BioPortal Virtual Appliance Release Notes

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This page contains software release notes for the BioPortal Virtual Appliance.

Please see the main release notes page to access release notes for the Stanford-hosted BioPortal application.

Contents

BioPortal Virtual Appliance 2.5 RC1 (2017-Aug)

Changes

  • Web UI is updated to V5.1.1 which is a major overhaul of the user interface. It has been refactored for rails 4.x support and adopted bootstrap UI framework.
  • Bundled-in UMLS Semantic Network (STY) ontology was updated to version 2016AA
  • Appliance includes scripts for facilitating minor in-place updates of the appliance components such as bioportal_web_up, ontologies_api and ncbo_cron.

Please refer to the main release notes page for more detailed information on the new features and bug fixes introduced in various Bioportal components.

Known issues

  • Web UI layout is not customized for the Appliance. It contains original bioportal.bioontology.org footer and header tool menu has a link to non-functioning resource index tool.

Components

  • bioportal_web_ui v5.1.1
  • ontologies_api v5.4.0
  • ncbo_cron v5.4.0


Application Stack

  • CentOS 6.9
  • Apache httpd 2.2.15
  • Apache Tomcat 6
  • Solr 4.10.4
  • MySQL 5.1
  • Ruby 2.3.3
  • Passenger 5.1.6
  • Redis 3.2.9
  • Memcached 1.4.4
  • 4store v1.1.5-122-g1788d29
  • nginx 1.12.1


BioPortal Virtual Appliance 2.4 (2015-Apr)

Components

  • Ontologies API (REST service) v4.15.3
  • Annotator
  • Recommender
  • BioPortal Web User Interface (including ontology visualization, widgets, and Annotator UI) v4.15.5
  • BioMixer

Note that release 4.15 was a silent release, implying that it contained bug fixes and other non-visible changes, and the third release number (.3, .5) indicates a patch number.

Application server stack

  • CentOS 6.6
  • Apache httpd 2.2.15
  • Apache Tomcat 6.0.24
  • Solr 4.10.4
  • MySQL 5.1.73
  • Ruby 2.1.5
  • Passenger 4.0.57
  • Redis 2.8.18
  • Memcached 1.4.4
  • 4store v1.1.5-122-g1788d29
  • nginx 1.6.3
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