Client library for communication with InterMine web-services
view intermine gene network interaction using cytoscape.js
Client library for communication with InterMine web-services
Visualize gene expression by tissue and stage with help of expression charts. Easily see which expressions are up- or down-regulated.
Visualize relation and linkages between the proteins associated with a particular gene.
Visualize gene and protein interaction networks using [cytoscape.js](http://js.cytoscape.org/).
Intermine's component library
InterMine Identifiers Widget
ui widgets for displaying query results in interactive tables
Generates a scaffold for BlueGenes tools
BlueGenes wrapper for protvista protein feature viewer
Bluegenes Pathway Visualizer is a tool made for [BlueGenes](http://bluegenes.apps.intermine.org) following BlueGenes Tool API. Add more description of your tool here! :)
Bluegenes Interaction Network is a tool made for [BlueGenes](http://bluegenes.apps.intermine.org) following BlueGenes Tool API. Add more description of your tool here! :)
Bluegenes JBrowse Tool is a tool made for [BlueGenes](http://bluegenes.apps.intermine.org) following BlueGenes Tool API. Add more description of your tool here! :)
Visualize protein structures using different types of 3D models. You can select from multiple [RCSB](https://www.rcsb.org/) PDB ID.
Bluegenes ESYN Viewer is a tool made for [BlueGenes](http://bluegenes.apps.intermine.org) following BlueGenes Tool API. Add more description of your tool here! :)
Bluegenes GWAS Visualizer is a tool made for [BlueGenes](http://bluegenes.apps.intermine.org) following BlueGenes Tool API. Add more description of your tool here! :)
GO Concept Relation is a tool made for [BlueGenes](http://bluegenes.apps.intermine.org) following BlueGenes Tool API. Add more description of your tool here! :)
Bluegenes Protein Tissue Localisation is a tool made for [BlueGenes](http://bluegenes.apps.intermine.org) following BlueGenes Tool API. Add more description of your tool here! :)
Bluegenes List Enrichment Visualizer is a tool made for [BlueGenes](http://bluegenes.apps.intermine.org) following BlueGenes Tool API. Add more description of your tool here! :)
Visualize gene ontology terms by their amount of matches for items in a list. Allows you to filter and adjust the enrichment results.
Bluegenes Human Tissue Expression Visualizer is a tool made for [BlueGenes](http://bluegenes.apps.intermine.org) following BlueGenes Tool API. Add more description of your tool here! :)
Visualize gene expression by disease using ArrayExpress data. Easily see which expressions are up- or down-regulated.
= Webservice Client Library for InterMine Data-Warehouses This library provides an interface to the InterMine webservices API. It makes construction and execution of queries more straightforward, safe and convenient, and allows for results to be used directly in Ruby code. As well as traditional row based access, the library provides an object-orientated record result format (similar to ActiveRecords), and allows for fast, memory efficient iteration of result sets. == Example Get all protein domains associated with a set of genes and print their names: require "intermine/service" Service.new("www.flymine.org/query"). new_query("Pathway") select(:name). where("genes.symbol" => ["zen", "hox", "h", "bib"]). each_row { |row| puts row[:name]} == Who is this for? InterMine data warehouses are typically constructed to hold Biological data, and as this library facilitates programmatic access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services may find it especially useful: * FlyMine (http://www.flymine.org/query) * YeastMine (http://yeastmine.yeastgenome.org/yeastmine) * RatMine (http://ratmine.mcw.edu/ratmine) * modMine (http://intermine.modencode.org/release-23) * metabolicMine (http://www.metabolicmine.org/beta) == How to use this library: We have tried to construct an interface to this library that does not require you to learn an entirely new set of concepts. As such, as well as the underlying methods that are common to all libraries, there is an additional set of aliases and sugar methods that emulate the DSL style of SQL: === SQL style service = Service.new("www.flymine.org/query") service.model. table("Gene"). select("*", "pathways.*"). where(:symbol => "zen"). order_by(:symbol). outerjoin(:pathways). each_row do |r| puts r end === Common InterMine interface service = Service.new("www.flymine.org/query") query = service.new_query("Gene") query.add_views("*", "pathways.*") query.add_constraint("symbol", "=", "zen") query.add_sort_order(:symbol) query.add_join(:pathways) query.each_row do |r| puts r end For more details, see the accompanying documentation and the unit tests for interface examples. Further documentation is available at www.intermine.org. == Support Support is available on our development mailing list: dev@intermine.org == License This code is Open Source under the LGPL. Source code for this gem can be checked out from https://github.com/intermine/intermine-ws-ruby
= Biological Extensions to the InterMine Webservice Client Library This library is a set of extensions to the InterMine Webservices client, providing access for data in biological formats. It directly extends the InterMine classes, providing extra methods to the Query class. == Example Get all sequences for proteins on "h", "r", "eve", "bib" and "zen": require "rubygems" require "intermine/service" require "intermine/bio" s = Service.new("www.flymine.org/query") puts s.query("Gene").select("proteins").where(:symbol => %w{h r eve bib zen}).fasta Process the locations of these genes one at a time: s.query.select("Gene").where(:symbol => %w{h r eve bib zen}).bed do |line| process line end == Who is this for? InterMine data warehouses are typically constructed to hold Biological data, and as this library facilitates programmatic access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services may find it especially useful: * FlyMine (http://www.flymine.org/query) * YeastMine (http://yeastmine.yeastgenome.org/yeastmine) * RatMine (http://ratmine.mcw.edu/ratmine) * modMine (http://intermine.modencode.org/release-23) * metabolicMine (http://www.metabolicmine.org/beta) These extensions are aimed at bioinformaticians looking to integrate these sources of data into other workflows. For details on constructing queries, see the intermine documentation. == Support Support is available on our development mailing list: dev@intermine.org == License This code is Open Source under the LGPL. Source code for all InterMine code can be checked out from svn://subversion.flymine.org/flymine
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