Last Updated Mon Sep 4 2006 Simbiome is a trusted, online electronic resource that organizes and presents relevant resources for physics-based simulation of biomedical structures and related entities in biology and life sciences. Simbiome is managed by te staff at the Simbios center at Stanford. The code to run Simbiome was built by Jonathan Dugan and Bill Katz at Stanford University. A poster describing te work is available here: http://www.bisti.nih.gov/ahm2006/abstracts/D-2.pdf#search=%22svn%2Fsimbiome%22 Contact: Jonathan Dugan dugan@matsonsystems.com dugan@biocontact.org Simbiome is released under the MIT Licence http://www.opensource.org/licenses/mit-license.php INSTALLATION 1) Get Ruby >1.8.4 installed. As of the latest update, the current stable release of Ruby is 1.8.5. Simbiome was build and tested to run on 1.8.4, as most of the pakages and automated installs support this version. Once installed, you can check the version: >ruby -v 2) Install the latest Rails "gem" >gem install rails and follow the instructions. Gem is an application that comes with Ruby to add functionality to the language. The Simbiome code depends on Rails being installed to function. 3) Get a local copy of postsgres installed and running see http://www.postgresql.org 4) Create a user and DB "simbiome" as the local user who owns the PostgreSQL database: >createuser simbiome >createdb simbiome 5) Follow instructions in simbiome/trunk/doc/00README.legacy_data to pull in legacy data >psql -f pg_dump_legacy_table -U simbiome This will create and populate a table called legacy in the simbiome databse with test data that works in Simbiome. Note that this data is now OLD and out of date, and it is provided for example purposes only. 6) Edit simbiome/rails/config/database.yml Access to the DB is controlled in config file simbiome/rails/config/database.yml - this needs to be eidted to "see" the database 7) Build the database tables >cd /simbiome/trunk/rails >rake migrate This will run the migration scripts located in /simbiome/trunk/rails/db/migrate These are Ruby scripts and will build the neccesary tables for Simbiome and take the data from the legacy table and populate the simbiome tables. 8) Test your database connection >cd simbiome/rails >./script/console This provides and interactive environment within the application Then type: >> r = Resource.find(1) This will set the variable r to the databse value of the first resource. If this works, then the Rails application is accessing the database, and you should see this: => # 9) Run the web application > ./simbiome/rails/script/server This will start a webrick (a minimal. local web server) and serve the application on port 3000 10) Customizing The root of the web application is located here simbiome/trunk/rails/public/ here you will fine images, stylesheets and javascripts The Rails application which generates most of the pages is located simbiome/trunk/rails/app and in the subdirectories The Rails configuration files are located simbiome/trunk/rails/config and includes the files for the environment setting for the Rails application, the database connections, and the routing that translates URLS into the Rails application