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Ben J Woodcroft wwood

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wwood / eupathdb_ubiquity.js
Created October 30, 2008 01:29
[DEPRECATED: a version for Ubiquity 0.5 is now available at http://gist.github.com/183528] Ubiquity 0.1 commands for EuPathDB databases such as PlasmoDB and ToxoDB.
CmdUtils.CreateCommand({
name: "plasmodb",
takes: {"plasmodb_id": noun_arb_text},
homepage: "http://gist.github.com/20872",
author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
contributors: ["Ben J. Woodcroft"],
license: "GPL3",
description: "Go to a PlasmoDB Gene page in a new window",
preview: "Go to a PlasmoDB Gene page in a new window.",
@wwood
wwood / scholar-search-non-br.js
Created November 3, 2008 05:32
[DEPRECATED - merged into upstream] A google scholar ubiquity command that is not brazil-specific. Adapted from http://static.isnotworking.com/scholar-search.html
var noun_type_article = {
_name: "article title",
suggest: function( text, html ) {
var suggestions = [CmdUtils.makeSugg(text)];
return suggestions;
}
}
CmdUtils.CreateCommand({
name: "scholar-search",
@wwood
wwood / gist:30621
Created December 1, 2008 04:27
Ubiquity access to wormbase gene pages
CmdUtils.CreateCommand({
name: "wormbase gene ",
takes: {"term": noun_arb_text},
homepage: "http://gist.github.com/30621",
author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
contributors: ["Ben J. Woodcroft"],
license: "GPL3",
description: "Search Wormbase",
preview: "Go to a Wormbase search in a new window.",
@wwood
wwood / orthomcl.js
Created December 1, 2008 06:08
Ubiquity command for OrthoMCL Gene and Group
CmdUtils.CreateCommand({
names: ["orthomcl"],
arguments: [{label: "gene_or_group_accession", nountype: noun_arb_text, role: 'object'}],
homepage: "http://gist.github.com/30649",
author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
contributors: ["Ben J. Woodcroft"],
license: "GPL3",
help: "Go to an OrthoMCL gene or group page in a new window",
description: "Go to an OrthoMCL gene or group page in a new window",
preview: "Go to an OrthoMCL gene or group page in a new window",
@wwood
wwood / ensemblUbiquity.js
Created January 10, 2009 05:41
Ubiquity Ensembl searching
CmdUtils.CreateCommand({
names: ["ensembl"],
arguments: [{label: "ensemble_gene_or_protein_or_transcript_id", nountype: noun_arb_text, role: 'object'}],
homepage: "www.ensembl.org",
author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
contributors: ["Ben J. Woodcroft"],
license: "GPL3",
description: "Search Ensembl",
preview: "Search Ensembl.",
@wwood
wwood / localhost.js
Created March 4, 2009 00:43
Commands for interacting with locally installed services (my Rails blast server and stuff)
CmdUtils.CreateCommand({
names: ["genbank-blast-local"],
arguments: [{role: 'object', nountype: noun_arb_text, label: 'genbank id'},
{role: 'goal', nountype: noun_arb_text, label: 'blast database'},
{role: 'instrument', nountype: noun_arb_text, label: 'blast program'},
{role: 'location', nountype: noun_arb_text, label: 'taxa'}],
homepage: "http://gist.github.com/73638",
help: 'genbank_blast_local <b>entrez_id</b> [with <b>blast_program</b>] [to <b>blast_database_name</b>]',
author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
contributors: ["Ben J. Woodcroft"],
@wwood
wwood / pfam.js
Created March 4, 2009 22:07
CmdUtils.CreateCommand({
name: "pfam",
takes: {"pfam_id": noun_arb_text},
author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
contributors: ["Ben J. Woodcroft"],
license: "GPL3",
description: "Go to a PFAM family page in a new window",
preview: "Go to a PFAM family page in a new window.",
execute: function(plasmodb_id) {
@wwood
wwood / texmed.js
Created March 24, 2009 11:50
CmdUtils.CreateCommand({
names: ["texmed_pmid"],
arguments: [{role: 'object', nountype: noun_arb_text}],
homepage: "http://www.bioinformatics.org/texmed",
author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
contributors: ["Ben J. Woodcroft"],
license: "GPL3",
description: "Retrieve the bibtex entry for a pubmed identifier.",
preview: "Retrieve the bibtex entry for a pubmed identifier.",
@wwood
wwood / ensembl.rb
Created April 23, 2009 00:03
# To change this template, choose Tools | Templates
# and open the template in the editor.
module Bio
class Ensembl
# Ensembl species taken from ensembl/modules/Bio/EnsEMBL/Registry.pm
# Ensembl version 52 (December 2009)
# transformed manually to hash form
ENSEMBL_SPECIES_HASH = {'ENSRNO'=>['Rat','Rattus norvegicus'],
'ENSMUS'=>['Mouse','Mus musculus'],
@wwood
wwood / tolweb.js
Created May 19, 2009 11:10
CmdUtils.CreateCommand({
names: ["life"],
arguments: [{label: "taxon", nountype: noun_arb_text, role: 'object'}],
author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
contributors: ["Ben J. Woodcroft"],
license: "GPL3",
description: "Go to tolweb.org page in a new window",
preview: "Go to tolweb.org page in a new window.",
execute: function(args) {