VANTED / News: Recent posts

[[url:Download Vanted 2.5.0:http://vanted.org/index.php?file=doc2.html]]
VANTED v2.5.0 has been released. Changes are listed below:
- Drawing speed improvement when loading and exploring large networks
- Reorganisation of menus and sidepanels
- Support for downloads of curated SBML models from Biomodels database [link]
- Reenabling support to create GO and KEGG hierarchies
- Better support for program preferences
- Tons of bug fixes

[[url:Download Vanted 2.2.1:https://sourceforge.net/projects/vanted/files/vanted2/v2.2.1/]]
VANTED v2.2.1 has been released. Changes are listed below:
- bug fixes regarding text encoding
- bug fixes and enhancements for the installation process

[[url:Download Vanted 2.2.0:https://sourceforge.net/projects/vanted/files/vanted2/v2.2.0/]]
VANTED v2.2.0 has been released. Changes are listed below:

• Support added for KEGG REST API
• Upgrade to official jSBML v1.0 library
• bug fixes

Please upgrade your Java Runtime to JAVA 1.7. We're not supporting JAVA 1.6 and lower anymore.
http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html

[[url:Download Vanted 2.1.0:https://sourceforge.net/projects/vanted/files/vanted2/v2.1.0/]]
VANTED v2.1.0 was released today. Changes are listed below:

* Support added for SBML based on JSBML
* Support added for BioPAX based on Paxtools
* bug fixes

Please go to http://www.vanted.org and download the new version. Feel free to comment or report any bugs to further improve the tool.

[[url:Download Vanted 2.01:https://sourceforge.net/projects/vanted/files/vanted2/v2.01/]]
VANTED v2.01 was released today. There are just minor changes (bug fixes). Furthermore support for Java 7 was added.

Please go to http://www.vanted.org and download the new version. Feel free to comment or report any bugs to further improve the tool.

[[url:Download Vanted 2.0:https://sourceforge.net/projects/vanted/files/vanted2/v2.0/]]
We proudly announce the release of VANTED v2.0. It was strongly revised in the last year and has been improved in various aspects. Most important changes are: 1) reorganised and optimised GUI for easy access of functions, 2) improved internal data handling to speed up data loading and to reduce memory consumption, 3) code clean up, 4) added support for new data input and output formats (ppt, metatool, excel2007...) and 5) many more... read more

You may experience problems when accessing information sourced from the KEGG system. The interface of this information system has changed, which is not yet reflected within the VANTED and KGML-ED tools. We are investigating the problem and will fix it as soon as possible.

The Web Start Version and the installer files available for download have been updated to correct a problem with the drawing of error bars.

The WebStart version of VANTED now contains an enhanced image export command. The size of the output files (PNG / JPG) can now much more easily be modified using three different mode settings (zoom level / absolute height or width in pixel / DPI).

The Download-Versions will be updated at a later time point.

[[url:Info about new version:https://sourceforge.net/news/?group_id=196037&id=283009]]
New installer files are available for Windows, Mac and a ZIP file for Linux or other operating systems. The WebStart version has been updated, too.

V1.8 (23th February, 2010):
* Add-on interface supports version-check.
* From the side panel experiments it is possible to load affymetrix and agilent annotation files. The entrez gene columns are interpreted and processed. Such array data may be mapped to KEGG or used for KEGG BRITE classification tree construction without further work.
* Image export (JPG and PNG) works optionally on all open graphs (click onto the interactive working set text field at the bottom of the parameter dialog, which appears as you click the menu item).
* Increased amount of maximum RAM usage for WebStart and Windows installer version
* Web Start Version for Java 64 bit compatible systems is available from the VANTED Website (utilizes a larger amount of maximum RAM)... read more

[[url:Web-Start:http://vanted.ipk-gatersleben.de/index.php?file=doc2.html]]

The Java Web Start version of VANTED has been updated to V1.78. The installers for Windows, Mac OS X and the generic ZIP version will be updated during this week.

The new version includes improved and enhanced features, mainly suited to Add-on development.

Additionally, problems with the GML import has been resolved, it is now for example possible to load GML files, saved from Cytoscape. ... read more

[[url:Download:http://sourceforge.net/projects/vanted/]]
New installer files are available for Windows, Mac and a ZIP file for Linux or other operating systems. The WebStart version has been updated.

V1.71 (25th August, 2009):
* A number of bug fixed, related to treatment of special characters, which need to be escaped in XML (<,>,')
* Fixed drawing bugs, for cases where data is mapped onto very small nodes
* Fixed small errors related to loading several graph files at once
* z-Level (ordering of drawing) is stored and restored (Layout/Move Elements to Front )

[[url:Download:http://sourceforge.net/projects/vanted/]]
New installer files are available for Windows, Mac and a ZIP file for Linux or other operating systems.

After additional testing the WebStart version will be updated.

V1.70 (10th August, 2009):
* Reduced memory consumption for large graphs with mapped experimental data
* Increased view-recreation speed for large graphs
* Improved Add-on handling, 'find updates'-function button available in Add-on manager dialog
* Basic macro recorder function (disabled by default in the Help/Settings tab), may be used to replicate simple tasks (currently not all functions are logged and stored in the macro file). This function may be a starting point to see how to develop new macros or Java code, which requires the use of existing VANTED functions
* New node shapes (e.g. one that looks like a sheet of paper) and new arrow types to enable improved SBGN graph editing
* Various improvements which enable more flexible Add-on development (e.g. the possibility to add new data-mapping algorithms or to develop views with toolbars on any side of the window)
* It is possible to add invisible labels to nodes. Double click node and add "Annotation" labels, where the position is set to "hidden (not shown)". Annotation labels are considered during data mapping
* Some commands (e.g. data mapping) may work on all open graphs instead of only working with the active graph. In case more than one graph is open, the algorithm properties windows allow the modification of the working set by clicking the corresponding label next to the OK/Cancel buttons. Commands without properties will ask the user for the working set of graphs upon execution with a special dialog
* Improved event handling, tabs stay activated when changing active graph
* "Unstructured" Excel files of experiment data (not structured according to the VANTED templates), can be loaded. The first column needs to contain the substance identifier. Subsequent columns contain experiment data for different conditions or time points. Upon loading such a file, VANTED asks the user to fill in annotation data such as genotype/condition, time point, replicate ID.

The Java Web Start version has been updated to V1.67. PDF and SVG export should now work correctly with non-latin characters. Additional small usability enhancements have been made. Installer files, stored at Source Forge will be updated at a later time point.

[[url:Info:http://sourceforge.net/project/shownotes.php?group_id=196037&release_id=664502]][[url:Download:http://sourceforge.net/project/showfiles.php?group_id=196037]]

(Java WebStart version performs automatic update)

New installer files are available for Windows, Mac and a ZIP file for Linux or other operating systems.

When selecting arrow types where the arrow-head or -tail is not fully filled, the whole edge may disappear after applying the new arrow-head or -tail style. As a work-around for this problem it is suggested, to modify the "Arrow Size" edge attribute at the same time as you modify the "Arrow Head" or "Arrow Tail/Shape" attributes. Change the arrow size from value 1 to a higher number, e.g. 15. Value 1 means, that the arrow size is variable, depending on the Thickness-value of the edge, other values specify the absolute size. This problem will eventually be resolved in one of the next versions.
If the edges are not visible any more and you can thus not select them with the mouse from the view to modify their settings, select all graph elements (Ctrl+A) and set the arrow size to e.g. 15 from the network/edge side panel. The edges will be visible again.

[[url:Release Infos:https://sourceforge.net/project/shownotes.php?group_id=196037&release_id=655500]][[url:Download:https://sourceforge.net/project/showfiles.php?group_id=196037]]A number of bug-fixes and feature enhancements have been implemented and are automatically available to Web Start users, and available for download from SourceForge.

After additional tests the VANTED WebStart version has been updated from v1.54 to v1.63. A list of changes and new features is available at this page: https://sourceforge.net/project/shownotes.php?group_id=196037&release_id=645111

If for one reason older versions of VANTED need to be downloaded and used, you may start older versions, by either clicking the corresponding WebStart (JNLP) links, available from this site:
http://vanted.ipk-gatersleben.de/beta/
or you may download older releases from the SourceForge website:
https://sourceforge.net/project/showfiles.php?group_id=196037&package_id=231514... read more

[[url:Release Infos:http://sourceforge.net/project/shownotes.php?group_id=196037&release_id=645111]]

New installer files are available for Windows, Mac and a ZIP file for Linux or other operating systems.

After additional testing the WebStart version will be updated.

Download Link:
http://sourceforge.net/project/showfiles.php?group_id=196037&package_id=231514&release_id=645111

The KGML Pathway Editor program has been updated to V1.1. A new feature is the automated download of database files, required for processing the KEGG Pathway hierarchy and for working with compound and enzyme identifiers and names. Available from the Help menu, under "Database Status", the database files may be downloaded or updated by clicking the corresponding buttons.

The preferences folder for the program has been modified, it will be migrated (moved) to a system-dependent location (different for Mac, Linux and Windows), so that users of these operating systems are not irritated by a out of place settings folder. The settings folder is opened in the file manager by opening the Help menu and choosing "Preferences". ... read more

A slight update has been made available via Web Start and as a downloadable ZIP/DMG file. A number of improvements, mainly related to SBGN processing have been implemented. A number of small bug fixes and performance improvements are applied.

A new settings folder is automatically used (on Windows and Mac, under Linux the old settings folder is used).

Drag & Drop support has been added, which works on Windows, Mac and Linux, by dragging a file from the file manager to the VANTED window. Under Mac OS X, it is possible to drag files onto the icon of VANTED in the dock or in the file manager. If not yet started, VANTED will be launched and the files will be opened. If the application is already running, the files will be opened.... read more

A new version of VANTED is available. It is modified to work on Java 1.5 and Java 1.6 and thus properly on Mac OS X V10.5. An application bundle for simplified start from the dock is included in the disk image file. Download link: http://vanted.ipk-gatersleben.de/bin.

The newest update includes the follwing new program features:

1) Preliminary support for the SGBN (http://sbgn.org) process diagram "level 1" standard is included. An example pathway, drawn using the new node and edge shapes is available from the side-panel Help/Example Visualizations. Adding SBML conform node shapes and setting corresponding edge-styles is possible with the side panel Pathways/SBGN Template. This side-panel is not visible if no graph file is open (choose File/New or open a file to see this tab).... read more

The Java Web Start version has been updated. The graphviz/dot layout processing has been improved, the edge routing is processed.

The limitation of "input template 1", is that Excel allows here only 255 columns, limiting the number of substances that may be entered in this template. From the experiments tab / save template command, the second button "save template 1 (transposed" now finally works correctly. A example template will be saved, showing how to use the partly transposed version of template 1. Use this template if you want to enter more than 250 substance in the excel template. Don't try to manually "convert" your normal templates to this format; several changes on different places are done, so that VANTED recognises the format correctly. If you need to enter even more data, which does not fit into one of these templates, create a text file from Excel (save as text), and put data for each condition / time point / ... in separate columns. The first column needs to contain the substance identify values. Upon loading VANTED asks for missing annotation data like time point, condition, line and so on. You could use the button "save binary" to save the prepared input data set, so next time you can open the saved ".bin" file, which avoids multiple entering of data annotation when working with text input files.... read more

An alternative launch configuration for VANTED is now available at http://vanted.ipk-gatersleben.de/bin/

As there is for some systems (e.g. 64 bit operating systems) no Java Web Start available, a command line start for VANTED may be useful for some users. Also in some other special use cases, this alternative start configuration may be useful.

The Java Web Start of VANTED is still recommended, as bug fixes and improvements are this way immeadiatly available. When using the ZIP file download, it is highly recommended to enable the checkbox "Download at program start" from the "Help/News" tab, to automatically download and show notices about bug fixes, improvements and newly available command line versions for download.... read more