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apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.

apple-snail-expression-pattern-ontology

Apple Snail Expression Pattern Ontology

biological-spatial-ontology

An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces

chado

the GMOD database schema

chickencoopcontroller

my chicken coop controller

class_test

cshl_ngs

NGS DNA analysis for the CSHL 2012 Programming for Biology course

cshlprogforbiol2018

CSHL Prog for Bio 2018, trinity rnaseq section

evop2018

findpackmule

Uses TIRs of a Mule to blast to the genome to see if the TE has picked up any other genomic sequence

gbrowse

the Generic Genome Browser

go-site

A collection of metadata, tools, and files associated with the Gene Ontology public web presence.

intermine

A powerful open source data warehouse system

jbplugin-screenshot

JBrowse plugin that adds button which uses phantomJS to take browser screenshot

learninggit

just some stuff to practice using git and github

mtea

Mosquito TE Annotation

obi

The Ontology for Biomedical Investigations

obofoundry.github.io

OBO Foundry Ontology Registry

ols-treeview

This is the standalone widget for the OLS treeview

ontology-starter-kit

Bootstrap an OBO Library ontology

ontology_search

Tripal extension module that carries out hierarchical ontology searches

owlery

Owlery is a set of REST web services which allow querying of an OWL reasoner containing a configured set of ontologies.

pato

PATO - the Phenotype And Trait Ontology

pfb.github.io

pfb2012

Code and samples from lecture and review sessions

pfb2017

Programming for Biology 2017

pfb2017_problemsets

Solutions for PFB2017 Problem Sets

pfb2018_testing

testing stuff

pfb_problemsets

Solutions for PFB Problemsets

pfb_web