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© 2010 - 2024 Thallinger Lab · Institute of Biomedical Informatics ·
Graz University of Technology · Stremayrgasse 16/I, 8010 Graz, Austria Tel +43-316-873-5343 · Fax +43-316-873-105343 · URL http://genome.tugraz.at · 
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| NEWS AND UPDATES | |
| 18 Jan 2017 | New release - 1.8.1
 Gene Ontology feature reworked. Greatly enhanced performance
and fixed several bugs in the Gene Ontology view. Added current EBI and Ensembl Gene Ontology databases in the
GO Database Connection dialog. Fixed several rare error messages when switching UI views
|
| 21 Dec 2016 | New release - 1.8.0
New feedback function! Send bug reports, feature requests,
and comments directly through Genesis! New linkage methods for HCL clustering: Ward, Centroid,
Median, Group Average (UPGMA) and Flexible Linkage New distance function: Mahalanobis distance
CA now also supports 2D scatter plots
Randomization test for variable (in)dependence in KMC
Ability to add gaps to expression view by holding shift and dragging
Ability to display filtering results directly in Genesis instead
of having to save them first Improved KMC results by performing multiple runs with randomized
starting clusters Added function save bottom and top N genes
Ability to multi-select and delete groups
Gene/sample groups can now be consolidated
Normalization function now ignores NA values
Added option to make KMC clusters private
Added heatmaps, centroid view and individual expression images
for HCL Sample clusters Fixed bug where previously stored KMC results from a project file
were loaded wrong Fixed external database search
Fixed display bug where very long sample names were cut off
Fixed image saving dialog hanging if no file type and no file
extension were provided Progress Bar at kmeansAnalysis now slightly more accurate
Range filtering now accepts all genes that match the critera instead
of removing them Fixed error when running HCL for a data set that had more
experiments than genes Improved sample names display on Mac OSX
Some other minor bugfixes
|
| 10 Apr 2015 | New release - 1.7.7
PCA now also available as 2D scatter plots!
Updated Java3D to version 1.6.0
Fixed previously saved KMC results read wrong
Fixed error when using HCL with more experiments than genes
Dual screen support should be more reliable now
PCA no longer fails if the dataset contains NaN values
SVG images that are larger than the window are no longer clipped
Sample names are no longer cut off in SVG images
Saved images now have a set margin (can be set in Program Properties)
Auto cropping blank areas from saved images
3D view menu bar now works better with Windows 7 Look and Feel
Proper error handling when saving an image with insufficient permissions
Genesis should no longer stall if your .genesis folder got corrupted
Choppy legend for PCA 3D view is now much smoother
|
| 29 Sep 2010 | New Release - 1.7.6
Semi-automatic cluster assignement after HCL
Use HCL from the command line without GUI
K-means Next Nearest Neighbor analysis
Gamma correction of color scales
Export entire gene list with cluster numbers
Log10 transform for better representation of p-values
Additional Sorting: Sort by Trend
Define cluster color and name in the same dialog
Extend "Data Table" panel
Extend the Eigenvalue table from PCA and CA
Allow Clipboard copy of "System Information" panel contents
Add "Cluster Information" to of clustering results
Change name of tree node for hierarchical clustering
PCA Eigenvector display in tabular form
Improve GO Database Connection Dialog
Fixed header width can be set from the View menu
Minimum and maximum for color scale can be set separately
Numerous bugfixes and improvements
|
| 04 Mar 2009 | New Release - 1.7.5 Fixed behaviour of color options Single/Double
Filter option Coefficient of Variation added
Issue with displaying Genesis Server jobs fixed
Numerous bug fixes and improvements in the display
of clustering results |
| 28 Jan 2009 | New Release - 1.7.4 Problem with launching on Mac OS fixed
Improved color grouping features
|
| 10 Nov 2008 | New Release - 1.7.3 Color Group definition added
Updated default GO Connection settings
Better handling of export to EPS format
Improved support for Linux and Mac OS
Numerous bug fixes and improvements
|
| 22 Nov 2006 | New Release - 1.7.2 Import of Genepix result files fixed Open file dialog behavior after using plugins fixed |
| 03 Nov 2006 | New Release - 1.7.1 Launch file for Mac OSX fixed |
| 14 Jul 2006 | New Release - 1.7.0 Numerous bug fixes and improvements New demo license valid until 31 August 2006 |
| 06 Jun 2005 | New Release - 1.6.0 Designed and developed for Java 5.0 (1.5.0) New algorithm: Gene Expression Terrain Maps New algorithm: Figure of Merit Single gradient color schemes for e.g. Affymetrix data Redesigned for the new GO database schemas New GO overview page Numerous bug fixes and improvements New demo license valid until 31 July 2005 |
| 01 Oct 2004 | New Release - 1.5.0 User definable properties for pie charts (Settings->Program properties) New
saving of gene and sample similarity matrices Numerous bug fixes and improvements New demo license valid until 30 November 2004 |
| 05 July 2004 | New Release - 1.5.0 Beta 1 Genes
can be searched in all cluster results and GO views Automatic scrolling to search results. New distance measurement: Chebychev distance. User
definable links to external databases Sorting genes by gene group affiliation. New data adjustment: Divide Genes/Experiments by Variance Numerous bug fixes and improvements New demo license valid until 31 August 2004 |
| 10 Mar 2004 | New Release - 1.4.0 Integration of the Gene Ontology (GO) into Genesis. Graphical view of GO terms. Mapping of gene clusters onto GO terms. Saving of images as Scalable Vector Graphics (SVG) Fixed header for better scrolling Saving of ordered cluster gene and sample lists. Merging of datasets now possible Improved GenBank flat file reader for new GenBank format Numerous bug fixes and improvements New demo license valid until 30 April 2004 |
| 17 Nov 2003 | New Release - 1.3.0 Saving of Project data (groups, settings, all clustering results)
in xml. One-way ANOVA for detection of differentially expressed genes Straightforward gene and sample group declaration New Color configuration dialog with much more settings Gradient painting in expression views All gene tree functions also for sample trees Complete rewriting of the code for better readability and maintenance
Improved GenBank flat file reader for new GenBank format Numerous bug fixes and improvements New demo license valid until 31 December 2003 |
| 31 July 2003 | New Release - 1.2.2 Some bugs fixed
Java 1.4.2 now officially supported and recommended Tree selections and clusters can now be saved as images
Windows XP and GTK+ look and feel supported New start script for MacOSX (GenesisMacOSX) New
start script for problems with DirectDraw (e.g. NVidia) New demo license valid until 30 September 2003 |
| 02 June 2003 | New Release - 1.2.1 Some bugs fixed
New demo license valid until 31 July 2003 |
| 08 April 2003 | New Release - 1.2.0 Redesign
of the client-server communication using SOAP Corresponence Analysis (CA) Complete redesign of the PCA and CA 3D-views Interactive
selecting of genes and/or experiments in the PCA view Fullscreen 3D-view Resetting the view to default values now possible New Range (Min/Max) filter Gene
groups and sample groups can be specified with an xml file Recovery
system to prevent file corruption by a program termination Better
pattern overview in SOM and KMC expression view Some bugs fixed |
| 31 Oct. 2002 | New Release - 1.1.3 Tasposition of expression matrix now possible Java 1.4.1 now officially supported and recommended New demo license valid until 30 November 2002 |
| 16 Sept. 2002 | New Release - 1.1.2 Unix, Linux and Max OS X starting problems fixed Problem using older java releases (prior 1.4) fixed Better debugging with system log in the program properties folder New demo license valid until 31 October 2002 |
| 03 Sept. 2002 | New Release - 1.1.1 Bugfix concerning Correlation Coefficients and KMC, SOM, SVM Improved transparancy which distance function is in use. | 30 July 2002 | New Release - 1.1 Full client-server functionality for clustering Sorting of genes (variety of different sorting methods) Java 1.4 now officially supported and recommended New demo license valid until 30 September 2002 |
| 29 May 2002 | New Release - 1.0.2 Scanning of GenBank files can now be aborted Saved images of GenBank entries now without the toolbar Font problem with Java 1.4.0 solved Mac OS X start script problem solved Rollover effect in images can be turned off (useful for Mac OS X) Case sensitive search option Marking of genes in images from searches can be turned off New demo license valid until 31 July 2002 |
| 28 Mar 2002 | New Release - 1.0.1 Much better SVM results presentation (expression images, plots, etc.) Full cluster functionality now also for SVM Results (public clusters....) Search function for genes based on unique-ids or gene names GenePix results file reader plugin Java3D check before PCA results are displayed GenBank flat-file parser improved (*.gbs files now supported) New icons with 256 colors New demo license valid until 31 May 2002 |
| 12 Mar 2002 | New Release - Installation and Yeast data New additional installation using InstallAnywhere Latest yeast GenBank files from 10 March 2002 incorporated |
| 28 Feb 2002 | New Release - Licensing New demo license valid until 31 March 2002 |
| 17 Feb 2002 | New Release - Bug fixing New thread architecture to fix problems with Linux Java 1.3.1 Minor changes to Genesis Look&Feel |
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