Comments on geWorkbench - Revision history

Bjagla: /* Promoter Panel */

2008-09-11T18:35:05Z

‎Promoter Panel

Bjagla: /* Sets */

2008-09-11T18:30:31Z

‎Sets

Bjagla: /* Project Folders */

2008-09-11T18:27:50Z

‎Project Folders

Bjagla: /* Programmatic features */

2008-09-11T18:15:39Z

‎Programmatic features

Bjagla: /* General Features */

2008-09-11T18:10:05Z

‎General Features

Bjagla: /* Feature requests not listed in Mantis */

2008-09-11T16:27:25Z

‎Feature requests not listed in Mantis

Bjagla: /* Feature requests not listed in Mantis */

2008-03-10T19:02:57Z

‎Feature requests not listed in Mantis

Bjagla: /* Feature requests not listed in Mantis */

2008-02-01T14:23:32Z

‎Feature requests not listed in Mantis

Bjagla: /* Feature requests not listed in Mantis */

2007-10-04T14:32:14Z

‎Feature requests not listed in Mantis

Bjagla: /* Feature requests not listed in Mantis */

2007-10-03T19:56:02Z

‎Feature requests not listed in Mantis

@@ Line 370: / Line 370: @@
 : After loading the attached transcription factor trough the "Add TF" button, the new TF entry appears in the Selected TF list (I was actually expecting it to appear in the TF Mapping list but this is not a big deal). When I double click on the new TF it moves (correctly) to the TF Mapping list. When I then go to the TF Mapping list and double click on the new TF again, I get an exception and the TF disappears from both lists
-* Mantis [http://mantis.cu-genome.org/view.php?id=0000712 0000712]: Promoter Panel Logo Tab needs a header
+<s>* Mantis [http://mantis.cu-genome.org/view.php?id=0000712 0000712]: Promoter Panel Logo Tab needs a header
-:It would be good to change the color of the currently selected TF. Now it is just a little bit darker blue. Try Black or red/ light red.
+:It would be good to change the color of the currently selected TF. Now it is just a little bit darker blue. Try Black or red/ light red. </s>
 * Mantis [http://mantis.cu-genome.org/view.php?id=0000653 0000653]: position of promoter panel
@@ Line 382: / Line 382: @@
 :Especially when changing parameters it can be really annoying.
-* Mantis [http://mantis.cu-genome.org/view.php?id=0000660 0000660]: selection is not used for pattern discovery
+<s>* Mantis [http://mantis.cu-genome.org/view.php?id=0000660 0000660]: selection is not used for pattern discovery
-:=> It is a known issue and need further discussion.
+:=> It is a known issue and need further discussion. </s>
 * Mantis [http://mantis.cu-genome.org/view.php?id=0000697 0000697]: progress bar color doesn't change to red if process is interrupted under MAC

@@ Line 344: / Line 344: @@
 === Sets ===
-* Mantis [http://mantis.cu-genome.org/view.php?id=0000381 0000381]: Renaming a label erases its class (case, control, etc.) status.
+<s>* Mantis [http://mantis.cu-genome.org/view.php?id=0000381 0000381]: Renaming a label erases its class (case, control, etc.) status.
-Renaming a label erases its class (case, control, etc.) status. To reproduce, set a label's class to 'case', then rename that label.
+Renaming a label erases its class (case, control, etc.) status. To reproduce, set a label's class to 'case', then rename that label. </s>
 * Mantis [http://mantis.cu-genome.org/view.php?id=0000451 0000451]: if filter after clustering, dendrograms become invalid

@@ Line 300: / Line 300: @@
 :1. load a data set with more than one array; 2. add both arrays to a new set called "a"; 3. add array 2 to a new set called "b"; 4. create a new phenotype set; collection by clicking on "New"; 5. save the data as "test.exp" on your desktop; 6. open the file again with geWorkbench; => only set "a" is retained. all information about set "b" is lost
-* Mantis [http://mantis.cu-genome.org/view.php?id=0000730 0000730]: feature request: union / intersection
+<s>* Mantis [http://mantis.cu-genome.org/view.php?id=0000730 0000730]: feature request: union / intersection
-: being able to combine e.g. fasta sequence/merge data sets
+: being able to combine e.g. fasta sequence/merge data sets</s>
-* Mantis [http://mantis.cu-genome.org/view.php?id=0000604 0000604]: select menu-file-open-workspace
+<s>* Mantis [http://mantis.cu-genome.org/view.php?id=0000604 0000604]: select menu-file-open-workspace
-:=> new workspace is not confirming deletion of old one
+:=> new workspace is not confirming deletion of old one </s>
 * Mantis [http://mantis.cu-genome.org/view.php?id=0000739 0000739]: right click image nodes should show option to export
 :if there is an image in the project panel there should be an additional option to export the image. Now one has to go through the File menu.
-* Mantis [http://mantis.cu-genome.org/view.php?id=0000633 0000633]: copy function
+<s>* Mantis [http://mantis.cu-genome.org/view.php?id=0000633 0000633]: copy function
-:Since all the operations are destroying the original data I believe it could be useful to have a copy function that copies a state of a data set to a new data set.
+:Since all the operations are destroying the original data I believe it could be useful to have a copy function that copies a state of a data set to a new data set. </s>
 * Mantis [http://mantis.cu-genome.org/view.php?id=0000643 0000643]: ask if should really remove

@@ Line 198: / Line 198: @@
 :There should have been no significant genes found once the marker selection had been made but the volcano plot was erroneously displaying the genes that had been selected as being significant. This is due to an inconsistency in the way the markers() method is implemented in CSMicroarraySetView. For the time being I've routed around this method but it should probably be changed at some point.
-* Mantis:   [http://mantis.cu-genome.org/view.php?id=0000509 0000509]: Error when trying to create network from saved workspace
+<s>* Mantis:   [http://mantis.cu-genome.org/view.php?id=0000509 0000509]: Error when trying to create network from saved workspace
-::[http://mantis.cu-genome.org/view.php?id=0000794 0000794]: Component state is not saved for any component
+::[http://mantis.cu-genome.org/view.php?id=0000794 0000794]: Component state is not saved for any component </s>
 ----

@@ Line 104: / Line 104: @@
 :save the parameters of matrix reduce; change parameters; save again under different name; go to first parameter settings by selecting first saved item; => nothing happens, still the latest parameters are displayed.
-* Mantis [http://mantis.cu-genome.org/view.php?id=0001004 0001004]: Add a "Delete Settings" button to the analysis panel
+<s>* Mantis [http://mantis.cu-genome.org/view.php?id=0001004 0001004]: Add a "Delete Settings" button to the analysis panel
-:It works, but on saving the parameter set an exception is thrown: java.io.NotSerializableException. Reopening bug for cleanup.
+:It works, but on saving the parameter set an exception is thrown: java.io.NotSerializableException. Reopening bug for cleanup. </s>
 * Mantis [http://mantis.cu-genome.org/view.php?id=846 846]: For every file import we need a warning message if the import didn't work and also a message what has been read in (how many markers, TF sites etc...)
-* [http://mantis.cu-genome.org/view.php?id=0000700 0000700]: progress bar for saving/loading (not only the workspace)
+<s>* [http://mantis.cu-genome.org/view.php?id=0000700 0000700]: progress bar for saving/loading (not only the workspace)</s>
-* Mantis: [http://mantis.cu-genome.org/view.php?id=0000482 0000482]: "All Markers" and "All Arrays" overrides are confusing
+<s>* Mantis: [http://mantis.cu-genome.org/view.php?id=0000482 0000482]: "All Markers" and "All Arrays" overrides are confusing
 :In order to successfully uses the marker and phenotype panels, the user must create selection sets, enable those, optionally set them as case/control and ensure that "All Markers" or "All Arrays" is not checked in their component. This seems very difficult for a user to learn, and is not a very intuitive approach. There must be a better way to manage selections.
-:It might be sufficient to describe the basic concepts of geWorkbench (like this one) in the documentation AND tutorial etc...
+:It might be sufficient to describe the basic concepts of geWorkbench (like this one) in the documentation AND tutorial etc...</s>
 * Mantis [http://mantis.cu-genome.org/view.php?id=0000410 0000410]/[http://mantis.cu-genome.org/view.php?id=494 494]: Rewrite Visual Builder.
@@ Line 171: / Line 171: @@
 :when moving a column (which is not necessarily bad) to the first position (row names) the row name is exchanged with a value but has this "button" look....
-* Mantis [http://mantis.cu-genome.org/view.php?id=0000547 0000547]: Inaccurate Error Message
+<s>* Mantis [http://mantis.cu-genome.org/view.php?id=0000547 0000547]: Inaccurate Error Message
 :When connecting to a MAGE-OM Server the error message is "can not connect to server" even when it does connect and authenticate the user.
 :I changed the related code to reflect the real error.
-:But right now I have no available caArray RMI server to test this bug, if John can give me access to his local caArray server, I can confirm the bug is fixed or need more work.
+:But right now I have no available caArray RMI server to test this bug, if John can give me access to his local caArray server, I can confirm the bug is fixed or need more work. </s>
 * Mantis [http://mantis.cu-genome.org/view.php?id=0000552 0000552]: remembering parameters for different sequences

@@ Line 17: / Line 17: @@
 * Version control for components
-* We need to define a standard way to deal with reading and writing files:
+* We need to define a standard way to deal with reading and writing files: (bug 1538)
 # writing files
 ## if file exists, ask if to overwrite
@@ Line 37: / Line 37: @@
 ## tell the user what has been read
-* Do we really need the "All markers" and "All Arrays" check boxes? It involves a lot of work for the programmer to 1. understand and then also implement everything that is related to this. 2. The user needs to understand this concept.
+<s>* Do we really need the "All markers" and "All Arrays" check boxes? It involves a lot of work for the programmer to 1. understand and then also implement everything that is related to this. 2. The user needs to understand this concept.</s>
 * Graphics export/printing should have publication quality, it should be standardized and more than one format should be implemented (jpeg, tiff, png). We need a use case for this.
@@ Line 43: / Line 43: @@
 <s>* list management: i.e. union, intersection, etc, visualization of sets: Venn diagrams should be possible to select from more than one data object or even between projects </s>
-* there is a gray box displayed when starting the application
+<s>* there is a gray box displayed when starting the application</s>
 * import projects by adding to existing live projects
@@ Line 53: / Line 53: @@
 * genomics visualization tools: plotting features on genomic regions with zooming functionality
-* visualization of multiple chips at the same time
+<s>* visualization of multiple chips at the same time</s>
 * more annotation features for graphics (Title, comments, regression lines, etc)
-* better linking of table cells and selected data (highlight OR display selected data within all data)
+<s>* better linking of table cells and selected data (highlight OR display selected data within all data)</s>
 * being able to deal with sequences as input for numerical calculations: what is needed here are different ways to encode nucleic and amino acids. There are different matrices that can be applied but also self adapting algorithms one of which I developed during my PhD thesis...
@@ Line 72: / Line 73: @@
 : currently there is a right click functionality called "view Annotations" but that only displayed the raw data as a tab delimited file
-* In the "open file menu - remote access" one has to right-click to get vital information about the data being retrieved. It is very unintuitive to hide essential information in a right-click.
+<s>* In the "open file menu - remote access" one has to right-click to get vital information about the data being retrieved. It is very unintuitive to hide essential information in a right-click.</s>
 * it should be possible to clean the temp folder from within Workbench to be able to revert to the initial installation configuration

@@ Line 2: / Line 2: @@
 == Feature requests for geWorkbench ==
 === Feature requests not listed in Mantis ===
 * There are preprocessing methods implemented in geWorkbench like normalization and others, but I am missing methods for dealing with replica, time course, and similar problems.

@@ Line 2: / Line 2: @@
 == Feature requests for geWorkbench ==
 === Feature requests not listed in Mantis ===
 * Marker sets have visual properties associated to them. The color and shape should be visible next to the name in the Marker Sets view. This way it is obvious what the displayed results refer to. It is better to have the symbol and color as a separate image next to the name rather than coloring the name because light color would make it impossible to see the names (e.g. light yellow)
-* Integrate JRE (see Genepattern PCA)
+* Integrate JRE with distribution (to handle genepattern problems)
 * Unit tests
@@ Line 42: / Line 44: @@
 * there is a gray box displayed when starting the application
-* import projects to existing live projects
+* import projects by adding to existing live projects
 * full support for cell files, chip chip data, all Affymetrix data type/formats ( cel files, cnt files, expression chp files, genotyping chp files (LOH Estimation and Genotyping Analysis), exp files, experimental result summary) chemical information (SD files), ODBC connections
-* 3D visualization of PCA projections
+<s>* 3D visualization of PCA projections</s>
 * genomics visualization tools: plotting features on genomic regions with zooming functionality
 * visualization of multiple chips at the same time
 * more annotation features for graphics (Title, comments, regression lines, etc)
-* better linking of table cells to selected data (highlight OR display selected data within all data)
+* better linking of table cells and selected data (highlight OR display selected data within all data)
 * being able to deal with sequences as input for numerical calculations: what is needed here are different ways to encode nucleic and amino acids. There are different matrices that can be applied but also self adapting algorithms one of which I developed during my PhD thesis...
@@ Line 62: / Line 62: @@
 * different kinds of artificial neural networks.
-* the application should be much more memory efficient
+'''* the application should be much more memory efficient'''
 * various kinds of visualization should be included/improved. 3D visualizations, box plot, ...
@@ Line 69: / Line 69: @@
 :=> All information that is read into the program should be visible through some interface.
 : Mantis [http://mantis.cu-genome.org/view.php?id=870 870]
-* In the open file menu, remote access one has to right-click to get vital information about the data being retrieved. It is very unintuitive to hide essential information in a right-click.
+* In the "open file menu - remote access" one has to right-click to get vital information about the data being retrieved. It is very unintuitive to hide essential information in a right-click.
 * it should be possible to clean the temp folder from within Workbench to be able to revert to the initial installation configuration