Intermine

Motivation
CCTS/BMI group plans to establish an Intermine server at UAB in order to support genomics (and other -omic) reseach. The tool provides a way to link datasets with disparate datatypes together in a single warehouse. We particularly expect it to be useful for the analysis of gene sets: storage, collaboration/sharing and researcher self-service.

Web Resources for Intermine

 * Home page http://www.intermine.org/


 * About Intermine http://intermine.org/wiki/InterMine


 * Intermine Overview http://intermine.org/wiki/InterMineOverview


 * Prerequisite and downloading     http://intermine.org/wiki/GettingStarted   http://intermine.org/wiki/Prerequisites
 * Hardware requirements   http://intermine.org/wiki/Hardware


 * QuickStart http://intermine.org/wiki/QuickStart


 * TroubleShooting http://intermine.org/wiki/TroubleshootingTips


 * Download/Get intermine http://intermine.org/wiki/SVNCheckout


 * Intermine use cases  http://intermine.org/wiki/InterMineUseCases

Examples of databases using Intermine

 * RatMine: http://ratmine.mcw.edu/
 * modENCODE: http://www.modencode.org/
 * Flymine: http://www.flymine.org/
 * Yeastmine : http://yeastmine.yeastgenome.org/yeastmine/begin.do
 * Targetmine : http://targetmine.nibio.go.jp/
 * Metabolicmine : http://www.metabolicmine.org/

Installation notes for Intermine on Ubuntu 64bit
Step A: Install all prerequistite tools required for Intermine installation

The basic notes for Installation are present on the Intermine website at http://intermine.org/wiki/Prerequisites

Additional install notes. This Installation is done on a Virtual box (running on win 7 64bits). 1. Install subversion sudo apt-get install subversion

2. Install sunjava6jdk sudo add-apt-repository "deb http://archive.canonical.com/ lucid partner" (added a source repository) Or add following to the /etc/apt/osurcelist deb http://archive.canonical.com/ubuntu lucid partner deb-src http://archive.canonical.com/ubuntu lucid partner Commands to run - sudo apt-get update sudo apt-get install sun-java6-jdk 3. Install ant a. Download ant from http://www.reverse.net/pub/apache//ant/binaries/apache-ant-1.8.2-bin.tar.gz or http://ant.apache.org/ b. export JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.26 c. export ANT_HOME=/home/ranjit/ant   (ant is in my home directory) d. export PATH=${PATH}:${ANT_HOME}/bin These variable can be included in a batch script which automatically runs after system login. 4. Install Tomcat Download tomcat, unzip it and place it at a location you know. Just start/stop the server as (ant is in my home directory) /home/ranjit/apache-tomcat-6.0.33/bin/startup.sh (to start the server) /home/ranjit/apache-tomcat-6.0.33/bin/shutdown.sh (to stop it) Add a manager for tomcat by editing file $CATALINA_HOME/conf/tomcat-users.xml   ($CATALINA_HOME is the installation directory)   

Add java memmory requirements To avoid java.lang.OutOfMemory errors, specify the JVM heap size in $TOMCAT_HOME/bin/tomcat.sh. You can specify '-Xmx256m -Xms128m' as part of TOMCAT_OPTS. OR  Edit the file $TOMCAT_HOME/bin/startup.sh and insert the following line, substituting for the desired value, eg. Bash Shell:  export CATALINA_OPTS=”-Xms(min heap)m -Xmx(max heap)m” If you get the error message: java.lang.OutOfMemoryError: PermGen space you need to add the argument -XX:MaxPermSize=128m to CATALINA_OPTS, in addition to any argument you use to set the heap size. 5. Install postgresql 8.4 sudo apt-get install postgresql-8.4 Make following changes in file as suggested in postgre installation section of intermine page at http://intermine.org/wiki/Prerequisites sudo vim /etc/postgresql/8.4/main/postgresql.conf Create/Identify a userid and password. (help https://help.ubuntu.com/8.04/serverguide/C/postgresql.html) Edit sudo vim /etc/postgresql/8.4/main/pg_hba.conf  to use "md5" MD5 authentication sudo /etc/init.d/postgresql-8.4 restart        (restart the server)

Install Bioseg into postgres sudo apt-get install postgresql-contrib-8.4 sudo apt-get install postgresql-server-dev-8.4 Download bioseg from http://www.bioinformatics.org/bioseg/wiki/ Unzip and Install it as  make USE_PGXS=t clean make USE_PGXS=t make USE_PGXS=t install When a database is created it can be added to it by  psql (database) <bioseg.sql psql (database) <btree_gist.sql To start/stop/restart postgressql do.. sudo /etc/init.d/postgresql-8.4 start   (replace start with stop/restart)

6.Install Junit Download from http://www.junit.org/ Copy to the ant lib directory, (may be apache-ant-1.6.5/lib/) Add to the java classpath with this command, replacing X.X with the version number. like export CLASSPATH=/home/ranjit/ant/lib/junit4.10/junit-4.10.jar

Step B: Download and Install Intermine svn co svn://subversion.flymine.org/branches/intermine_0_98 Thats all :)

Step C: Creating a example database using Malaria called Malariamine. Please follow the steps given at http://intermine.org/wiki/GettingStarted