Ben J Woodcroft wwood
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| CmdUtils.CreateCommand({ | |
| names: ["plasmodb"], | |
| arguments: [{label: "plasmodb_id", nountype: noun_arb_text, role:'object'}], | |
| 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
/ scholar-search.js
Created
September 3, 2009 02:08
Google Scholar Ubiquity Plugin (Ubiquity 0.5 compatible) Another copy of http://static.isnotworking.com/scholar-search.html
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| var noun_type_article = { | |
| _name: "article title", | |
| suggest: function( text, html ) { | |
| var suggestions = [CmdUtils.makeSugg(text)]; | |
| return suggestions; | |
| } | |
| } | |
| CmdUtils.CreateCommand({ | |
| names: ["scholar"], |
wwood
/ pubmed0.5.js
Created
September 3, 2009 01:19
A pubmed search plugin for ubiquity that works with Ubiquity 0.5. Inspired by http://hublog.hubmed.org/archives/001747.html
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| /* This is a template command. */ | |
| CmdUtils.CreateCommand({ | |
| names: ["pubmed"], | |
| icon: "http://www.ncbi.nlm.nih.gov/favicon.ico", | |
| description: "Searches <a href='http://www.ncbi.nlm.nih.gov/pubmed'>pubmed</a>.", | |
| help: "type 'pubmed something', enter. The something is like searching from the front page of PubMed", | |
| author: { name: "Ben J. Woodcroft", email: "b.woodcroft near pgrad.unimelb.edu.au"}, | |
| license: "GPL", | |
| arguments: [{role: 'object', nountype: noun_arb_text}], | |
| execute: function execute(args) { |
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| CmdUtils.CreateCommand({ | |
| names: ["amigo", "go"], | |
| arguments: [{label:"GO term query", nountype:noun_arb_text, role:'object'}], | |
| author: { name: "Ben J. Woodcroft", email: "b.woodcroft before pgrad.unimelb.edu.au"}, | |
| contributors: ["Ben J. Woodcroft"], | |
| license: "GPL3", | |
| description: "Go to AmiGO search result for your query of GO terms", | |
| preview: "Go to AmiGO search result for your query of GO terms", | |
| execute: function(args) { |
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| CmdUtils.CreateCommand({ | |
| names: ["entrez-nucleotide"], | |
| arguments: [{role: 'object', nountype: noun_arb_text, label: 'entrez_id'}], | |
| author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"}, | |
| contributors: ["Ben J. Woodcroft"], | |
| license: "GPL3", | |
| execute: function(args) { | |
| var urlString = "http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore&term="+args.object.text; | |
| Utils.openUrlInBrowser(urlString); |
wwood
/ ezproxy.js
Created
June 14, 2009 08:52
commands to reload the current page through an EZproxy. Written so that different proxies from different universities to gain access to scholarly articles
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| CmdUtils.CreateCommand({ | |
| DEFAULT_EZPROXY_PREF: "extensions.ubiquity.ezproxy_default", | |
| names: ["set default ezproxy"], | |
| arguments: [{label: "ezproxy_stub", nountype: noun_arb_text, role: 'object'}], | |
| homepage: "http://gist.github.com/129610", | |
| author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"}, | |
| contributors: ["Ben J. Woodcroft"], | |
| license: "GPL3", | |
| description: "Sets the default proxy. Eg. set-default-ezproxy http://ezproxy.library.uq.edu.au/login?url=", |
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| 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) { |
wwood
/ ensembl.rb
Created
April 23, 2009 00:03
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| # 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'], |
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| 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.", | |
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| 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) { |