Category:NCBO Virtual Machine Image

The NCBO Virtual Machine Image contains a pre-installed, pre-configured version of commonly used NCBO software. The image was created using VMWare and is available for download from NCBO ADD_DOWNLOAD_LOCATION_HERE.

The following software is included on the image:

• BioPortal Ontology Services (BioPortal Core)
• BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)
• BioPortal Admin (a UI for administering BioPortal Ontology Services)
• Annotator
• Resource Index

Please see below for how-to documentation for managing the software and running data population for Annotator and Resource Index.

Getting Started

• You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer as this hostname as 'example'.
• Change default passwords
  • Operating System
    • Username: root
    • Password: changemeNOW
  • BioPortal Admin User
    • Username: admin
    • Password: changeme
• Add an ontology using the BioPortal Admin User here: http://example/ontologies/new
  • BioPortal Ontology Services will automatically process new ontologies every hour at 30 minutes past the hour. This processing includes:
    • Parsing any new, unparsed ontologies
    • Calculating a set of metrics for these ontologies
    • Indexing these ontologies for use with search
• Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://example/bioportal_admin

Population Workflows

When storing an ontology using the BioPortal Ontology Services, some amount of processing is done automatically so that the ontologies can be visualized using the Web UI. However, the Annotator and Resource Index require separate, manual data population workflows in order to function with the provided ontologies. Details on running these populations can be found in the "Howto" sections located at the bottom of this page.

Image Format and Machine Details

The NCBO Virtual Machine Image is created using the Open Virtualization Format, which should allow the machine to be used in a variety of environments.

The operating system is CentOS 5.5 running Tomcat 6, Java 6, Rails 2.3.5, and Ruby Enterprise Edition 1.8.7, and memcached.

The following applications use these services/runtime environments:

• Tomcat, Java
  • BioPortal Ontology Services (BioPortal Core)
  • BioPortal Admin (a UI for administering BioPortal Ontology Services)
  • Annotator
  • Resource Index
• Rails, Ruby, memcached
  • BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)

Basic System Administration

• Most of our administration scripts and build environment assume that you will be running as the root user.
• Helper commands:
  • ncbostart: the required services are started on boot automatically, but if they need to be started automatically
  • ncbostop: manually stop services
  • ncborestart: manually start/stop services
• Start individual services:
  • /sbin/service httpd start
  • /sbin/service memcached start
  • /sbin/service tomcat6 start
  • /sbin/service mgrep start
• Stop individual services:
  • /sbin/service httpd stop
  • /sbin/service memcached stop
  • /sbin/service tomcat6 stop
  • /sbin/service mgrep stop