Timothy Danford

Login: tdanford

Company: null

Location: Cambridge, MA

Bio: null

Blog: http://pinboard.in/u:arthegall

Blog: http://pinboard.in/u:arthegall

Repositories

adam

A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

avocado

A Variant Caller, Distributed

battleship

Board games for my daughter

BayesDB

A Bayesian database for querying the probable implications of data as easily as SQL databases query the data itself

bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.

bdg-services

Utility classes for wrapping services or other interfaces around a Spark/ADAM cluster. Apache 2 licensed.

bdg-utils

General (non-omics) code used across BDG products. Apache 2 licensed.

bigwig4j

A BigWig Reader, in Java

bioinfo-algorithms

Experimentation

bwa

Burrow-Wheeler Aligner

cavitynesting

"Cavity Nesting" Wildlife Database

cell-type

Code for working with the Cell Type (CL) Ontology

chrome-cli

Control Google Chrome from the command line

cnv

CNV calling functions and scripts

ContEst

Spark implementation of the ContEST contamination estimation algorithm.

dartmouth-atlas

Java utilities for data from the Dartmouth Atlas of Health Care.

datacleaning

Simple scripts for data munging and cleaning.

datalog-experiment

Scala experiments with Datalog

datamining-36-350-homework

Source Code for Fall 2009 36-350 Homework

data-use-ontology

A simple ontology for representing data use and research purpose constraints.

djeocoder

A standalone geocoder, derived from the OpenBlock use of GeoDjango.

docs

My writings.

dotfiles

Colourful & robust OS X configuration files and utilities.

dropwizard-configurable-assets-bundle

An implementation of an AssetBundle for use in Dropwizard that allows user configuration.

ffauto

Tools for managing my fantasy football draft and team.

ga4gh-flask-api

Flask implementation of part of the GA4GH WS API

graphite-experiment

Setting up Graphite inside of Vagrant.

gse-stereo-t

Mirror of SVN Repository for the STEREO-T project.

ideals

Experimentation with computer algebra in Java

java-json-schema

Java implementation of a JSON Schema loader and validator

java-obo

Java library for parsing and handling OBO ontologies.

letterplayer

An interface to evaluate Letterpress games, and suggest alternative plays.

load_tools

Tools for efficient and error-tolerant loading of data into SciDB

luigi-workflows

null

metamodel_extras

Extra pluggable modules for Apache MetaModel (but licensed with LGPL)

nci_design

null

neurocommons

Mirror(s) of Packages from Neurocommons

noaa-postgis

Enabling searching geo data from NOAA using Postgis and Postgresql

nrc-wildlife

Code for Rachel's Wildlife Projects

obroker

An implementation of a web-broker for new term requests to an ontology.

ontologies

Work-related Ontology Development

ontology-broker-tests

Validation and Test Code for the Ontological Term Broker

osm-utils

Utilities for OSM (Open Street Map) Data.

ott-data

null

pybamview

Browser based application for viewing bam alignments

qc-metrics

Read and variant metrics, useable for pipeline quality control purposes

rasch-model

Implementation of a Rasch Model

rdf-utils

Utilities for working with RDF data.

RNAdam

An RNA fusion transcript pipeline built on top of ADAM. Apache 2 licensed.

scheduling-simulator

Simulator for writing and evaluating cloud schedulers

snark

A nested vector library for Scala.

spark

Mirror of Apache Spark

spark-start

Template for starting with Spark

spark-template

A template for projects using Spark, Avro, and Parquet.

spring-jersey-template

Personal template for creating web services with Spring and Jersey

sunfish

Sunfish: a Python Chess Engine in 111 lines of code

table-service

Turning simple text tables into web services.

tdanford.github.io

null

text-corrector

Text Rewriting Rules for Free-Text Parsing and Validation

turtle-graphics

Turtle Graphics, String Rewriting, and L-Systems.

vcfc

An experimental VCF flattener in C

vcf_loader

Prototype loader for the Variant Call Format files

Commits To