Category:NCBO Virtual Appliance

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NCBO VIRTUAL APPLIANCE v2.0 IS NOW AVAILABLE

The NCBO Virtual Appliance has been updated to use NCBO's new v4.0 software infrastructure, including the use of an RDF triplestore as the primary data storage mechanism. Please read below as much of the Appliance workflow has changed.

For documentation of v1.0 Virtual Appliances, please see our archive.

Virtual Appliance Basics

The NCBO Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source NCBO software running on a Linux operating system. The image was created using VMWare and is available for download by contacting support@bioontology.org.

The following software is included on the image as of v2:

  • Ontologies API (REST service)
  • Annotator
  • Recommender
  • BioPortal Web User Interface (including ontology visualization, widgets, and Annotator UI)

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

Getting Started

  • To obtain the Virtual Appliance, contact NCBO Support and include your BioPortal account username. You can create a BioPortal account at: http://bit.ly/bioportal-account
  • The download is provided as a tar archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be converted to work in your virtualization environment.
  • You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer to this hostname as 'example'.
  • Change default passwords
    • Operating System
      • Username: root
      • Password: password is prompted on the first boot
    • BioPortal Admin User
      • Username: admin
      • Password: changeme
  • Add an ontology using the BioPortal Admin User here: http://{YourDomainName}/ontologies/new
    • The ncbo_cron project is configured to automatically process new ontologies every 5 minutes (see documentation for enabling the scheduler). This processing includes:
      • Parsing any new, unparsed ontologies
      • Calculating a set of metrics for these ontologies
      • Indexing these ontologies for use with search
      • Processing the ontology for use with the annotator
  • REST services are available at the following location:

System Requirements

The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.

Note: these requirements are for basic usage. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.

  • Minimum
    • 1 CPU (2 GHz)
    • 4GB RAM
    • Hard disk space: 3GB
  • Recommended for heavier usage
    • 2 CPU (3 GHz)
    • 6GB RAM (When using more than 4GB RAM, you should configure Tomcat to use the additional memory)
    • Hard disk space: 10GB (or more depending on number/size of ontologies)

Image Format and Operating System Details

The NCBO Appliance image was created using the Open Virtualization Format, which should allow the machine to be used in a variety of environments.

The operating system is CentOS 5.7 64-bit running Tomcat 6.0.26, Java 6, MySQL 5.1.x, PHP 5.1.6, Rails 2.3.x, and Ruby Enterprise Edition 1.8.7, and memcached.

The following applications use these services/runtime environments:

  • Sinatra, Ruby, 4store, redis
    • Ontologies API
    • Annotator
    • Recommender
  • Rails, Ruby, memcached, mysql
    • BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)
  • Tomcat, Solr
    • Search index

Basic System Administration

  • Most of our administration scripts and build environment assume that you will be running as the root user.
  • Helper commands:
    • bpstart: the required services are started on boot automatically, but if they need to be started automatically
    • bpstop: manually stop services
    • bprestart: manually start/stop services
  • Start individual services:
    • /sbin/service httpd start
    • /sbin/service memcached start
    • /sbin/service tomcat6 start
    • /sbin/service mgrep start
    • /sbin/service 4store start
    • /sbin/service unicorn start
  • Stop individual services:
    • /sbin/service httpd stop
    • /sbin/service memcached stop
    • /sbin/service tomcat6 stop
    • /sbin/service mgrep stop
    • /sbin/service 4store stop
    • /sbin/service unicorn stop

License

All NCBO software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.

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