geWorkbench

Functionality Comments

Rich, add functionality comments and new feature suggestions here.

One quick inital suggestion. geWorkbench should be able to import files in the following GCG formats: sequence, mutiple sequence, and rsf.

(3/23/06) A more robust couterpart of k-means clustering with statistical estimates for micorarray analysis is described in the following papers:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12801869&query_hl=11&itool=pubmed_docsum

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12184810&query_hl=11&itool=pubmed_docsum

3/30/06 I don't like the slider to change arrays in the microarray widow. The identity of an array is a fixed, not a variable quantity. I suggest that a pull-down window for this would be better.

4/7/06 I suggest asking "are you sure" when a user asks to remove a project.

Tutorials Comments

Tutorials comments go here.

The initial download should come with all of the datasets in the tutorial (the cardio set was missing when I installed) OR the tutorial should show where these can be downloaded.

3/30/06: Some mention of what the micorarray viewer does should be included in the manual - i.e that it shows a raw image of the chip.

3/30/06: What it means to merge microarray files should be stated more explicitly.

4/07/06 That the chip recognition message is only shown once should be stated. Alternatively maybe it should be shown each time - but not require an okay button.