Revision as of 11:05, 25 May 2006

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.

4/26/06 It would be very helpful if the workbench could display an hourglass, or a watch, or a sundial or something, when it ia loading or working - for example when it is loading micorarray files from a remote database.

5/25/06. I just installed Version 1.03. In the Windows menu it says version geWorkbench 1.0 and on top of the geWorkbench GUI its says geWorkbench 1.0. I suggest that all labels give the full workbench version.

5/25/06 The two tutorial sets should be included in the download automatially.

5/25/06 I would like to ammend my recommendation of 4/26/06 to inlcude an estimate of the time a task will take, so that people may use it more easily.

5/25/06 When I spoke to the group, Ken had stated that the intensities in the microarray viewer did not correspond to an image of the chip. In which case the phrase "microarray viewer" is misleading. In fact I am not sure to what the intensities an spacing in microarray viewer corresponds.

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.

4/10/06 How to save a merged affy dataset so that one may open it again shoudl be described more clearly. The following points (courtesy of Ken) should be mentioned (and illustated).

1. The set should be saved with an exp suffix.

2. The set can be reopened with the filter set to "Affymatrix Matrix file".

4/24/06 The tutorials comments for opening a remote site are misleading. It should state: 1. Go is clicked for getting the list of micorarray experiments. 2. "Get Bioassays" is necessary for getting a list of arrays in the

  experiment-not for retreival.

3. "open" will retrieve the selcted bioassays. I found this veyr hard to use and required correspondence with Kem and a visit from Xiaoqing in orfer to learn to use it.

4/26/06 I suggest that the tutorial not mention adding a new site for remote downlaod umtil such sites are commonly available. Otehrwise it just begs questions from the reader/

5/25/06 I suggest that the tutorial pages state to which version of geWorkbench they apply. This is implicit in the label of the window, that appears in the screenshot, but it should also be on the web-page that the user unloads.

5/25/06 I suggest that the tutorial pages be downlaodable as a pdf file.

5/25/06 I suggest that there be a public mailing list where users can be notified of updates.

5/25/06 I suggest to what the intensities and layout on the microarray viewer slide be discussed.

5/25/06 I suggest that what is meant by merging microarray datasets be discussed explicitly.