Summary of software requirements and optional tools
completely written in
||Windows (*)||MacOS (*)||Unix||Unix is required to
interface with Pathway Tools through JavaCyc|
Pathway Tools is necessary to interface Cyclone with BioCyc.|
||...||Oracle||pgSQL||mySQL||The distribution is pre configured for mySQL.|
Run Java programs
includes the OQL Editor
Cyclone is an open source API.|
To visualize graphs interactively
can already be exported as graphs and manipulated using Jung included in the Cyclone distribution.|
To browse XML files
XML files manually
opens and saves XML files.|
(*) Cyclone Core can work with a Windows or a MacOSX machine.
List of requirements and strongly recommended tools
Memory: 1 Gb Ram is really a minimum.
Storage: free 2 Gb minimum
Processor: 1 GHz minimum
Cyclone runs on any computer equipped with a Java virtual machine that complies with the Java 2 Standard Edition (J2SE)
Java implementations for Linux, Windows, and Solaris are available for download from Sun's java
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
Macos X JDK version 1.5 is required.
Java is also available on many other platforms. To check your version of Java type in the terminal:
Cyclone has been tested on mySQL and PostgreSQL.
In principle, RDBMS that are compatible with Hibernate should be usable with Cyclone: Oracle,
, Sybase, SAP DB,
MS SQL Server, IBM DB2,
HSQL, JNDI Datasource, Mckoi SQL, JSQL Driver, JTURBO, WebLogic, jTDS, Interbase (more).
You can use Cyclone with several RDBMS. 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 'cyclonedb' and a mySQL user, 'cycloneuser', with all privileges on cyclonedb.
Ask your RDBMS/database administrator to create it if needed.
If you want to use mysql, the procedure to install mySQL should be like this:
These commands are for quick reference only and should not be entered if you do not know what you do exactly.|
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');
To run Pathway Tools (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 and of course Pathway Tools.
If you have Pathway Tools already installed, you can skip this step but note that you will need to run Pathway Tools on the same computer as Cyclone.
To install BioCyc, read the installation guide.
This step is optional because Cyclone distributions provide a sample CycloneML file, containing an entire Pathway Genome database,
to be directly loaded into cyclonedb. It concerns Pseudomonas entomophila (Pseen58.xml)
"Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila PMID: 16699499".
But in normal configuration, Cyclone will generate a CycloneML file for each Pathway Genome DataBases in Pathway-Tools ( EcoCyc, MetaCyc, HumanCyc ... ).
We will be using the Eclipse software and some plugins for writing,
compiling, and testing programming assignments in the tutorial,
but you are welcomed to use your own Java Integrated Development Environment (JDE).
We recommend the use of 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
MacOS X users should use Eclipse instead of the JBOSS JDE. Download
eclipse-SDK-3.1.2 for MacOS X.
To install JBoss, follow these instructions:
- 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:
- Specify your workspace (example
- Exit Eclipse.
To run Cytoscape (optional)
You will need Cytoscape !