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 upper section is the menu. Some of the menu items may be disabled depending on environment parameters or group selection.
From the "File" menu, you can manage the Active Group, and external data.
"Exit" closes the CyDAS application.
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 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 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 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 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.
Access to other windows of the CyDAS application is planned but not yet implemented.
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.
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.
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.
The info panel is planned to be used for showing further information on the group.