Cyclone

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Quick install

Download and extract the Cyclone archive Cyclone_Core.tar.gz

Chmod the configuration file chmod -R 777 ./CyClone_Core

Edit the file ./CyClone_Core/hibernate.properties to enter the properties of your mySQL database. By default the mySQL database 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/cyclone where localhost is the ip of the computer that hosts mysql. 3306 is the standard port for mysql connections. 'cyclone' is the name of the database that should exist. Login and Password should correspond to an account that has all privileges on the database, cyclone.

Requirements and Installations

Hardware
Memory: 1 Gb Ram is really a minimum.
Storage: free 2 Gb minimum
Processor: 1 GHz minimum

Java
Cyclone runs on any computer equipped with a Java virtual machine which complies with the Java 2 Standard Edition (J2SE) 5.0 (or later) specifications. Java implementations for Linux, Windows, and Solaris are available for download from Sun's java website. Recent versions of MacOS X (version greater than 10.4) include an old version of Java implementation as standard. On such platforms, installation of the J2SE 5.0 Macos X JDK version 1.5 is required. Java is also available on many other platforms: if in doubt, contact your vendor. To check your Java version type in the terminal: java -version

Database
The following database management systems can be used with Cyclone: mySQL, Oracle, PostgreSQL, Sybase, SAP DB, MS SQL Server, IBM DB2, HSQL, JNDI Datasource, Mckoi SQL, JSQL Driver, JTURBO, WebLogic, jTDS, Interbase (more).

To run BioCyc (optional)
You will need Linux -- any that uses a version 2.2 or higher kernel, OpenMotif (not LessTif), glibc 2.1+, Perl, mySQL or Oracle.

To run Cytoscape (optional)
You will need cytoscape.

All the sources of Cyclone are distributed. Cyclone binaries are distributed in .jar (Java ARchive) format configured for mysql. You can always get the latest release version from the binaries directory of the download area or from CVS.

We will guide you in installing Cyclone : We will guide you through the installation process of Cyclone. We first provide guidelines for the installation of BioCyc/PathwayTools and Eclipse. These steps are not required if you already have these softwares installed, or if you do not want to use them.

Then we will guide you to install Cyclone. Finnally a tutorial demontrates how to use Cyclone.
Some basic knowledge about Java, BioCyc and development tools is required.

Pathway Tools Installation (optional)

If you have Pathway Tools already installed, you can skip this step but take care that you need to run Pathway Tools on the same computer as Cyclone. The installation guide is at http://bioinformatics.ai.sri.com/ptools/installation-guide/released/unix.html; here you will find a quick installation guide.

The Pathway Tools software is a bioinformatics software system for pathway analysis of genomes, and for creating Pathway/Genome Databases (PGDBs). A pathway/genome database (PGDB), such as EcoCyc, is a bioinformatics DB that integrates genomics data with detailed functional annotations of the genome, such as descriptions of metabolic and signaling pathways. A PGDB is a type of model-organism DB. The tool is freely available to academics for research purposes, and is available for a fee to commercial institutions. Pathway Tools was developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International.
For more information, visit http://bioinformatics.ai.sri.com/ptools/
You will also find a Pathway Tools Installation Guide there (includes Solaris and Linux system requirements and tutorials).
Follow the steps of the installation process and become familiar with biocyc. Browse Ecocyc for example for 1 hour or two if you are not familiar with it.

- Download ptools-linux.tar.gz. The URLs pointing to these distributions can be found in the confirmation email that is sent after signing the BioCyc license agreement.
- Here we use the example of the installation of Pathway Tools version 9.5, don't hesitate to follow the exact procedure of installation of our version.
- Extract ptools tar xzf ptools-linux.tar.gz (it should take about 2 minutes)
- run ./aic-export/ecocyc/genopath/9.5/install/config-ptools then type Enter.
- Chmod the executable file chmod -R 775 ./aic-export
- Download to your home directory some additional libs that are required: pathwaytools.libs.tar.gz
- Extract them gunzip pathwaytools.libs.tar.gz
- Extract them tar -xvf pathwaytools.libs.tar
- Now you should have a folder pathwaytools.libs
- Add at the end of your profile .bashrc file in your home directory the line: export LD_LIBRARY_PATH=HOME_DIRECTORY/pathwaytools.libs:${LD_LIBRARY_PATH} that links to the directory you have just extracted.
- Close and open a new terminal (load your new profile, to be sure you can execute : echo $LD_LIBRARY_PATH or type ~/.bashrc
- Make a symbolic link to execute Pathway Tools easily : ln -s ./aic-export/ecocyc/genopath/9.5 released
- Now you can test if the Pathway Tools installation has been achieved.
- You can run Pathway Tools with its interface: ./aic-export/ecocyc/genopath/released/pathway-tools
- Quit
- You can run Pathway Tools with its server: ./aic-export/ecocyc/genopath/released/pathway-tools -api or ./aic-export/ecocyc/genopath/released/pathway-tools -lisp depending of your Pathway Tools version.
- Exit Pathway Tools, type :exit

Java 5.0 Installation (required)

If you have java 5.0 or greater already installed, you can skip this step.
- Download Java 5.0
- Follow the installation guide provided by Sun Installation notes

mySQL Installation (optional)

You can use Cyclone with several databases. Here we will help you to install mySQL quickly. Furthermore, you will find many tutorials on the web to install mySQL on your platform. For more information, see http://mysql.org

You will need a dedicated Database that we will name 'cyclone'. Ask your database administrator to create it if you do not know how to create it.

Here are only some lines to remind you how to install mysql if you have not installed it before.

bin/mysqld_safe --user=mysql &

Then Securing the Initial MySQL Accounts

bin/mysqladmin -u root password new_password_here
bin/mysql -u root -p 
CREATE DATABASE Cyclone;

/usr/local/mysql/bin/mysql -u root
mysql> SET PASSWORD FOR ''@'localhost' = PASSWORD('newpwd');

Eclipse Installation (advised)

We will be using the Eclipse software and some plugins for writing, compiling, and testing programming assignments in this tutorial, but you can use your own Java Integrated Developement Environment (JDE) to access Cyclone.
Eclipse is an Open Source community whose projects are focused on providing an extensible development platform and application frameworks for building software. Eclipse provides extensible tools and frameworks that span the software development lifecycle, including support for modeling, language development environments for Java. Note : Eclipse does not include a Java runtime environment (JRE). You will need at least a 5.0 level Java runtime or Java development kit (JDK) installed on your machine in order to run Eclipse.

We advise you to use the JBoss Eclipse IDE which is a special version of Eclipse already packaged with different plugins to enable easy managing of hibernate, xml files instead of Eclipse. JBoss is a special distribution of Eclipse with additional features.

- Go to http://www.jboss.com/products/jbosside/downloads and download JBossIDE-1.5-Bundle-linux-gtk.tar.gz

- Extract the file (tar xzf JBossIDE-1.5-Bundle-linux-gtk.tar.gz)

- chmod -R 777 ./eclipse/

- Run eclipse: ./eclipse/eclipse

- Specify your workspace (example /home/user/workspace)

- Exit Eclipse.

MacOS X users should use Eclipse instead of the JBOSS JDE. Download eclipse-SDK-3.1.2 for MacOS X.

Cyclone Installation & Configuration

- Download and extract the Cyclone archive Cyclone_Core.tar.gz

- Chmod the configuration file chmod -R 777 ./CyClone_Core

- 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

If you want to use mySQL
Edit the file ./CyClone_Core/hibernate.properties to enter the properties of your database. By default the mySQL database 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/cyclone where localhost is the ip of the computer that hosts mysql. 3306 is the standard port for mysql connections. 'cyclone' is the name of the database that should exist. Login and Password should correspond to an account that has all privileges on the database, cyclone.

If you want to use a distinct data base.
If you use a distinct database other than mySQL, you will need to make additional modifications. (Cyclone has been tested also with pgSQL and hsql) :
1/ Comment the mysql paragraph in ./CyClone_Core/hibernate.properties , fill in and uncomment the corresponding paragraph of your data base.
2/ 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.
3/ 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 database.
4/ Edit the ./CyClone_Core/cyclone.build.xml and edit the paragraph hyperjaxb2.db.path: uncomment the line corresponding to your 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-1.0.beta.jar 
-function:Biocyc2Xsd -orgids:Meta -max:10

.
For more information about how to use Cyclone in the terminal, see the usage example page.

Cyclone in Eclipse

This is an optional step. It is required only if you want to use Eclipse.

- Copy or move the Cyclone directory into your eclipse workspace: cp -r ./CyClone_Core /home/user/workspace/Cyclone_Core or mv ./CyClone_Core /home/user/workspace/Cyclone_Core

- Run eclipse: ./eclipse/eclipse &

- Close the Eclipse welcome page if any.

- Select in the Eclipse menu File>Import... and then select 'Existing Projects into Workspace'.

- Next select your root directory (should be /home/user/workspace/CyClone_Core).

- Click the Finish button. Then Eclipse will build the workspace.

- If any error appears, please check that your project is configured for Java 5.0: Right click on Cyclone Project > Java Compiler> Enable project specific settings > Set Compiler compliance level to 5.0

- On the 'Package Explorer' tab on the left of the screen, open CyClone_Core > src/config > cyclone.conf.xml. The file will open in the main tab.

- If not already done, open the property gproot4Server and set it to the command that enables you to start Pathway Tools in server mode.

- Save the file.

Right-click on cyclone.build.xml and select menu 'Run as>2 Ant Build...'
In the pop-up window, in the 'Classpath' tab, click on 'User Entries' and 'Add JARs'.
In the second pop-up window, select Cyclone_core>lib>junit>junit.jar
Click Apply and Run this will execute the default task described at Architecture-Pipeline
Note: don't be afraid if the log show the error : [junit] test fr.cns.genoscope.cyclone.db.tests.RoundtripTestCase FAILED

The Ant Build should take between 1 and 10 minutes.

- Now you can run the Tutorial examples. Jump to the Code Examples page.

Testing and Reporting

Any test of compatibility on other platforms or in a different setting than the one presented here is welcome. You are invited to report results of such tests to us. Do not hesitate (feel encouraged, in fact) to dump as much output as possible when reporting any problem you might experience to our bug report system.

In any case, include at least the following informations 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

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