Diff for "New_File_Menu"

New File Menu

In 2.3, the File munu will be re-organized for new features including session saving and XGMML writer. The default save action will be session saving, and other menus will be moved to export menu.

Save Menu

• Save session (Overwrite file, CTL-S)
• Save session as...
• Save current network as XGMML

Load Menu

• Open session (CTL-O)
• Load XGMML Network File
• Load sif file
• Load annotation
• Load Expression Matrix

Export Menu

Currently, Export menu is used for exporting graphics. In 2.3, this will be reorganized as follows:

• Export Network as graphics
• Export network as...
  • sif file
  • sif with annotation (Rowan's format)

• Transform Network with [http://www.w3.org/Style/XSL/ XSL]

By adding XSL transformer, users and developers can transform network files into all kinds of file formats (for example, HTML). Sample XSL files will be provided.

Discussion:

• GaryBader - Jan.13.2006 - You could make the menu simpler by just saying "Save" instead of "Save session". If there is only one save option, it is simpler and you don't have to specify what is saved. Save as... could shortcut to CTRL-SHIFT-S (not very important). Same for 'open session' to 'open'. Also, load could be renamed 'import' - do CYS is the only basic format for Cytoscape and everything else is imported or exported. Also, the import/export should be grouped by data type, so you would have import/export network (GML, XGMML, sif, etc.), annotation (e.g. obo), expression data (e.g. .pvals), image (.png, gif, pdf, etc.). I think that transform could be an option via Cytoscape to make things simpler - so instead of creating a new concept called 'transform' that people must learn, we could just have import and export - they could transform by importing a sif and then exporting to GML. Tranform XSL might be useful as a developer tool, however, so we might want to provide some command line scripts to do common transformations.