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Martina Summer-Kutmon edited this page Oct 3, 2024 · 10 revisions

Release Notes for PathVisio 3.4.0-alpha

  • October 3, 2024: Minor release
  • BridgeDb update - version 3.4
  • New interaction type in panel - mim-translocation
  • New status bar
  • Two new templates (reversible reaction, phosphorylation)
  • Improvements in data import dialogs
  • Default species for new pathways set to Homo sapiens
  • Sorting of identifiers in search result is fixed (correct element is selected) - contributed by larsgw
  • Bug fixes

Release Notes for PathVisio 3.3.0

  • January 22 2018: Minor release
  • BridgeDb update - version 2.2.1
  • Wikidata is now available as database for metabolite annotations
  • User gets asked to fill in pathway title and organism when creating new pathway
  • Updates to the datanode annotation search dialog (position and sortable table)

Release Notes for PathVisio 3.2.4

  • November 24 2016: Bug fix release
  • Increased default WIN_W to support pref panel viewing
  • Updated base URL for PubMed citation look ups

Release Notes for PathVisio 3.2.3

  • September 20 2016: Bug fix release
  • Default font size for data nodes increased
  • New command line argument "wpid" that installs WP plugin if needed and loads defined pathway from WikiPathways
  • Updated templates
  • Bug fixes

Release Notes for PathVisio 3.2.2

  • May 03 2016: Bug fix release

Release Notes for PathVisio 3.2.1

  • October 07 2015: Bug fix release
  • Started code cleanup
  • PathVisio core lib now also reads information about ontology tags
  • Bug fixes: #1781, #1787, #1794

Release Notes for PathVisio 3.2.0

  • February 28 2015: Bug fix release
  • Issues with Java 8 have been resolved
  • Code signing certificate provided by NRNB (via the Cytoscape Consortium non-profit organization) is now used - * Java security issues resolved
  • Bug fixes in the data import module and statistics module
  • Improvements in the plugin manager interface
  • New page for available key shortcuts in PathVisio: http://www.pathvisio.org/documentation/shortcuts/

Release Notes for PathVisio 3.1.3

  • January 31 2014: Bug fix release
  • GeneOntology terms are now removed from Search results for annotations
  • DataNodes need to be annotated with ID and Datasource or nothing (saving data nodes with only ID or datasource is not allowed anymore)

Release Notes for PathVisio 3.1.2

Release Notes for PathVisio 3.1.1

  • October 04 2013: Bug fix release 3.1.1
  • New data tab: show imported expression data
  • Lots and lots of bug fixes and improvements

Release Notes for PathVisio 3.1.0

  • July 02 2013: Feature release 3.1.0
  • Plugin manager improvements - browse feature by category, status information
  • Advancements in legend tab: missing data and criteria not met are added
  • Bug fix: External references for lines will show up immediately
  • Several bug fixes

Release Notes for PathVisio 3.0.1

  • June 06 2013: Bug fix release 3.0.1
  • fixed problem with publication references that got deleted when clicking undo

Release Notes for PathVisio 3.0.0

  • Mar 28 2013: Major release 3.0.0
  • basic plugin manager included
  • interaction annotation enabled
  • new gpml schema: GPML2013a
  • new object graphical line as another graphical shape
  • new structure of object panel
  • bug fixes in PathVisio and WikiPathways

Release Notes for PathVisio 3.0.0beta3a

  • Feb 20 2013: Point release
  • Disable dialog to warn about old Ensembl identifiers
  • Hide species specific Ensembl linkouts in the backpage (temporary fix for problem in BridgeDb)
  • Bug fix 1528

Release Notes for PathVisio 3.0.0beta3

  • Jan 25 2013
  • new backpage layout
  • possibility to select all lines in pathway editor, right click -> Select -> Select all lines
  • splash screen when starting PathVisio standalone application
  • new core module org.pathvisio.data was added to PathVisio as a separate API for biological data import
  • several bug fixes

Release Notes for PathVisio 2.0.11

  • Autosave
  • Zoom using scroll wheel
  • Selection of lines is easier: no longer necessary to click on the exact pixel
  • Now with two methods for over-representation analysis; one pathway-oriented and one data-oriented

Release Notes for PathVisio 2.0.10

  • New way of drawing rounded rectangles to avoid stretching effect
  • Various small bugfixes

Release Notes for PathVisio 2.0.9

  • New connector type for connector of arbitrary length and arbitrary angles
  • New "cellular component" property for storing the biological meaning of a compartment
  • New "double" line type (especially useful for double-membraned organelles)
  • Clickable hyperlinks in pathways

Release Notes for PathVisio 2.0.8

  • Improved shapes for cellular components
  • A few usability improvements such as copy / paste in the popup menu

Release Notes for PathVisio 2.0.7

  • toolbar icons and new side panel to make it easier to select arrow types and shapes (thanks liubing)
  • Pathway databases are included as data source, so that you can add links from one pathway to another
  • BioPAX converter has been improved and produces more valid BioPAX documents.
  • new connector type where individual points can be manipulated (thanks leonth)
  • Number of data sources has been increased to over 180

Release Notes for PathVisio 2.0.6

  • The number of anchors on a shape can be increased from the default 12.
  • A legend of the data visualization can now be shown on the pathway image itself. Previously it was only visible in a side panel.

Release Notes for PathVisio 2.0.5

  • Datanodes can now have states to represent e.g. phosphorylation and other protein modifications

Release Notes for PathVisio 2.0.4

  • This is a relatively big release. Many new drawing capabilities have been introduced:
  • improved text formatting of shapes, labels and datanodes
  • many more shapes for datanodes
  • simple pixel coordinates
  • set background color on datanodes

Release Notes for PathVisio 2.0.3

  • Most notable in this release is the new XML Schema for the GPML pathway format (version 2010a). This new pathway format will enable many new graphical capabilities the future, you can look forward to some of those appearing in the next release.
  • Other new features:
  • Invisible anchors are really invisible, at least when something is connected to them (Thanks to Margot)
  • Extra -v command line option (thanks to Mark)
  • Currently selected database is displayed properly in the status bar again
  • Many new extension points for plugin developers

Release Notes for PathVisio 2.0.2

  • This is a minor release, with mostly bug fixes. New in this release:
  • data visualization: behavior of rows in a split gene box is more predictable
  • dragging an anchor along a complex path is more smooth
  • added hooks to give plugins more freedom to modify the preference panel
  • improved speed of identifier search when using BridgeWebservice? as back-end

Release Notes for PathVisio 2.0.1

  • This is a minor release, with mostly bug fixes. New in this release:
  • Improved algorithm for automatic connectors that point to an anchor.
  • Improved drawing of arrow types that have a short "gap" at the end.
  • Because the thawte freemail service has been cancelled, we updated our Security Certificate
  • The Pathway History viewer had a bug where each line was considered modified, even if it wasn't. This has been fixed.

Release Notes for PathVisio 2.0.0

  • This is a major release
  • Visualization, Gene Expression and Statistics plugin are upgraded to core plugin status.
  • Color Rules have been improved, made more efficient, new operators and String comparison were added
  • Quickly toggle visualization styles with a Visualization Combo on the main window
  • Dynamic Visualization: visualization is loaded on the fly and updated to changes in the current pathway

Release Notes for PathVisio 1.1.7

  • This was a bug-fix release

Release Notes for PathVisio 1.1.6

  • Pathway statistics: ZScore calculation was reviewed and checked against MAPPFinder

Release Notes for PathVisio 1.1.5

  • This release focused on memory usage: PathVisio now uses significantly less memory, which means that bigger maps can be handled by the same computer. Also, a major memory leak has been fixed.
  • Recent pathways - menu item to provide quick access to recently used pathways.

Release Notes for PathVisio 1.1.4

  • New gene databases: Arabidopsis thaliana and Oryzia sativa japonica (rice) thanks to the help of Gramene. As a result of this, support for new external datasources has been added as well.
  • The Gex plug-in can now import expression data without the intervention of a gene database. This only works if the references in your pathway match your data exactly, but this can be a great help for species that don't currently have a gene database.
  • Gex plug-in can import data with missing (or extra) header rows, which makes data import much more flexible

Release Notes for PathVisio 1.1.3

  • Preparations for addition of many new species, including Arabidopsis and rice. New system codes have been added
  • Reworked selection combo's to make it easier to select the right data source.
  • Bugs related to running the PathVisio applet twice in the same browser have finally been fixed, after a large code restructuring.
  • Increased memory limits in webstart for larger pathways.
  • Many small bugs have been fixed

Release Notes for PathVisio 1.1.2

  • "States" have been added to GPML, which can be used to represent e.g. protein modifications.
  • GPML namespace has been adjusted to reflect a new version. From now on, each change to the schema will be accompanied by a namespace change. See EverythingGpml for details.
  • Arbitrary attributes can now be edited from within PathVisio
  • Many bug fixes

Release Notes for PathVisio 1.1.1

  • This is a minor release, mainly with bug fixes and small usability enhancements. New since PathVisio 1.1:
  • The comments dialog tab has been reworked to make adding comments easier.
  • Literature references are visible as small numbers above a pathway element.
  • Editor distinguishes between groups that have biological meaning and groups that are just there to help editing.
  • Ordering of shapes (which shape overlaps which) is now stored in GPML.
  • GPML allows arbitrary attributes.
  • The mouse cursor changes to reflect editor state.

Release Notes for PathVisio 1.1

  • What is new since PathVisio 1.0?
  • Mac OS X and Linux compatibility
  • Add literature references and comments more easily by double-clicking and searching on pubmed id
  • Connect lines to shapes easily with drag and drop
  • Elbow- and curved connectors
  • Line anchors and the possibility to make arrows point to other lines.
  • Multi-line labels
  • Redesigned group selection model and appearance to make it easier to find grouped items
  • Easier database references: search for genes and metabolites by name instead of database identifier
  • Numerous bugfixes
  • Modeless editor (removed edit mode button)
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