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| When you load a lot of plugins at once, sometimes Cytoscape crashes even if you have a lot of memory in your machine. This is because | When you load a lot of plugins at once, sometimes Cytoscape crashes even if you have a lot of memory in your machine. This is because Java heap called ''Permanent'' region is full. To avoid this problem, you can do the following: |
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In the file, you can see the following options: {{{ -Xss5M -Xmx1024M -XX:MaxPermSize=128m |
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In general, if you increase '''''-XX:MaxPermSize''''', you can load many plugins at once. Default size is 64M, so probably 128M is enough in most cases. |
(Under construction!!)
Introduction
From version 2.6, Cytoscape works as a web service client for public biological databases.
What is a Web Service?
Web Service is a standardized mechanism for computers to communicate to each other to exchange data. There are lots of public databases in
Goal of this Tutorial
You can learn the following functions of Cytoscape from this tutorial:
- How to import networks from public databases
- How to mapping IDs
- Merge networks from multiple data sources
Setup
To do this tutorial, you need to install the following plugins:
- Pathway Commons plugin (installed by default)
- NCBIClient Plugin
- NCBIEntrezGeneUserInterface Plugin
- IntActWSClient Plugin
BiomartClient Plugin
AgilentLiteratureSearch Plugin
- MiMI plugin
AdvancedNetworkMerge Plugin
Note: Out of Memory Problem
When you load a lot of plugins at once, sometimes Cytoscape crashes even if you have a lot of memory in your machine. This is because Java heap called Permanent region is full. To avoid this problem, you can do the following:
# for Mac/Linux cytoscape.sh
# for Windows cytoscape.bat
In the file, you can see the following options:
-Xss5M -Xmx1024M -XX:MaxPermSize=128m
In general, if you increase -XX:MaxPermSize, you can load many plugins at once. Default size is 64M, so probably 128M is enough in most cases.
Tutorial 1: Start from Keyword
In this exercise, you are going to learn how to search interactions by keyword.
Select File-->
Open NCBI Client and search pparg and human[ORGN]
- Import annotations
Use Pathway Commons and search PPARG for human
- Load all pathways and merge them into one big network
Tutorial 2: Start from List of Genes
Tutorial 3: Merge Multiple Networks
== Tutorial 4:
Optional
How did I get the list of genes on a specific pathway?
This is a bit out of focus of this protocol, but here is how I got the original list of genes. To do the following, you need to install RubyScriptingEngine Plugin.
Here is how:
Open the BioRuby Console and get list of genes by using KEGG API
# First, get list of genes for KEGG Pathway mmu03320 (PPAR Signaling Pathway) . . . B i o R u b y i n t h e s h e l l . . . Version : BioRuby 1.2.1 / Ruby 1.8.6 bioruby> gene_list = keggapi.get_genes_by_pathway("path:mmu03320") JRuby limited openssl loaded. gem install jruby-openssl for full support. http://wiki.jruby.org/wiki/JRuby_Builtin_OpenSSL ==> ["mmu:103968", "mmu:104086", "mmu:108078", "mmu:11363", "mmu:11364", "mmu:113868", "mmu:11430", "mmu:11450", "mmu:11770", "mmu:11806", "mmu:11807", "mmu:11814", "mmu:11832", "mmu:12140", "mmu:12491", "mmu:12894", "mmu:12895", "mmu:12896", "mmu:13117", "mmu:13118", "mmu:13119", "mmu:13122", "mmu:13124", "mmu:13167", "mmu:14077", "mmu:14079", "mmu:14080", "mmu:14081", "mmu:14626", "mmu:14933", "mmu:15360", "mmu:16202", "mmu:16204", "mmu:16592", "mmu:16956", "mmu:17436", "mmu:18534", "mmu:18607", "mmu:18830", "mmu:19013", "mmu:19015", "mmu:19016", "mmu:20181", "mmu:20182", "mmu:20183", "mmu:20249", "mmu:20250", "mmu:20280", "mmu:20411", "mmu:216739", "mmu:22190", "mmu:22227", "mmu:22259", "mmu:225579", "mmu:235674", "mmu:26457", "mmu:26458", "mmu:26459", "mmu:26569", "mmu:30049", "mmu:433256", "mmu:50790", "mmu:56473", "mmu:57875", "mmu:622384", "mmu:66113", "mmu:669888", "mmu:74147", "mmu:74205", "mmu:74551", "mmu:78070", "mmu:80911", "mmu:83995", "mmu:83996", "mmu:93732"] bioruby> query = gene_list.join(" ").gsub(/mmu:/, "") ==> "103968 104086 108078 11363 11364 113868 11430 11450 11770 11806 11807 11814 11832 12140 12491 12894 12895 12896 13117 13118 13119 13122 13124 13167 14077 14079 14080 14081 14626 14933 15360 16202 16204 16592 16956 17436 18534 18607 18830 19013 19015 19016 20181 20182 20183 20249 20250 20280 20411 216739 22190 22227 22259 225579 235674 26457 26458 26459 26569 30049 433256 50790 56473 57875 622384 66113 669888 74147 74205 74551 78070 80911 83995 83996 93732" bioruby>
By learning simple BioRuby commands, you can access lots of functions to access KEGG and other databases. For more information, please visit: