The CyDAS Main Window

The CyDAS main window serves for controlling and accessing all the functions of the CyDAS application. It is divided into four sections:

The Menu (1)

The upper section is the menu. Some of the menu items may be disabled depending on environment parameters or group selection.

The File Menu

From the "File" menu, you can manage the Active Group, and external data.

"Open" displays the dialog for selecting a group or subgroup.
"Close" closes the currently active group and all windows pertaining to it.
"New" opens the dialog for creating a new group or subgroup.

"Import" opens the utility for data import.
"Export" is a preliminary export utility for data originating from the Mitelman database.

"Exit" closes the CyDAS application.

The Group Menu

From the "Group" menu, you can retrieve statistical information on the group composition, information on bogus karyotypes, and edit the data proper.

The Edit Menu

The "Edit" menu leads to data (parameter) manipulation forms.

"Drawing Parameters" are explained in the Analysis chapter.
"Mining Parameters" are explained in the Data Mining chapter.
"Group" allows for the editing of the group (which patients are part of the group).
"Classification" leads to Clinical Classification Systems.
"Breakpoint Search" adds breakpoints for common aberrations which are often omitted (e.g. t(9;22)->t(9;22)(q34;q11).
"Clean Up DB" removes unlinked data from the data base.

The Analyse Menu

The "Analyse" menu leads to basic analysis of the karyotypes of the active group. Gains and losses, and break points are calculated per chromosomal band and displayed as sensitive graphical maps or as a table.

The Mine Menu

The "Mine" menu offers deeper analysis of the cytogenetic data. It searches for patterns in the data.

"Evolution Tree" displays putative pathways of karyotype evolution and information on selected steps.
"Dependence Network" shows dependence of pairs of aberrations.
"Aberration Count Distribution" shows the distribution of aberration towards the complexity of the karyotype.
"Cluster Analysis" clusters similiar karyotypes into groups (not yet implemented).

The "Other" Menu

The "Other" menu points to functionality which does not require a group or subgroup to be activated.

"Develop Karyogram": You may develop a karyogram from an ISCN formula and add additional rearrangements using a graphical interface.
"Derivative Chromosome" is a utility for drawing ideograms of derivative chromosomes.
"Analyse ISCN" allows for the analysis of a simple or composite ISCN formula showing virtually all information which can be extracted from such a formula.

The Window Menu

From the windows menu, you can control the appearance of the main window (see the chapters on the Toolbar and Status Line,resp.).

Access to other windows of the CyDAS application is planned but not yet implemented.

The Help Menu

The "Help" menu is intended to provide you some information on the forms and fucntionality of the CyDAS application. It has not yet been implemented upto now.

The "About" submenu displays the "About" form informing you on the authors and licence agreement of CyDAS.

Toolbar (2)

Below the menu, there is space for a toolbar. This toolbar is not yet implemented, and can be made invisible by deselecting "Window - Show Toolbar" in the menu.

Status Line (3)

The status line shows which group or subgroup is presently selected as active group.

It can be made invisible by deselecting "Window - Show Status" in the menu.

Info Panel (4)

The info panel is planned to be used for showing further information on the group.