What is RRiki?

• Type in notes, cross-reference them and attach keywords.
• Enter citations - sources - by hand or import from pubmed.
• User interface is any webbrowser (Firefox was used during development).
• Use intuitive plain text (markdown) to format notes.
• See cross-referenced notes/sources at a glance.
• Use auto-generated BibTeX file in your LaTeX documents.
• Insert figures in notes using scalable vector graphics (svg)

Screenshots

• Front page showing database summary and list of keywords
• Example of a note with equations using latex and mathml
• Note with inline svg image
• v2.0 screenshots
• v1.2 screenshots
• v1.0 screenshots

Initial Setup

Linux

1. Install Ruby and Ruby on Rails [instructions and software here]
2. Install bluecloth if needed gem install bluecloth --include-dependencies
3. Install MySQL [go]
   Don't forget to create a user account and give it a password
4. Install CVS
5. Go to or create a directory (mydirectory) where you would like to keep the code. 
6. Grab the latest code from rubyforge:
   cvs -d :pserver:anonymous@rubyforge.org:/var/cvs/rriki login
   cvs -d :pserver:anonymous@rubyforge.org:/var/cvs/rriki checkout rriki
7. Under /mydirectory/rriki/config edit the database.yml file to fill in the username and password for MySQl.
8. Create the RRiki database via MySQL:
   cd /mydirectory/rriki/db [change to the rriki directory with database creationg scripts]
   mysql -uUser -pPassword [start the MySQL commandline client]
   mysql>create database rriki [create the RRiki database]
   mysql>use database rriki [tell MySQL to use this new database]
   mysql>source empty_rriki_db.sql [use the supplied script to create the tables in the database]
9. Start RRiki:
   cd /mydirectory/rriki
   ruby rrikiserver.rb [get ruby to run the server]
10. Open a webbrowser and goto http://localhost:3000/

Windows

1. Install Ruby and Ruby on Rails [instructions and software here]
2. Install bluecloth if needed gem install bluecloth --include-dependencies
3. Install MySQL (use the 'complete' install, not 'essentials') [go]
   Give root a password
4. Install tortoiseCVS.
5. Go to or create a directory (mydirectory) where you would like to keep the code. 
6. Right click in mydirectory and select 'CVS checkout'.
   protocol is :pserver
   server is rubyforge.org
   repository folder is /var/cvs/rriki
   user name is anonymous
   module is rriki
   Click OK and let the code flow in
7. Under /mydirectory/rriki/config edit the database.yml file to fill in the username and password for MySQL.
8. Create the RRiki database via MySQL:
   Got to Programs->MySQL->MySQL administrator, enter username and password
   Click on 'Restore' in the left hand pane
   Click 'Open Backup File' on right hand pane
   Find /mydirectory/rriki/db/empty_rriki_db.sql and click OK
   Then click 'Start Restore'. You can also use this to restore an existing RRiki database
   
   OR
   
   Open a commandline window
   mysql -uUser -pPassword [start the MySQL commandline client]
   mysql>create database rriki [create the RRiki database]
   mysql>use database rriki [tell MySQL to use this new database]
   mysql>source empty_rriki_db.sql [use the supplied script to create the tables in the database]
9. Start RRiki:
   cd /mydirectory/rriki
   ruby rrikiserver.rb [get ruby to run the server]
   Remember to allow Ruby Interpreter past the windows firewall
10. Open a webbrowser and goto http://localhost:3000/
11. If you like RRiki, set it up as a service:
    gem install mongrel_service [more details here]
    cd /mydirectory/rriki
    mongrel_rails service::install -Nrriki -eproduction -p3000

Updating

1. Backup your database:
   mysqldump -uUser -pPassword rriki > backupfile.sql
2. Backup your database
3. You did back up your database right?
4. Note the release date for your version of RRiki. Click on 'Front'. The summary page contains the text 'You are using RRiki YYYY.MM.DD...' this is the release date
5. Use CVS to update the code.
   Linux:
   cd /mydirectory/rriki [go into the code directory]
   cvs -d :pserver:anonymous@rubyforge.org:/var/cvs/rriki login
   cvs -d :pserver:anonymous@rubyforge.org:/var/cvs/rriki update rriki
   Windows:
   Navigate to the rriki directory
   Right click and select 'CVS update' and let the code update
6. Navigate to /db and look at the .sql files named update_YYYY.MM.DD.sql . In sequence, starting at the first date after your release date apply the updates as follows:
   mysql -uUser -pPassword
   mysql>use database rriki
   mysql>source update_YYYY.MM.DD.sql
7. Open a webbrowser and goto http://localhost:3000/
   

Also see:

• Zotero
• Kaspaliste
• NeuroScholar
• citer
• TiddlyWiki
• TiddlyMath