PathVisio

Software Screenshot:
PathVisio
Software Details:
Version: 3.1.3
Upload Date: 18 Feb 15
Developer: PathVisio
Distribution Type: Freeware
Downloads: 47

Rating: nan/5 (Total Votes: 0)

PathVisio is an open source and completely free graphical application implemented in the Java programming language and designed from the ground up to be used for displaying, analyzing and editing biological pathways under a GNU/Linux operating system.

Can be used to draw pathways, link biological entities

The software lets users to draw pathways, link biological entities (proteins or genes) to biological data, using database identifiers, edit pathways, as well as to analyze pathways. With PathVisio you will also be able to map experimental data, such as microarray data, and visualize it on top of the existing pathway drawing.

In addition, you will be able to select a gene database, select a metabolic database, view statistics, import expression data, select expression dataset, search pathways, view legend, manipulate objects, import projects, as well as to install and manage plugins, which can add additional functionality to the app.

Requires no installation

The application can be used without installing it on your GNU/Linux operating system. All you have to do is to download the binary package from Softoware, save the archive on a location of your choice, extract it using an archive manager utility, open the extracted directory, and double click on the pathvisio.jar file.

Under the hood

While taking a quick look under the hood of the PathVisio software, we’ve noticed that the application is written entirely in the Java programming language, and that its graphical user interface is designed with the latest Java Swing technologies. We’ve successfully tested the application on computers supporting either of the 32 or 64-bit CPU architectures.

Runs on any OS where Java is supported

Being written in the Java programming language, PathVisio can be declared a platform-independent application that supports GNU/Linux, Microsoft Windows, Mac OS X, BSD, Solaris, and any other operating system where the latest Java technologies are supported.

What is new in this release:

  • 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)

What is new in version 3.1.2:

  • Major bug in file import module fixed: http://developers.pathvisio.org/ticket/1697

What is new in version 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

What is new in version 2.0.10:

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

What is new in version 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
  • see milestone:"milestone_27" for a complete list of bug-fixes

What is new in version 2.0.8:

  • Improved shapes for cellular components
  • A few usability improvements such as copy / paste in the popup menu
  • see milestone:"milestone_26" for a complete list of bug-fixes

What is new in version 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
  • see milestone:"milestone_25" for a complete list of bug-fixes

What is new in version 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.
  • see milestone:"milestone_24" for a complete list of bug-fixes

What is new in version 2.0.4:

  • improved text formatting of shapes, labels and datanodes
  • many more shapes for datanodes
  • simple pixel coordinates
  • set background color on datanodes

What is new in version 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
  • see milestone:"milestone_21" for a complete list of bug-fixes

What is new in version 2.0.1:

  • 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.

Requirements:

  • Oracle Java Standard Edition Runtime Environment

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