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THALLINGER LAB
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NEWS AND UPDATES

18 Jan 2017New release - 1.8.1
    icon  Gene Ontology feature reworked. Greatly enhanced performance
        and fixed several bugs in the Gene Ontology view.
    icon  Added current EBI and Ensembl Gene Ontology databases in the
        GO Database Connection dialog.
    icon  Fixed several rare error messages when switching UI views
21 Dec 2016New release - 1.8.0
    icon  New feedback function! Send bug reports, feature requests,
        and comments directly through Genesis!
    icon  New linkage methods for HCL clustering: Ward, Centroid,
        Median, Group Average (UPGMA) and Flexible Linkage
    icon  New distance function: Mahalanobis distance
    icon  CA now also supports 2D scatter plots
    icon  Randomization test for variable (in)dependence in KMC
    icon  Ability to add gaps to expression view by holding shift and dragging
    icon  Ability to display filtering results directly in Genesis instead
        of having to save them first
    icon  Improved KMC results by performing multiple runs with randomized
        starting clusters
    icon  Added function save bottom and top N genes
    icon  Ability to multi-select and delete groups
    icon  Gene/sample groups can now be consolidated
    icon  Normalization function now ignores NA values
    icon  Added option to make KMC clusters private
    icon  Added heatmaps, centroid view and individual expression images
        for HCL Sample clusters
    icon  Fixed bug where previously stored KMC results from a project file
         were loaded wrong
    icon  Fixed external database search
    icon  Fixed display bug where very long sample names were cut off
    icon  Fixed image saving dialog hanging if no file type and no file
        extension were provided
    icon  Progress Bar at kmeansAnalysis now slightly more accurate
    icon  Range filtering now accepts all genes that match the critera instead
        of removing them
    icon  Fixed error when running HCL for a data set that had more
        experiments than genes
    icon  Improved sample names display on Mac OSX
    icon  Some other minor bugfixes
10 Apr 2015New release - 1.7.7
    icon  PCA now also available as 2D scatter plots!
    icon  Updated Java3D to version 1.6.0
    icon  Fixed previously saved KMC results read wrong
    icon  Fixed error when using HCL with more experiments than genes
    icon  Dual screen support should be more reliable now
    icon  PCA no longer fails if the dataset contains NaN values
    icon  SVG images that are larger than the window are no longer clipped
    icon  Sample names are no longer cut off in SVG images
    icon  Saved images now have a set margin (can be set in Program Properties)
    icon  Auto cropping blank areas from saved images
    icon  3D view menu bar now works better with Windows 7 Look and Feel
    icon  Proper error handling when saving an image with insufficient permissions
    icon  Genesis should no longer stall if your .genesis folder got corrupted
    icon  Choppy legend for PCA 3D view is now much smoother

29 Sep 2010New Release - 1.7.6
    icon  Semi-automatic cluster assignement after HCL
    icon  Use HCL from the command line without GUI
    icon  K-means Next Nearest Neighbor analysis
    icon  Gamma correction of color scales
    icon  Export entire gene list with cluster numbers
    icon  Log10 transform for better representation of p-values
    icon  Additional Sorting: Sort by Trend
    icon  Define cluster color and name in the same dialog
    icon  Extend "Data Table" panel
    icon  Extend the Eigenvalue table from PCA and CA
    icon  Allow Clipboard copy of "System Information" panel contents
    icon  Add "Cluster Information" to of clustering results
    icon  Change name of tree node for hierarchical clustering
    icon  PCA Eigenvector display in tabular form
    icon  Improve GO Database Connection Dialog
    icon  Fixed header width can be set from the View menu
    icon  Minimum and maximum for color scale can be set separately
    icon  Numerous bugfixes and improvements

04 Mar 2009New Release - 1.7.5
    icon  Fixed behaviour of color options Single/Double
    icon  Filter option Coefficient of Variation added
    icon  Issue with displaying Genesis Server jobs fixed
    icon  Numerous bug fixes and improvements in the display
        of clustering results

28 Jan 2009New Release - 1.7.4
    icon  Problem with launching on Mac OS fixed
    icon  Improved color grouping features

10 Nov 2008New Release - 1.7.3
    icon  Color Group definition added
    icon  Updated default GO Connection settings
    icon  Better handling of export to EPS format
    icon  Improved support for Linux and Mac OS
    icon  Numerous bug fixes and improvements

22 Nov 2006New Release - 1.7.2
    icon  Import of Genepix result files fixed
    icon  Open file dialog behavior after using plugins fixed

03 Nov 2006New Release - 1.7.1
    icon  Launch file for Mac OSX fixed

14 Jul 2006New Release - 1.7.0
    icon  Numerous bug fixes and improvements
    icon  New demo license valid until 31 August 2006

06 Jun 2005New Release - 1.6.0
    icon  Designed and developed for Java 5.0 (1.5.0)
    icon  New algorithm: Gene Expression Terrain Maps
    icon  New algorithm: Figure of Merit
    icon  Single gradient color schemes for e.g. Affymetrix data
    icon  Redesigned for the new GO database schemas
    icon  New GO overview page
    icon  Numerous bug fixes and improvements
    icon  New demo license valid until 31 July 2005

01 Oct 2004New Release - 1.5.0
    icon  User definable properties for pie charts (Settings->Program properties)
    icon  New saving of gene and sample similarity matrices
    icon  Numerous bug fixes and improvements
    icon  New demo license valid until 30 November 2004

05 July 2004New Release - 1.5.0 Beta 1
    icon  Genes can be searched in all cluster results and GO views 
    icon  Automatic scrolling to search results.
    icon  New distance measurement: Chebychev distance.
    icon  User definable links to external databases
    icon  Sorting genes by gene group affiliation.
    icon  New data adjustment: Divide Genes/Experiments by Variance
    icon  Numerous bug fixes and improvements
    icon  New demo license valid until 31 August 2004

10 Mar 2004New Release - 1.4.0
    icon  Integration of the Gene Ontology (GO) into Genesis. 
    icon  Graphical view of GO terms.
    icon  Mapping of gene clusters onto GO terms.
    icon  Saving of images as Scalable Vector Graphics (SVG)
    icon  Fixed header for better scrolling
    icon  Saving of ordered cluster gene and sample lists.
    icon  Merging of datasets now possible
    icon  Improved GenBank flat file reader for new GenBank format
    icon  Numerous bug fixes and improvements
    icon  New demo license valid until 30 April 2004
 
17 Nov 2003New Release - 1.3.0
    icon   Saving of Project data (groups, settings, all clustering results) in xml. 
    icon  One-way ANOVA for detection of differentially expressed genes
    icon  Straightforward gene and sample group declaration
    icon  New Color configuration dialog with much more settings
    icon  Gradient painting in expression views
    icon  All gene tree functions also for sample trees
    icon  Complete rewriting of the code for better readability and maintenance
    icon  Improved GenBank flat file reader for new GenBank format
    icon  Numerous bug fixes and improvements
    icon  New demo license valid until 31 December 2003

31 July 2003New Release - 1.2.2
    icon  Some bugs fixed
    icon  Java 1.4.2 now officially supported and recommended
    icon  Tree selections and clusters can now be saved as images
    icon  Windows XP and GTK+ look and feel supported
    icon  New start script for MacOSX (GenesisMacOSX)
    icon  New start script for problems with DirectDraw (e.g. NVidia)
    icon  New demo license valid until 30 September 2003

02 June 2003New Release - 1.2.1
    icon  Some bugs fixed
    icon  New demo license valid until 31 July 2003

08 April 2003New Release - 1.2.0
    icon  Redesign of the client-server communication using SOAP
    icon  Corresponence Analysis (CA)
    icon  Complete redesign of the PCA and CA 3D-views
    icon  Interactive selecting of genes and/or experiments in the PCA view
    icon  Fullscreen 3D-view
    icon  Resetting the view to default values now possible
    icon  New Range (Min/Max) filter
    icon  Gene groups and sample groups can be specified with an xml file
    icon  Recovery system to prevent file corruption by a program termination
    icon  Better pattern overview in SOM and KMC expression view
    icon   Some bugs fixed

31 Oct. 2002New Release - 1.1.3
    icon  Tasposition of expression matrix now possible 
    icon  Java 1.4.1 now officially supported and recommended
    icon  New demo license valid until 30 November 2002

16 Sept. 2002New Release - 1.1.2
    icon  Unix, Linux and Max OS X starting problems fixed 
    icon  Problem using older java releases (prior 1.4) fixed
    icon  Better debugging with system log in the program properties folder
    icon  New demo license valid until 31 October 2002

03 Sept. 2002 New Release - 1.1.1
    icon  Bugfix concerning Correlation Coefficients and KMC, SOM, SVM 
    icon  Improved transparancy which distance function is in use.

30 July 2002 New Release - 1.1
    icon  Full client-server functionality for clustering 
    icon  Sorting of genes (variety of different sorting methods)
    icon  Java 1.4 now officially supported and recommended
    icon  New demo license valid until 30 September 2002

29 May 2002 New Release - 1.0.2
    icon  Scanning of GenBank files can now be aborted 
    icon  Saved images of GenBank entries now without the toolbar
    icon  Font problem with Java 1.4.0 solved
    icon  Mac OS X start script problem solved
    icon  Rollover effect in images can be turned off (useful for Mac OS X)
    icon  Case sensitive search option
    icon  Marking of genes in images from searches can be turned off
    icon  New demo license valid until 31 July 2002

28 Mar 2002 New Release - 1.0.1
    icon  Much better SVM results presentation (expression images, plots, etc.) 
    icon  Full cluster functionality now also for SVM Results (public clusters....)
    icon  Search function for genes based on unique-ids or gene names
    icon  GenePix results file reader plugin
    icon  Java3D check before PCA results are displayed
    icon  GenBank flat-file parser improved (*.gbs files now supported)
    icon  New icons with 256 colors
    icon  New demo license valid until 31 May 2002
 
12 Mar 2002 New Release - Installation and Yeast data
    icon  New additional installation using InstallAnywhere 
    icon  Latest yeast GenBank files from 10 March 2002 incorporated

28 Feb 2002 New Release - Licensing
    icon  New demo license valid until 31 March 2002

17 Feb 2002New Release - Bug fixing
    icon   New thread architecture to fix problems with Linux Java 1.3.1 
    icon   Minor changes to Genesis Look&Feel
 
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