Cyclone

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Cyclone distributions

Cyclone is available as two different distributions. This table will help you to choose the one you need. Please, check the requirements before installing.

Cyclone Platform	Cyclone Core
All Cyclone Java API functionalities (connect to Biocyc server, upload a Pathway Genome database from Biocyc into Cyclone database ...)	All Cyclone Java API functionalities (connect to Biocyc server, upload a Pathway Genome database from Biocyc into Cyclone database ...)
Include a graphical user interface to query in Object Query Language the database provided by JBoss Eclipse IDE	-
Pre-configured for mySQL	-
Works with Linux	Works with Linux, Windows or MacOS
Easy to install	For good developers only
About 240 MB	About 40 MB

These two distributions are both available at Sourceforge web site. Please register before downloading them.

Cyclone Platform

Installation

-Download Cyclone Platform. Please register before.
-Uncompress the archive: tar zxvf cyclone.platform.[version].tar.gz
-Execute eclipse: ./cyclone.platform/cyclone-eclipse

Configuration

-To configure which workspace to use go tto the File menu>'Switch Workspace...' and enter the path of your workspace './workspace'
-To configure Cyclone database parameters, edit Cyclone_Core/hibernate.properties to match your configuration (database url, user, password).
-To configure Cyclone path to Pathway-Tools, edit Cyclone_Core/src/config/cyclone.conf.xml to link to Pathway-Tools executable. [Optional]
-To deploy Cyclone with this minimal customization, run the ant default build of Cyclone_Core/cyclone.build.xml. To do so, click on the second green arrow, the one with the small case or direct right click on the file and 'Run as Ant build'. The console panel should inform you on the different executed steps: creation of the java classes based on the default schema Cyclone_Core/schema/cyclone.xsd, creation of the database.
-Then refresh the eclipse environment by doing a right-click on Cyclone_Core on the left frame, followed by 'Refresh' action.

Two Flash illustrations of these steps are available:

Configure Cyclone to match with your configuration (database, pathway-tools localisation)
Flash Tutorial.

Test the connection between Biocyc and Cyclone Platform
Flash Tutorial

You can now go to the Tutorial page.

Cyclone Core

Installation
- Download and extract the Cyclone distribution ( Cyclone Core or Cyclone Platform), please register before downloading.
- To verify checksum, type cksum Cyclone-[].tar.gz you should get the number provided in the file information on the sourceforge website (Optional).
- Then extract the file, tar -xvf Cyclone-[].tar.gz
- Change rights on the configuration file, chmod -R 777 ./CyClone_Core

Configure Cyclone access to Pathway Tools Server.

- Edit this file ./CyClone_Core/src/config/cyclone.conf.xml and set the property of gproot4Server to the command that enables you to start Pathway Tools in server mode. ( depends on your version) For example : ./aic-export/ecocyc/genopath/released/pathway-tools -api or ./aic-export/ecocyc/genopath/released/pathway-tools -lisp

Configure CycloneDB

- Edit the file ./CyClone_Core/hibernate.properties to enter the properties of your RDBMS. By default the mySQL RDBMS is selected. If you want to use Oracle or an other DB, comment the mySQL code and uncomment your DB code.
- Create Database (default name should be 'cyclonedb').
- Enter the url, login and password to access your DB. The url for mySQL looks like this: jdbc:mysql://localhost:3306/cyclonedb where localhost is the ip of the computer that hosts mysql. 3306 is the standard port for mysql connections. Login and Password should correspond to an account that has all privileges on the database, cyclonedb.

If you want to use mySQL:
- Edit the file ./CyClone_Core/hibernate.properties to enter the properties of your RDBMS/database. By default the mySQL RDBMS is selected. If you want to use Oracle or an other DB, comment the mySQL code and uncomment your DB code.
- Enter the url, login and password to access your DB. The url for mySQL looks like this: jdbc:mysql://localhost:3306/cyclonedb where localhost is the ip of the computer that hosts mysql. 3306 is the standard port for mysql connections. 'cyclonedb' is the name of the database that should exist. Login and Password should correspond to an account that has all privileges on the database, cyclonedb.

If you want to use another RDBMS:
If you use another RDBMS other than mySQL, you will need to make additional modifications. (Cyclone has been tested also with pgSQL and hsql) :
- Comment the mysql paragraph in ./CyClone_Core/hibernate.properties , fill in and uncomment the corresponding paragraph of your data base.
- Create a directory ./CyClone_Core/lib/MYDB and put the Java Data Base Connector (jdbc) of your db in this folder. If you do not have it, you can try the Sun jdbc drivers page.
- Edit the ./CyClone_Core/hyperjaxb2.paths.xml and correct the paragraph that starts with CYCLONE COMPATIBLE DB, you have to fill in and uncomment the corresponding paragraph of your RDBMS/Database.
- Edit the ./CyClone_Core/cyclone.build.xml and edit the paragraph hyperjaxb2.db.path: uncomment the line corresponding to your RDBMS/database path. Example: keep the line <path refid="mysqldb.path" /> in cyclone.build.xml and

 <path id="mysqldb.path">   <fileset id="mysqldb.fileset" dir="${hyperjaxb2.lib.dir}/mysql">        <include name="mysql-connector-java-3.1.10-bin.jar"/>      </fileset>   </path>

in hyperjaxb2.db.path

Now you can try Cyclone!

- Jump to the Tutorial page.
- Run your commands in the terminal, like for example:

java -jar CyClone_Core_fat-[].jar 
-function:Biocyc2Xsd -orgids:Meta -max:10

Testing and Reporting

Bug and test reports are very welcome. Do not hesitate to dump as much output as possible when reporting any problem you might experience to our bug report system.

In any case, please include at least the following information in your bug report :
- the version of Cyclone you are using (or the date of the daily snapshot)
- the version of BioCyc
- your operating system
- the version of Java
- the way you use Cyclone : as a standalone application or as a tool program for BioCyc

Cyclone is an Open Source project: future development depends on the contributions that will be made by its user community. Please do not hesitate to submit your suggestions for new functionalities (email: cyclone at genoscope.cns.fr ).

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