Cytoscape Wiki|
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| I have been playing around with using [http://db.apache.org/derby/ Derby] to associate databases with cytoscape networks. Derby can serve as an embedded relational database in Java applications. This may be a solution for use cases that need real-time access relatively stable data, such as gene aliases and annotations. Getting Derby to work within a Cytoscape plugin was not trivial, so I wanted to share that experience. | Derby can serve as an embedded relational database in Java applications. This may be a solution for use cases that need real-time access to relatively stable data, such as gene aliases and annotations. Getting Derby to work within a Cytoscape plugin was not trivial, so I wanted to share that experience. |
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http://db.apache.org/derby/ - Offical Apache Derby site http://db.apache.org/derby/quick_start.html - Useful Quick Start site for newbies [http://db.apache.org/derby/derby_downloads.html#Software+required+to+build+Derby Related software] - Reference to OSGi (osgi.jar) * Relevant discussion threads relating to OSGi * [http://mail-archives.apache.org/mod_mbox/db-derby-dev/200512.mbox/%3C001001c602ae$adcdd270$6400a8c0@Apollo%3E thread#1] * [http://mail-archives.apache.org/mod_mbox/incubator-felix-dev/200603.mbox/%3C44061826.7010505@ungoverned.org%3E thread#2] |
* http://db.apache.org/derby/ - Offical Apache Derby site * http://db.apache.org/derby/quick_start.html - Useful Quick Start site for newbies * [http://db.apache.org/derby/derby_downloads.html#Software+required+to+build+Derby Related software] - Reference to OSGi (osgi.jar) * Relevant discussion threads relating to OSGi * [http://mail-archives.apache.org/mod_mbox/db-derby-dev/200512.mbox/%3C001001c602ae$adcdd270$6400a8c0@Apollo%3E thread#1] * [http://mail-archives.apache.org/mod_mbox/incubator-felix-dev/200603.mbox/%3C44061826.7010505@ungoverned.org%3E thread#2] |
Derby can serve as an embedded relational database in Java applications. This may be a solution for use cases that need real-time access to relatively stable data, such as gene aliases and annotations. Getting Derby to work within a Cytoscape plugin was not trivial, so I wanted to share that experience.
Important Links
http://db.apache.org/derby/ - Offical Apache Derby site
http://db.apache.org/derby/quick_start.html - Useful Quick Start site for newbies
[http://db.apache.org/derby/derby_downloads.html#Software+required+to+build+Derby Related software] - Reference to OSGi (osgi.jar)
- Relevant discussion threads relating to OSGi
Overview
...more to come