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Release Notes

Features Updates

This site is published using the Open Source journal management and publishing framework being developed by Ambra. This site is updated regularly as new features become available. This page summarizes features and known bugs in each updated version.

Ambra 2.10.1

Released July 15, 2014

Features Implemented in Ambra 2.10.1

  • Update taxonomy thesaurus to 2014-3
  • Introduces a content-repo that is a versioning object store service. Ambra is now configured to use this external file store

Ambra 2.9.22

Released Jun 17, 2014

Features Implemented in Ambra 2.9.22

  • An enhancement to administrative functionality around article taxonomy
  • An optimization to database queries on home and issue pages
  • Enhancements to handling of reference DOI
  • Adding support for different content repositories

Ambra 2.9.21

Released Jun 10, 2014

Features Implemented in Ambra 2.9.21

  • A bugfix to taxonomy classification to narrow the criteria for analysis

Ambra 2.9.20

Released May 27, 2014

Features Implemented in Ambra 2.9.20

  • An enhancement to registration verification
  • An enhancement to the display of article data availability statements

Ambra 2.9.19

Released May 20, 2014

Features Implemented in Ambra 2.9.19

  • An enhancement to registration surrounding password reset reminders
  • An enhancement to the display of article metadata in mobile
  • An enhancement to taxonomic analysis - allowing multiple abstract to be utilized
  • An enhancement to Administrative functions around user import
  • A UI change around the User Profile screen

Ambra 2.9.18

Released May 6, 2014

Features Implemented in Ambra 2.9.18

  • A bugfix to ensure new registration emails are unique
  • A bugfix in registration verification
  • Administrative enhancements to user import
  • A refinement for a test function for displayName uniqueness
  • An update to the Administrative environment

Ambra 2.9.17

Released April 29, 2014

Features Implemented in Ambra 2.9.17

  • Patching Struts to version 2.3.16.2
  • A bugfix for display of Data Availability Statement on newly published articles
  • A bugfix for article ingestion when article payload included striking images
  • A bugfix for a test function for displayName uniqueness
  • A minor bugfix for a recent SSO migration around welcome email content

Ambra 2.9.16

Released April 22, 2014

Features Implemented in Ambra 2.9.16

  • A bugfix for inline figure and table display for certain articles

Ambra 2.9.15

Released April 15, 2014

Features Implemented in Ambra 2.9.15

  • A bugfix in how we manage reference DOI
  • Additional administrative changes: small bug fixes and integration enhancements
  • A bugfix for a 500 error retrieving article comments

Ambra 2.9.14

Released April 8, 2014

Features Implemented in Ambra 2.9.14

  • A bugfix in the password change workflow
  • Administrative changes: small bug fixes and integration enhancements

Ambra 2.9.13

Released April 1, 2014

Features Implemented in Ambra 2.9.13

  • Update to taxonomy synonyms
  • Changes to article logging implementation
  • Administrative changes to support additional authentication integration

Ambra 2.9.12

Released March 25, 2014

Features Implemented in Ambra 2.9.12

  • Bug fix in socket management, ensuring streams are properly closed

Ambra 2.9.11

Released March 18, 2014

Features Implemented in Ambra 2.9.11

  • Integration of CrossMark by CrossRef in our article pages
  • Minor bug fix around the ORCID integration

Ambra 2.9.10

Released March 11, 2014

Features Implemented in Ambra 2.9.10

  • Code refactoring around ArticleService
  • Code refactoring around annotationCitation
  • Enhancement to taxonomy cli

Ambra 2.9.9

Released March 4, 2014

Features Implemented in Ambra 2.9.9

  • Support for Collection Review article type
  • Fix for comment border display bug

Ambra 2.9.8

Released February 25, 2014

Features Implemented in Ambra 2.9.8

  • Support for ORCID linking with PLOS user accounts
  • Fix for white space display bug on some corrections articles
  • Syndication queue of citation and abstract data to PubMed
  • Exclusion of amendments from taxonomy backfill

Ambra 2.9.7

Released February 18, 2014

Features Implemented in Ambra 2.9.7

  • Migration of corrections and retraction annotation types to article types
  • Migration of minor correction annotation type to comment
  • Search index inclusion of retractions, expression of concerns and corrections
  • UI improvments for above mentioned article types
  • Preparation work to support CrossMark for article pages
  • Fix for figure lightbox use on tablets
  • Fix for an edge case lightbox display bug

Ambra 2.9.6

Released February 11, 2014

Features Implemented in Ambra 2.9.6

  • New figure lightbox for the article pages
  • Updated permissions service
  • Another fix for input error handling on article list curation tool for PLOS One homepage

Ambra 2.9.5

Released February 4, 2014

Features Implemented in Ambra 2.9.5

  • Reposition of article page media coverage submission link
  • Fix for the return of 'unkown' in the article page's media coverage section
  • Removal of article page references use of CrossRef backfill for DOI citations
  • Increased salt in Ambra's password service
  • Break of relationship between DB schemas and Ambra releases (this is backwards compatible)
  • Auto login of users after clicking on email verification link

Ambra 2.9.4

Released January 28, 2014

Features Implemented in Ambra 2.9.4

  • Fix for error under certain initial database conditions - originating from an OSS community user
  • Fix for input error handling on article list curation tool for PLOS One homepage

Ambra 2.9.3

Released January 14, 2014

Features Implemented in Ambra 2.9.3

  • Article page media coverage: fix for incorrect date display
  • Article page media coverage: suppression of date display for non-media and blog coverage links
  • Fixes for minor article page display bugs when navigating the across tabs
  • Population of description tag for CrossRef syndication

Ambra 2.9.2

Released December 26, 2013

Features Implemented in Ambra 2.9.2

  • URL validation for crowdsourced media coverage form
  • Fix for advanced search article type facet
  • Reapplying Ambra 2.8.7 mapping for taxonomy synonyms

Ambra 2.9.1

Released December 17, 2013

Features Implemented in Ambra 2.9.1

  • Fix for CSS file path mistake
  • Crowd sourced media coverage form on article page
  • Update to article page references section style, linking, and doi display logic

Ambra 2.9.0

Released December 10, 2013

Features Implemented in Ambra 2.9.0

  • Follow up fix for touch interaction with figure viewer
  • Follow up fix for twitter card meta fields
  • Added links to Figshare tile dialog on article metrics tab

Ambra 2.8.9

Released December 3, 2013

Features Implemented in Ambra 2.8.9

  • Fix for Google Scholar article metrics tab link
  • Fix for Figshare article metrics tab data display
  • Fix for display errors on user's preferences tab in community journals
  • Fix for author search facet "where my keywords appear"
  • Fix for abbreviated publication date month on article page
  • Fix for cross browser alphabetized display of subject areas on article page

Ambra 2.8.8

Released November 26, 2013

Features Implemented in Ambra 2.8.8

  • New ALMs on article metrics tab: Wordpress, PMC Europe, PMC Europe DB, Datacite DB, Reddit
  • New PubChase share badge on article page
  • Fix for sorting bug with pagination on PLOS One browse pages and all journal search results pages
  • Fix for article page download links on html5 tables
  • Fix for touch interaction with figure viewer
  • Media tracking data display on article page

Ambra 2.8.7

Released November 19, 2013

Features Implemented in Ambra 2.8.7

  • Version 6 of taxonomy terms
  • DOI search optimization
  • Return of solr debugging feature
  • Fix for a letter casing issue in the user registration system

Ambra 2.8.6

Released November 12, 2013

Features Implemented in Ambra 2.8.6

  • Article page refresh phase I: new metadata, figure lightbox display, block quotes, metrics signposts, article tweets widget, publication date and DOI display
  • Change of article references DOIs to CrossRef DOIs
  • Fix to properly open article reference links to CrossRef, PubMed and Google Scholar in new tabs(user settings permitting)

Ambra 2.8.5

Released October 29, 2013

Features Implemented in Ambra 2.8.5

  • Featured, Most Shared, and Most Viewed article blocks on PLOS One Subject Area browse pages
  • Article page Metrics tab Wikipedia tile bug fix
  • Article page Metrics tab bug fix for subset of newly published articles with metrics display issues

Ambra 2.8.4

Released October 22, 2013

Features Implemented in Ambra 2.8.4

  • PLOS One Editorial Board performance optimization
  • Fix for author display on browse page figure view results
  • Remapped notion of citations for article ALMs
  • New download button display on article page
  • Fix for article page right rail display bug
  • Canonical URL on PLOS One Browse pages
  • Removed accompaniment article types from Relative Metrics

Ambra 2.8.3

Released October 8, 2013

Features Implemented in Ambra 2.8.3

  • Minor improvement to SOLR API response format
  • Fixed signpost bug
  • Fixed for plos one taxonomy page
  • Added new signposts link in article page Metrics tab
  • Browse url refactor
  • Removed Relative Metrics accompaniment article types
  • Added SEO to PLOS One subject area browse pages

Ambra 2.8.2

Released October 1, 2013

Features Implemented in Ambra 2.8.2

  • Added of FASTA and FASTQ mime types
  • Removed obsolete links at bottom of article page metrics tab
  • Added canonical URL to article page
  • Added taxonomy term synonym mapping
  • Added field to enable Twitter Cards for PLOS abstracts
  • Fixed figure lightbox bug on ONE homepage

Ambra 2.8.1

Released September 24, 2013

Features Implemented in Ambra 2.8.1

  • Added article counts to PLOS One homepage taxonomy browser
  • Fixed post launch ONE hp bugs

Ambra 2.8.0

Released September 17, 2013

Features Implemented in Ambra 2.8.0

  • New PLOS One homepage
  • New taxonomy browser and taxonomy browse pages
  • New article type for service layer
  • Fix for search filter bugs
  • Fix for Scopus tile on article page Metrics tab

Ambra 2.7.9

Released September 10, 2013

Features Implemented in Ambra 2.7.9

  • Added new ALM Source, figshare, to the Article Metrics tab.

Ambra 2.7.7

Released August 27, 2013

Features Implemented in Ambra 2.7.7

  • Minor bug fixes

Ambra 2.7.6

Released August 20, 2013

Features Implemented in Ambra 2.7.6

  • Minor bug fixes

Ambra 2.7.5

Released August 13, 2013

Features Implemented in Ambra 2.7.5

  • Minor bug fixes

Ambra 2.7.4

Released August 6, 2013

Features Implemented in Ambra 2.7.4

  • Added support for ALM API Key
  • Updated RSS links on the taxonomy page
  • Twitter widget returns to the journal home pages
  • Performance improvement on the PLOS ONE Editorial board page

Ambra 2.7.3

Released July 30, 2013

Features Implemented in Ambra 2.7.3

  • Etocs feature live
  • Revise ALM classification for search, signpost and metrics tab
  • Bug fix for email this article

Ambra 2.7.2

Released July 23, 2013

Features Implemented in Ambra 2.7.2

  • Etocs feature enhancements and bug fixes
  • Upgrade Ambra to use ALM API v3
  • ALM signposts tooltip will have fade in/out feature
  • Users can choose no. of results to see on search result page
  • Incorporate security fix from Struts 2.3.15.1
  • Version 4 of taxonomy terms

Ambra 2.7.1

Released July 16, 2013

Features Implemented in Ambra 2.7.1

  • Etocs feature enhancements and bug fixes
  • Mathjax equations font size change and alignment fix
  • Fix for date filter in search
  • Fix for twitter spinner
  • Fix for broken PNGs in lightbox

Ambra 2.7.0

Released July 02, 2013

Features Implemented in Ambra 2.7.0

  • For tablets, enable swiping in figure carousel and lightbox

Ambra 2.6.9

Released June 25, 2013

Features Implemented in Ambra 2.6.9

  • Distinguish Authors and Editors in Affiliation on the Solr search backend
  • Addition of figure DOIs to Solr search API
  • Fix for article page user flows to Comments without page refresh
  • Use of CrossRef for citation count if Scopus unavailable in ALM signposts on the article page
  • Addition of LinkedIn share button for article pages
  • Correction of merge mistake from 2.6.8 in which changeset for eToCs and PubGet datasource removal was omitted

Ambra 2.6.8

Released June 18th, 2013

Features Implemented in Ambra 2.6.8

  • eToCs feature development
  • Advanced Search page journal specific "Filter by Article Type" search options
  • Deprecation of PubGet as a datasource

Ambra 2.6.7

Released June 11th, 2013

Features Implemented in Ambra 2.6.7

  • Restricted launch of eToCs
  • CrossRef API change support
  • Enhanced CrossRef support
  • PLOS-flavored Relevance sort option in search results

Ambra 2.6.6

Released June 4th, 2013

Features Implemented in Ambra 2.6.6

  • PLOS One Edboard search optimizations
  • Taxonomy tracking update
  • Reference DOI backfill

Ambra 2.6.5

Released May 28th, 2013

Features Implemented in Ambra 2.6.5

  • Tablet optimization - ONE header dropdown alignment
  • Fix for DOI formatting issues
  • Fix for PDF download name
  • Fix for eToCs browser specific display bug

Ambra 2.6.4

Released May 21st, 2013

Features Implemented in Ambra 2.6.4

  • Updated taxonomy rules
  • Citation display for Formal Corrections and Retractions
  • Tablet optimizations - search results page
  • Refactor URL rewrites to remove hardcoded paths
  • Client side article PDF viewing
  • Fix for Find this article online display edge case
  • Minion configuration for datasource dependency skipping
  • Fix for error message in Admin if article publishes when queue is not running

Ambra 2.6.3

Released May 14th, 2013

Features Implemented in Ambra 2.6.3

  • Provenance display support on article pages for subset of articles with unconventional XML
  • Fix for table title bolding on article pages
  • Ambra upgrade to Spring 3.2
  • Saved search threading fix
  • Ambra support for recent CrossRef API changes
  • PLOS Queue error handling optimizations
  • Find this article online link display - initial changes
  • XHTML tables follow up fix
  • Tablet optimizations - initial changes

Ambra 2.6.2

Released May 7th, 2013

Features Implemented in Ambra 2.6.2

  • Early integration of XHTML table support
  • Solr and PLOS Queue refactoring
  • User preferences tab clean up and enhancement
  • Logic to send PMC usage total, PMIDs and PMCIDs to Solr
  • Fix for margin bug on article page metrics tab
  • Fix for search alerts deletion behavior

Ambra 2.6.1

Released April 30th, 2013

Features Implemented in Ambra 2.6.1

  • Early integration of mathjax support
  • Find this article online link mapping fix

Ambra 2.6.0

Released April 23rd, 2013

Features Implemented in Ambra 2.6.0

  • Subject Areas display on Related Content article page tab for all PLOS journals(new to community journals)
  • Subject Area terms for all articles derive from machine aided indexing(MAI) of the full text of the article - excluding Reference lists
  • Support for all paths through the taxonomy polyhierarchy in indexing and search
  • AI thesaurus configurable from Ambra
  • Fix for XLST bug in taxonomy backfiller
  • Fix for "More by these authors" display on Related Content article tab
  • Saved search queue multithreading optimization
  • Refactor of article syndication flow

Ambra 2.5.9

Released April 16th, 2013

Features Implemented in Ambra 2.5.9

  • Relative metric front end support for Metrics tab
  • Article page client side tabs navigation instead of full page refresh tabs navigation
  • Bug fixes

Ambra 2.5.8

Released April 9th, 2013

Features Implemented in Ambra 2.5.8

  • New Science Seeker tile on article page metrics tab
  • Bug fixes

Ambra 2.5.7

Released March 26th, 2013

Features Implemented in Ambra 2.5.7

  • Added figure DOI information in the figure viewer
  • Gather DOI information for article citations

Ambra 2.5.6

Released March 19th, 2013

Features Implemented in Ambra 2.5.6

  • Displays Supporting Information DOIs
  • Many bug fixes

Ambra 2.5.5

Released March 5th, 2013

Features Implemented in Ambra 2.5.5

  • Expressions of Concern displays at the top of the article
  • Many bug fixes

Ambra 2.5.4

Released February 26th, 2013

Features Implemented in Ambra 2.5.4

  • Many bug fixes

Ambra 2.5.3

Released January 22nd, 2013

Features Implemented in Ambra 2.5.3

  • Reworked edboard search
  • Upgrade to SOLR4
  • Figshare integration
  • Many bug fixes

Ambra 2.5.2

Released December 20th, 2012

Features Implemented in Ambra 2.5.2

  • Taxonomy Improvements
  • Various code cleanups
  • Many bug fixes

Ambra 2.5.1

Released December 6, 2012

Features Implemented in Ambra 2.5.1

  • Global reskin of existing sites
  • Removal of inline annotations
  • Removal of ratings
  • Removed browse page
  • New about the authors tab
  • New article page
  • New figure viewer
  • Added figure search results
  • Replacement of Dojo with jQuery

Ambra 2.5.0

Released December 4, 2012

Features Implemented in Ambra 2.5.0

  • Implement a new taxonomy.

Ambra 2.4.9

Released November 19, 2012

Features Implemented in Ambra 2.4.9

  • Database cleanup.
  • Additional database fields added for features to come

Ambra 2.4.8

Released November 08, 2012

Features Implemented in Ambra 2.4.8

  • Saved Search: The User is now able to save search criteria and receive email alerts for newly published articles matching the criteria on a weekly and monthly basis.

Ambra 2.4.7

Released October 25, 2012

Features Implemented in Ambra 2.4.7

  • Fixing bug related to RSS feeds on the search results page.

Ambra 2.4.6

Released October 23, 2012

Features Implemented in Ambra 2.4.6

  • ALM: show percentage of HTML views that lead to a PDF download.
  • Registration: streamlined initial login to require fewer steps.

Ambra 2.4.5

Released October 4, 2012

Features Implemented in Ambra 2.4.5

  • Improved ping back logging.
  • Fixed bug that resulted in duplicate doi information in reference sections of articles.
  • Fixed bug that resulted in missing links in reference section.

Ambra 2.4.4

Released September 25, 2012

Features Implemented in Ambra 2.4.4

  • New ALM search & browse sort by Most Bookmarked and Most shared in social media
  • Fixed search errors and issue management errors.
  • Improved transaction management code.
  • Added Captcha challenge to "Email this article" functionality.

Ambra 2.4.3

Released September 18, 2012

Features Implemented in Ambra 2.4.3

  • Added the ability to Subscribe (RSS) to a search result.
  • Trial Registration field was added to advanced search.
  • Publication date was added to the Metrics box.
  • "Find this article online" feature retrieves results faster.
  • Several fixes to social media display such as twitter and facebook.
  • Added new ALM Source, Wikipedia, to the Article Metrics tab.

Ambra 2.4.2

Released September 4, 2012

Features Implemented in Ambra 2.4.2

  • Added functionality to clear css and javascript cache from browsers to prevent stale display of information.
  • Improved the code structure to facilitate deployment of registration application separately from the main web app.
  • Made logo changes to facilitate the new logo design.

Ambra 2.41

Released August 28, 2012

Features Implemented in Ambra 2.41

Ambra 2.40

Released August 2, 2012

Features Implemented in Ambra 2.40

  • The server now can receive pingbacks, and article pages are pingback-enabled. Received pingbacks will be stored in the database, but will not be visible in the Web application yet.

Ambra 2.38

Released July 12, 2012

Features Implemented in Ambra 2.38

  • We now have the capability to add multiple roles per user and a set of permissions associated with those roles. There are no functional changes to existing users/permissions. ie Everything works as it did before.

Ambra 2.37

Released July 3, 2012

Features Implemented in Ambra 2.37

Ambra 2.36

Released June 21, 2012

Features Implemented in Ambra 2.36

  • Upgrade to Struts 2.3.1.2 to fix a vulnerability that allows for a code injection attack.

Ambra 2.35

Released June 12, 2012

Features Implemented in Ambra 2.35

Ambra 2.32

Released April 26, 2012

Features Implemented in Ambra 2.32

  • Refactored the Annotation model.
  • Performance improvements:
    • Improved performance of the AdminTop when displaying a large number of unpublished articels.
    • Reduced the number of database queries for FetchArticleAction.

Ambra 2.31

Released April 12, 2012

Features Implemented in Ambra 2.31

Ambra 2.22

Released March 8, 2012

Features Implemented in Ambra 2.22

  • Refactored the User Profile model and underlying data.

Ambra 2.21

Released February 16, 2012

Features Implemented in Ambra 2.21

  • Added PMC Data to ALM Metrics chart (completely revamped the chart look and feel).
  • Pulled out the Administrative functions into a new stand alone web application.

Ambra 2.20

Released January 13, 2012

Features Implemented in Ambra 2.20

  • Refactored article data and associated objects.
  • Added new parameters to the annotation feed to display the entire annotation body and the competing interests statement.
  • Updated the Browse By functionality.

Ambra 2.10

Released December 6, 2011

Features Implemented in Ambra 2.10

  • Cleanup of Ambra objects.
  • Updated scripts that generate reports on annotations.

Ambra 2.0

Released November 11, 2011

Features Implemented in Ambra 2.0

  • Topaz, Fedora and Mulgara are no longer supported.
  • Ambra 2.0 uses a back-end architecture comprised of MogileFS, an open source distributed filesystem, and MySQL, an open source relational database. Hibernate has replaced Topaz as the object-relational mapping (ORM) library.

Ambra 1.7

Released August 4, 2011

Features Implemented in Ambra 1.7

  • Upgrade to CAS 3.4.7. CAS (Central Authentication Service) is the single sign-on used by Ambra.
  • Migrate CAS from the PostgeSQL database to the MySQL database.
  • Upgrade to Struts 2.1.8.
  • Allow italic, bold, superscript and subscript HTML markup in notes and comments.
  • Added citation_journal_title to the Google Scholar indexing metadata.
  • Bug fixes:
    • In Browse By Publication Date, clicking on a month hyperlink was not displaying the appropriate articles.
    • Print Article button on article tabs would print the article tab content, not the actual article.
    • Entities added to Correction Notes were not displaying correctly.
    • Superscripted Xrefs were not displaying correctly in the article slideshow.

Ambra 1.6

Released June 10, 2011

Features Implemented in Ambra 1.6

  • Added figure and table captions to advanced search.
  • Decoupled sending CrossRef metadata from the publishing process. This will allow article publishing to continue if there is a failure sending the CrossRef metadata.
  • Updated the CrossRef deposit schema to version 4.3.0.
  • Improvements to the Google Scholar indexing metadata in the article HTML:
    • Fixed corresponding authors and publisher fields.
    • Added citing articles.

Ambra 1.5

Released April 22, 2011

Features Implemented in Ambra 1.5

  • Replaced the Browse by Publication Date and Browse by Subject Categories to use the Solr API. Article-level Metrics is now included in the browse results.
  • RSS feeds are now pulling research article content directly from the Solr API.
  • A number of bugs were fixed in the RSS feeds:
    • The complete list of authors, including collaboration authors, has been added to each article.
    • The article publication time was changed from 2011�04�21T07:00:00Z to 2011�04�21T00:00:00Z .
    • HTML formatting has been removed from article titles.
    • The main article abstract is now included in the RSS feed.
  • Updated the templates used for user registration, login and profile pages.
  • Fixed the copyright XSL transform to accommodate a new public domain wording.

Ambra 1.4

Released March 11, 2011

Features Implemented in Ambra 1.4

  • Added Google Scholar indexing metadata in the article HTML. See Google Scholar's indexing guidelines for more information.
  • Updates to the Administration page:
    • Add the article publication date.
    • Sort articles by DOI or the article publication date.
    • Select all or none for publication of articles.
  • Added collaboration authors to articles on the Browse By pages and Issue Table of Contents.
  • Support for mp4 and mv4 mime types.

Ambra 1.3

Released November 18, 2010

Features Implemented in Ambra 1.3

  • Added an auto-ingest feature to allow for scheduling the ingest of articles.

Ambra 1.2

Released September 24, 2010

Features Implemented in Ambra 1.2

  • XSL stylesheet improvements for NLM 2.3 DTD.
  • Update Ambra to use Topaz 0.9.5.3. This release of Topaz removes objects filters and improves query performance.

Ambra 1.1

Released July 22, 2010

Features Implemented in Ambra 1.1

  • Support for NLM 2.3 DTD and new XSL stylesheets. The single XSL stylesheet has been split into two stylesheets: a generic XSL stylesheet to handle NLM 2.3 DTD and an XSL stylesheet specifically for Ambra.
  • Support for HTML iframes for advertising blocks.
  • Caching of CrossRef search results on the "Find this Article Online" page.
  • Updates to the copyright information.
  • Bug fixes:
    • Fix to author and editor search facet sorting.

Ambra 1.0

Released June 2, 2010

Features Implemented in Ambra 1.0

  • Now using Solr/Lucene for search with new look and feel and increased performance:
    • Integrate ALM/COUNTER data into search.
      • Display number of Downloads by document type, Number and source of Cited and bookmarked.
      • Ability to sort results by date and most viewed.
    • Faceted searching of result set by Journal, Subject Category, Article Type, Where my keywords appear.
    • See a list of your Most Recent Searches.
    • Explore More about the Authors, Academic Editors and Institutions in the result set.
  • Reciprocal Linking in Research Articles.
  • Remove formal corrections and retractions from ToC.
  • Enable Odyssey Press EZ Reprint servic.
  • Enable PubGet on Cross Ref Page.
  • Automate most recently published blocks.
  • Add cross ref links for article references.
  • Add Twitter to Share This Article.
  • Update Dojo to 1.4.

For a complete list of 1.0 features and bug fixes, please see the Ambra 1.0.0 RC1 Tickets , Ambra 1.0.0 RC2 Tickets and Ambra 1.0.0 RC3 Tickets

Ambra 0.9.6 beta

Released January 6, 2010

Features Implemented in Ambra 0.9.6

  • No new features were implemented. Happy New Year!
  • Bug fixes:
    • Changed the article RDFa subject from the publisher to the article URL.
    • Minor fixes to Email This Article.
    • Encode the plus sign (+) for new user confirmation emails.
    • Minor fixes to annotation display.

For a complete list of 0.9.6 features and bug fixes, please see the Ambra 0.9.6 RC1 Tickets

Ambra 0.9.5 beta

Released December 3, 2009

Features Implemented in Ambra 0.9.5

  • Added a new syndication service to the Admin panel. This will allow administrators to export article files and metadata to external sources. PLoS is using this syndication service with an internal application built on Apache Camel to send published files to PubMed Central and other external repositories. This is not an out-of-the-box solution as only the service hooks are available in Ambra.
  • Added RDFa for the Dublin Core elements in the article HTML.
  • Added a new action to support a Google Scholar XML feed for published articles.
  • Update to the article RHC to display articles cross-published in other journals.
  • Bug fixes:
    • Promote a note to a formal correction and the annotation body was removed.
    • Templates from other journals were displayed if freemarker.properties template_update_delay was set.
    • Templates changes to fix a number of formatting errors encountered in IE6, IE7 and IE8.
    • Minor fixes to annotation displays, formal corrections, formatting and messaging.

For a complete list of 0.9.5 features and bug fixes, please see the Ambra 0.9.5 RC1 Tickets and the Ambra 0.9.5 RC2 Tickets

Ambra 0.9.4 beta

Released September 11, 2009

Features Implemented in Ambra 0.9.4

  • Maven build separation of Ambra and Topaz. Ambra can now be built independently of Topaz.
  • A new article tab in the PLoS templates to display a graph with article pageviews, PDF downloads and XML downloads.
  • Bug fixes:
    • Fixed a prepare-sip NullPointerException for articles that have different DOI format.
    • Headings in Issue and Collection table of contents are made plural when appropriate.
    • The "Page Not Found" error page, "Site Error" page and an incorrect article DOI return correct Apache error codes.
    • CSS fixes.

For a complete list of 0.9.4 features and bug fixes, please see the Ambra 0.9.4 RC1 Tickets

Ambra 0.9.3 beta

Released August 7, 2009

Features Implemented in Ambra 0.9.3

  • Allow users to search across multiple journals.
  • Display CrossRef citations per article. A new action was created to display citations to articles as recorded by CrossRef.
  • Allow admins to override annotation citation information. Correction citations used to be dynamically generated from the article information. If this article information was part of the correction (e.g. title, author name), then the error is propagated in the Correction citation. Now, admins can update the citation information for any annotation to display the correct citation.
  • Display plural section headings in BrowseIssue.action if more than one article is displayed (configurable in ambra.xml).
  • Display an explanation icon per article type (configurable in ambra.xml).
  • Provide the article DOI in the page source. This will be used for serving targeted advertisements.
  • A number of outstanding bugs were fixed.
  • Separation of the PLoS and Ambra journal templates and CSS re-organization.
  • A new annotation feed that includes new notes, comments and ratings per journal.

For a complete list of 0.9.3 features and bug fixes, please see the Ambra 0.9.3 RC1 Tickets, the Ambra 0.9.3 RC3 Tickets and the Ambra 0.9.3 RC3 Tickets

Ambra 0.9.2 beta

Released March 25, 2009

Features Implemented in Ambra 0.9.2

  • Redesigned article page to accommodate new features and give a better visual experience to the user.
  • Tabs are included on the article page for Related Content and Comments.
  • Data from external sources is provided on the Related Content tab. Sources include the number of citations from PubMed Central and Scopus; the number of bookmarks from CiteULike and Connotea; and the number of blog posts linking to the article from Postgenomic, Nature Blogs and Bloglines. More sources will be added in the future.
  • Links to related articles appear in the right hand column of the article page.
  • Links to the appropriate issue or collection appear in the right hand column of the article page.
  • Competing interest statements were added to all notes, comments and ratings.
  • Related subject categories can be displayed in the right hand column of the article page and the Related Content tab.
  • The creation of retraction annotation types.
  • The Most Recently Published homepage block can be configured to display a set number of articles, articles from within a published date range and an article white list (e.g. display only research articles).
  • Articles can be ordered within an issue and in the table of contents.
  • Formal corrections and retractions are now displayed in the table of contents next to the appropriate article.
  • The administration portal was overhauled to provide a better workflow for creating volumes and issues.
  • The administration portal was updated to allow manual ordering of articles within an issue.

For more detail on Ambra 0.9.2, see the Ambra 0.9.2 Tickets

RC 0.9.1 beta

Released January 29, 2009

Features Implemented in RC 0.9.1 beta

  • Revamp of Ambra search to use Mulgara (does not include update to the search UI)
  • Support of article packages greater than 4Gb in size
  • Support of article packages in tar format
  • Support for very large assets (e.g. supporting info files) outside of memory
  • Fixes to formal corrections
  • Fixes to citations
  • Fixes to citation downloads
  • Article-level feeds for top-level notes/comments on an article
  • Updates to admin panel for administering notes/comments
  • Many fixes to the UI including line wrap for long gene sequences, browser-specific bugs, wrapping long URLs in annotations/articles, etc.
  • Cleanup of content models, back-end bug fixes, etc.

RC 0.9.0 beta

Released September 1, 2008

Features Implemented in RC 0.9.0 beta

  • Upgrade to Mulgara 2.0.1
  • Upgrade to Ehcache 1.4.1
  • Moved to Bitronix Transaction Manager because of bug in JOTM
  • Object level caching for applications
  • Rework of ingest to perform image processing pre-ingest and improve performance
  • Upgrade to Dojo 1.1
  • Mulgara write-lock cleanup
  • Many enhancements to improve performance and stability
  • Many fixes to the UI including volumes/issues, correction annotations, ratings, slideshow figures, etc.
  • Cleanup of content models, back-end bug fixes, etc.

RC 0.9.0 rc1 beta

Released July 16, 2008

Features implemented in RC 0.9.0 rc1 beta

  • Pre-ingest script (prepare-sip) for images transforms.
  • Re-architected the cache code.
  • Moved transactions to read-only queries where possible.
  • Optimized slideshow retrieval/display.
  • Optimized many actions (e.g. FetchArticleAction, GetAverageRatingsAction, etc.).
  • Lots of Ambra code improvements.
  • Upgraded to Dojo 1.1.
  • Upgraded to Mulgara 1.2 (multi-core!).
  • Upgraded to Lucene 2.3.
  • Upgraded to ehCache 1.4.1.
  • Many Ambra configuration changes for ease of installation.

RC 0.8.2.1 beta

Released February 26, 2008

Features Implemented in RC 0.8.2.1 beta

  • Minor corrections on articles
  • Formal corrections on articles
  • "View All" corrections page
  • Admin interface for converting notes to corrections
  • Citations for formal corrections
  • Advanced search:
    • Search by author name
    • Search article text
    • Search by date published
    • Search by subject category
  • Support for note DOIs in the DOI resolver
  • Dynamic "Most Viewed" tab for journal home pages

RC 0.8.2 beta

Released January 11, 2008

Features implemented in RC 0.8.2 beta

  • Fixes to Browse by Issue (Table of Contents) to add more article types and next/previous links
  • A dynamic Browse by Journal (Journal Archive) page
  • A single rating field for all front matter articles (e.g. Editorial, Opinion)
  • Affiliation footnote links are displayed for group authors
  • Minor FreeMarker and CSS fixes
  • Updates to the volume and issue object models
  • Migration from OSCache to ehcache for faster performance
  • Administrative interface for viewing and releasing caches

RC 0.8.1 beta

Released October 25, 2007

Features implemented in RC 0.8.1 beta

  • Display links to related articles on Article and Browse pages
  • Administrative interface for collecting Articles into Issue and Issues into Volumes
  • Administrative interface for attaching Issue Image article to Issues, and setting the current Issue
  • Browse by Issue (Table of Contents) page

RC 0.8 beta

Released September 20, 2007

Features implemented in RC 0.8 beta

  • Enable multiple journals using a single repository
  • Skins for multiple journals
  • Filter search results by journal using OTM
  • Trackback links for articles
  • Citation download for the published article
  • A fix to a rating display issue in IE7
  • Allow multiple e-mail addresses for "E-mail this Article"
  • Administrative modifications to annotations
  • Administrative interface for multiple journals
  • Migration to the Struts 2 web application framework

RC 0.7 beta

Released July 9, 2007

Features implemented in RC 0.7 beta

  • Ratings feature
  • Architecture overhaul
  • Removal of a layer of web services and increased performance
  • Object Triple Mapping (OTM) which speeds retrieval of objects
  • Object Query Language (OQL) that is similar to HQL, an object-oriented query language from Hibernate
  • Atom syndication format

RC 0.6 beta

Released April 20, 2007

Features implemented in RC 0.6 beta

  • Browse features
  • Full Safari support
  • Cross section and cross paragraph annotations now work correctly
  • Image cache is properly flushed when an article is deleted via the admin console
  • Fix issue where jsession id was appended to search button and JavaScript file requests
  • Resend address verification e-mail feature
  • Removed alerts e-mail address
  • After submitting profile for a new user, you get directed to alerts tab
  • Users can change their e-mail address now
  • New templates for the profile pages are available for customization
  • New organization types on profile page
  • Article title and journal title is in title of page now
  • Fixed RDF header in Ambra Journal pages

Site Credits

Many of the icons are adapted from the Silk Icon set, courtesy FamFamFam.