Changelog

Caleydo 1.3, February, 2, 2010

New Features

General:

  • Added Mouse (Mus musculus) support.
  • Project save, restore support including auto-save.
  • Support for several gene identifiers when importing data.
  • Pathways are now re-distributed with Caleydo - no more fetching is necessary.
  • New Radial Layout view for exploring cluster hierarchies.
  • It is now possible to bookmark both genes and experiments.
  • New sample project which makes it easier to explore the Caleydo functionality.

Hierarchal heat map:

  • Added dendrograms for both experiments and genes including sub-dendrograms on the detail levels.
  • Added cut-off sliders to dynamically determine clusters when using dendrograms.
  • Added group (cluster) visualization.
  • When right-clicking a group this group can now be exported, or pathways containing more than one gene in the group can be searched.

Fixed Bugs

For fixed bugs refer to our bug tracker.

Caleydo 1.2.5, August, 4, 2009

Fixed Bugs

  • Fixed pathway fetching error caused by external database updates

Caleydo 1.2.4, June, 8, 2009

Fixed Bugs

  • List heat map works as intended

Caleydo 1.2.3, May, 29, 2009

New Features

  • Caleydo now remembers the type of analysis (gene or general) you used previously
  • Caleydo now only shows the buttons that actually make sense in general data analysis mode
  • When exporting you can now decide which data, associated with which view to export (heat map, bucket or parallel coordinates)
  • Reduced startup speed and memory footprint of general data analysis significantly

Fixed Bugs

  • Tabular data viewer now shows the original, not the normalized values
  • Tabular data viewer now works in the general data analysis mode
  • Again a lot of clustering problems are fixed
  • Exporting in general data mode now works
  • Caleydo now truly treats empty cells in a file to import as NaN
  • Update of color-mapper when loading files during runtime now works correctly
  • Fixed a bug concerning the connection lines in the bucket - they wrongly connected axes when an axes was selected.

Caleydo 1.2.2, May, 25, 2009

Fixed Bugs

  • Fixed issues with clustering and clustering dialogs.

Caleydo 1.2.1, May, 20, 2009

Fixed Bugs

  • Fixed issue with connection lines in bucket, which were wrong in some cases
  • Fixed some bugs in clustering dialogs

Caleydo 1.2, May, 18, 2009

New Features

  • New extensive Help Section
  • Added support for general data (non gene-expression data)
  • Clustering: Caleydo now supports four different cluster algorithms, two partitional (Affinity Propagation and K-Means) and two hierarchical (CobWeb and Average Linkage) for genes and also experiments
  • Keyboard can now be used to browse through the heat maps (cursor keys)
  • Context menu: a newly added context menu simplifies the triggering of actions such as loading pathways, bookmarking genes etc.
  • Completely redesigned color mapping view including a histogram
  • Completely redesigned and improved search view
  • The zoomed view now shows the pool and the gene bookmark
  • The zoomed view now adapts to the screen resolution
  • The gene book mark (previously called "list heat map") can be cleared now
  • When a pathway is loaded from an external view, the bucket is made visible automatically
  • Improved stability, improved thread-safety
  • New method for expression mapping: by activating expression mapping, the nodes are shown in the color associated with the expression value of the currently selected experiment. By selecting other experiments, the colors of all nodes change
  • The heat map now reacts to deselections from the parallel coordinates, by fading out the corresponding values
  • New logging view
  • Hierachical heat map now can handle small datasets as well

Caleydo 1.1, March 10th, 2009

New Features

  • New Hierarchical Heat Map that allows to browse all genes
  • New Tabular Data View that shows you your data in a spreadsheet - which is synchronized with the other views
  • Many newly designed elements
  • New export functionality that enables you to save and re-read results of your analysis
  • New method for browsing a set of selected genes by propagating them and viewing them in a "list heat map" next to the bucket and the parallel coordinates
  • New way of applying random sampling: only the displayed elements are sampled, all operations are executed on the whole dataset. Also the sample automatically adapts to the number of visible element resulting in all elements being visible once a selection was narrowed down.
  • New user interface that improves clarity
  • New navigation features in the Bucket including drag and drop and removing of views.
  • Re-ordering, duplicating and removing of experiments is now synchronized across all views.
  • Drag and drop for re-ordering axes in the parallel coordinates
  • New global brush in the parallel coordinates that allows you to filter out all genes that never leave a threshold
  • New way to handle NaN values in the parallel coordinates
  • Experiment selection now possible in heat map

Caleydo 1.0.2, November 11th, 2008

New Features

  • Views have a new "reset view" function that clears all changes
  • Genes in pool layer are highlighted as well
  • Added log base 2 support
  • Added an XP classic style mode. (Enable via Preferences -> General)
  • Added support for different filter levels (all genes - genes with DAVID mapping - genes that occur in pathways). All genes mode is slow, needs improvement.
  • Data loader is now a view, not only a dialog. This allows runtime changes to data.

Fixed Bugs

  • Color mapping now uses correct values on reset default
  • Default color for NaN set to gray
  • Improved mouse events under windows, needs further testing
  • Min and max works now separately
  • Pathways can be loaded more than once now
  • Selection consistency when moving views improved
  • Data RefSeq mapping loader ignores version of RefSeqs (NM_*.* -> NM_*).
  • Multiple RefSeq numbers per micro-array spot in data files are ignored because they all point to the same DAVID gene ID.
  • All experiments in data loader are selected by default.
  • Corrected mapping of genes to actual values
  • Browser now does not complain all the time when it is offline
  • All delimiters for data import work now (not only Tab)

Caleydo 1.0.1, October 21th, 2008

  • Added proxy support for pathway download
  • Added NAN (not a number) support
  • Improved connection lines by using curved edge bundling
  • Improved look and feel

Version 1.0, October 6th, 2008

  • Initial release version

Application

The usage of the Caleydo is free for non-commercial use. You may not sell, rent, lease or sublicense Caleydo. You may not use Caleydo to further a business purpose. By downloading Caleydo you agree to these terms.

If you have troubles running Caleydo please refer to the Help Section.

Webstart

The webstart version runs on Windows and Linux. If you are running into problems with the webstart version, please try the stand-alone application.

Start Caleydo
Caleydo 1.2.5, All Platforms

Stand-alone Application

The stand-alone version of Caleydo is available for Windows and Linux 32-bit machines. A 64-bit version can be provided upon request. You have to download the compressed file and extract it to your local hard disk.


Caleydo 1.2.5, Windows XP, 2000 - 32-bit (zip-compressed)

Caleydo 1.2.5, Windows Vista - 32-bit (zip-compressed)

Caleydo 1.2.5, Linux - 32-bit (tar.gz-compressed)

Changelog

Caleydo 1.2.5, August, 4, 2009

Fixed Bugs

  • Fixed pathway fetching error caused by external database updates

Caleydo 1.2.4, June, 8, 2009

Fixed Bugs

  • List heat map works as intended

Caleydo 1.2.3, May, 29, 2009

New Features

  • Caleydo now remembers the type of analysis (gene or general) you used previously
  • Caleydo now only shows the buttons that actually make sense in general data analysis mode
  • When exporting you can now decide which data, associated with which view to export (heat map, bucket or parallel coordinates)
  • Reduced startup speed and memory footprint of general data analysis significantly

Fixed Bugs

  • Tabular data viewer now shows the original, not the normalized values
  • Tabular data viewer now works in the general data analysis mode
  • Again a lot of clustering problems are fixed
  • Exporting in general data mode now works
  • Caleydo now truly treats empty cells in a file to import as NaN
  • Update of color-mapper when loading files during runtime now works correctly
  • Fixed a bug concerning the connection lines in the bucket - they wrongly connected axes when an axes was selected.

Caleydo 1.2.2, May, 25, 2009

Fixed Bugs

  • Fixed issues with clustering and clustering dialogs.

Caleydo 1.2.1, May, 20, 2009

Fixed Bugs

  • Fixed issue with connection lines in bucket, which were wrong in some cases
  • Fixed some bugs in clustering dialogs

Caleydo 1.2, May, 18, 2009

New Features

  • New extensive Help Section
  • Added support for general data (non gene-expression data)
  • Clustering: Caleydo now supports four different cluster algorithms, two partitional (Affinity Propagation and K-Means) and two hierarchical (CobWeb and Average Linkage) for genes and also experiments
  • Keyboard can now be used to browse through the heat maps (cursor keys)
  • Context menu: a newly added context menu simplifies the triggering of actions such as loading pathways, bookmarking genes etc.
  • Completely redesigned color mapping view including a histogram
  • Completely redesigned and improved search view
  • The zoomed view now shows the pool and the gene bookmark
  • The zoomed view now adapts to the screen resolution
  • The gene book mark (previously called "list heat map") can be cleared now
  • When a pathway is loaded from an external view, the bucket is made visible automatically
  • Improved stability, improved thread-safety
  • New method for expression mapping: by activating expression mapping, the nodes are shown in the color associated with the expression value of the currently selected experiment. By selecting other experiments, the colors of all nodes change
  • The heat map now reacts to deselections from the parallel coordinates, by fading out the corresponding values
  • New logging view
  • Hierachical heat map now can handle small datasets as well

Caleydo 1.1, March 10th, 2009

New Features

  • New Hierarchical Heat Map that allows to browse all genes
  • New Tabular Data View that shows you your data in a spreadsheet - which is synchronized with the other views
  • Many newly designed elements
  • New export functionality that enables you to save and re-read results of your analysis
  • New method for browsing a set of selected genes by propagating them and viewing them in a "list heat map" next to the bucket and the parallel coordinates
  • New way of applying random sampling: only the displayed elements are sampled, all operations are executed on the whole dataset. Also the sample automatically adapts to the number of visible element resulting in all elements being visible once a selection was narrowed down.
  • New user interface that improves clarity
  • New navigation features in the Bucket including drag and drop and removing of views.
  • Re-ordering, duplicating and removing of experiments is now synchronized across all views.
  • Drag and drop for re-ordering axes in the parallel coordinates
  • New global brush in the parallel coordinates that allows you to filter out all genes that never leave a threshold
  • New way to handle NaN values in the parallel coordinates
  • Experiment selection now possible in heat map

Caleydo 1.0.2, November 11th, 2008

New Features

  • Views have a new "reset view" function that clears all changes
  • Genes in pool layer are highlighted as well
  • Added log base 2 support
  • Added an XP classic style mode. (Enable via Preferences -> General)
  • Added support for different filter levels (all genes - genes with DAVID mapping - genes that occur in pathways). All genes mode is slow, needs improvement.
  • Data loader is now a view, not only a dialog. This allows runtime changes to data.

Fixed Bugs

  • Color mapping now uses correct values on reset default
  • Default color for NaN set to gray
  • Improved mouse events under windows, needs further testing
  • Min and max works now separately
  • Pathways can be loaded more than once now
  • Selection consistency when moving views improved
  • Data RefSeq mapping loader ignores version of RefSeqs (NM_*.* -> NM_*).
  • Multiple RefSeq numbers per micro-array spot in data files are ignored because they all point to the same DAVID gene ID.
  • All experiments in data loader are selected by default.
  • Corrected mapping of genes to actual values
  • Browser now does not complain all the time when it is offline
  • All delimiters for data import work now (not only Tab)

Caleydo 1.0.1, October 21th, 2008

  • Added proxy support for pathway download
  • Added NAN (not a number) support
  • Improved connection lines by using curved edge bundling
  • Improved look and feel

Version 1.0, October 6th, 2008

  • Initial release version

Videos

The video presenting Caleydo on YouTube, December 2009

The video presenting Caleydo and the Bucket on YouTube, December 2008

Demonstration video for EuroVis08 paper, also available on YouTube, November 2007


website maintained by Marc Streit and Alexander Lex
last updated on 2010-07-29