby code analyzer, based on the community Ruby style guide.
ruby-factorial-cached: This is a ruby gem which adds cached factorial operation to your code.
sailfish: Rapid Alignment-free Isoform Quantification from RNA-Seq Reads
salmon: Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments
samtools: fork of samtools from sourceforge
sciencefair: search, browse, and download open access papers (WIP)
sciencetoolbox: An index of open scientific software
scraperJSON-demo-paper: scraperJSON and ContentMine stack demo paper for WOSP 2014
search-index: A persistent, network resilient, full text search library for the browser and Node.js
search-index-adder: The indexing module for search-index
seqtk: Toolkit for processing sequences in FASTA/Q formats
seqtkrb: Fast FASTA/FASTQ operations. Ruby gem wrapper for seqtk (https://github.com/lh3/seqtk)
sequenceserver: Intuitive local web frontend for the BLAST bioinformatics tool
Shannon: RNA-Seq
share-archive: archive all the data from OSF share
sheetify: :sparkles: Modular CSS bundler for browserify
shoco: shoco is a compressor for small text strings
Sigil: Sigil is a multi-platform EPUB ebook editor
sleuth: Inspect kallisto RNA-Seq output
slidewinder: This repo has moved to the slidewinder organisation
smoothscroll: Scroll Behavior polyfill
snap: Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
sodium-native: Low level bindings for libsodium
solvers: Solvers - improve our world
solvers-gene-motifs: Solvers.io project to predict gene expression from motif combinations in promoters
ssi_fellowship_application: My application to the SSI fellowship [http://www.software.ac.uk/fellowship-programme]
statsample: A suite for basic and advanced statistics on Ruby.
studyGroup: null
studyGroupLessons: One-hour introductory lessons on ideas and tools in coding and data wrangling for research.
styles: Repository of CSL citation styles.
Sublime-IJulia: An IJulia Frontend for Sublime Text 3
swc_concept_graph: null
tagma: The organisational tool we've always wanted, but haven't been able to find
tape-run-electron: run tests in electron like a boss
templates: Personal project templates for use with mafintosh/create-project
tensorflow: Open source software library for numerical computation using data flow graphs.
TGAC-2014-genome-annotation: Course materials for the genome annotation part of the TGAC SeqAhead course 2014
TGAC-2014-transcriptome-optimisation: Course materials for the transcriptome assembly optimisation part of the TGAC SeqAhead course 2014
theme-leap-day: A Jekyll Bootstrap theme based on Leap-day
timetrap: Simple command line timetracker
transfuse: Merge transcriptome assemblies
transrate: Understand your transcriptome assembly
transrate-paper: Paper for transrate
transrate-tools: Reading bam files and aggregating read mapping information about sequences
transrate-viewer: experiments in d3.js for viewing transrate results
unist-util-find: Unist node finder utility. Useful for working with remark, rehype or retext.
unmark: An open source to do app for bookmarks. Made by Plain.
vms: My virtual machine (docker/vagrant) file collection
WebMemex: The refactored version of the (Re)search-Engine
website: The prosemirror.net website
which: the 'which' gem on rubygems.org
windowmover: Position windows on a screen
working-open-workshop: A repo to collect all materials and resources related to Mozilla Science Lab's Working Open Workshop
yeoman.github.io: Yeoman website
YRDropdownView: YRDropdownView is a view library for displaying stylish alerts, warnings, and errors.
yunodb: A portable, persistent, electron-embeddable fulltext search + document store database for node.js

Commits To

Repository	Most Recent Commit	# Commits
lh3/seqtk	2015-06-17 17:37:36.0	1
pjotrp/bioinformatics	2014-02-20 08:29:53.0	1
BioJulia/BioFmtSpecimens	2014-08-28 09:08:02.0	1

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.