Release Notes

• Features Updates
• Site Credits

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 1.1

Released July 22, 2010

Features Implemented in Ambra 1.1

• Support for NLM DTD 2.3 and new XSL stylesheets. The single XSL stylesheet has been split into two stylesheets: a generic XSL stylesheet to handle NLM DTD 2.3 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.