geWorkbench

Feature requests for geWorkbench

General Features

• Mantis 0000480: Workflow support

Would be nice to have true workflow support for regular users (without the need for scripting). (agreed: Bernd)

• Not in Mantis:

There are problems related to memory management. geWorkbench uses too much memory for storing Microarray data internally. When loading 9 U133 chips one needs more than 512MB.

• Mantis 0000114: Persisting configuration settings designated through the visual builder

At present, changes to the start up configuration effected during the application execution (through the Visual Builder) do not get persisted: when the application is launched the original start up configuration is used again.

It is desirable that changes introduced by the Visual Builder be persisted in the application's configuration file so that they can be "remembered" at the next launch.

• Mantis 0000115: Choosing among available application "flavors"

During application launch, a start up window (which the user can opt to hide for subsequent application invocations) should prompt the user to select one among the available application configuration "flavors". This functionality should be available not only at start up but also from within the application, through a "Preferences" type of menu option.

• Mantis 0000077: Context sensitive online help

We need to make online help available in a context sensitive manner: from within a component, a user should be able (using F1 or by pressing a Help button) get access to the online help associated with the component.

• Mantis 0000156: Extension of event exchange model
  Entering this here as a placeholder regarding the proposed re-engineering of the event model. Some of the design suggestions that have been mentioned include:
  • Making it a rule that event data are always interfaces.
  • Removing the need to specify within the throwEvent() method the listener interface and the method to invoke in that interface.
  • Using annotations (or some other mechanism) in order to provide a direct reference to a service provider so that methods can be invoked directly rather than through event exchanges.

• Mantis 0000157: Extend framework to bring to focus components that receive appropriate events

An issue with the GUI is that one needs to know which components respond to which events in order to inspect the results of some action. E.g., when executing the hierarchical clustering analysis and in order to review the results one needs to explicitly select the Dendrogram tab.

The framework needs to be extended so that components can gain the focus as appropriate when they receive certain events.

• Mantis 0000173: UI Tab Display.

Tabs should be displayed in alphabetical order. It's difficult to find tabs as they are ordered currently.

If the user cannot view all the tabs without scrolling, the tab headers should become drop down values.

• Mantis 0000478: File save/load operations are memoryless in terms of last directory used.
  There are many places in the app where data are being loaded from or saved to disc. When such an operation is used for the *second* time the app should remember the directory the user navigated to the *first* time. Some specific examples where this is not the case:
  • Exporting an image node from within the projects folders.
  • Saving a data node from within the projects folders.
  • Saving a panel from the Markers component.

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Programmatic features

• Mantis 0000400: Inconsistent t-test results based on phenotype/panel activation order

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.

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Menu

• Mantis 0000166: main menubar controls for Project Folders Area are confusing.

The problem is caused by the differences in type and semantics between workspace folder and project folders. For example, The "File" submenu offers "Open" and the pop-up choices are "File" or "Workspace". Select Workspace and you are offered a dialog box. Select "File" and you are told you must first select a project node. Or if you select "New" (an adjective) from the submenu, you get a choice of "Workspace" or "Project". Select "Workspace" and the current workspace folder is cleared of its contents. Thus New Workspace actually REMOVES the Workspace folder, whereas the submenu item "Remove" does not include "workspace" as an option. Select "Project" and a new project folder is added without replacing an existing one. I think the whole thing could be made more obvious and logical by making the File submenu items "Workspace" and "Projects" and perhaps "Files". Then the choices under each could be actions (verbs) - e.g Open, Remove, Load, Delete, Save, etc. In other words, you consider the folder that you want to do something to, select it in the file menu and choose the action that you want to take. Also the other file items "Export" etc. have nothing to do with the Project Folders Area and are positioned awkwardly.

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File

• Mantis 0000345: File Loading Confusion

No choice to list all files in directory. The file selection box should contain an option to see all the files in a directory, otherwise unclear which file postfix goes with which loading option.

• Mantis 0000347: Prompt to Save

No prompt to save workspace when application exits, there should also be a way to exit the application from the file menu.

• Mantis 0000452: filtered datasets misrecognized on read in

If a dataset is filtered, written out, and then read in again, the "magic marker" that defined the chip type may be deleted, and the dataset can be recognized as another entirely. For example, my HG_U95 dataset, after filtering out half the markers, was recognized as HG_133_Plus2.

• Mantis 0000479: Enable the "Export" functionality for data nodes.

This functionality is supposed to be similar to the "Open file" functionality, where a number of pluggable export filters can be used to export a dataset into another format. At the vry least we should support exporting microarray data into the Cluster (http://rana.lbl.gov/EisenSoftware.htm) [^] format.

• Mantis 0000484: At the File menu, an "Exit" menu item should be provided.

Many many other softwares do have it. Maybe an option for saving the workspace should be provided before exit.

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Help

• Mantis 0000466: Add "shortcuts" screen

Add a "shortcuts" screen (maybe under the "Help" main menu item?) to list available shortcuts like the very useful F12.

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Project Folders

• Mantis 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.

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Sets

• Mantis 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.

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FASTA sequences

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5. Sequence alignment

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BLAST

• related to 0000541: blastall is not complete

using local / own databases

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Microarray data

The following panels/functionalities are requested specifically for Microarray data:

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Microarray viewer

• related to (closed) Mantis 0000225: Microarray panel details

It would be nice to have the values (min, max) displayed next to the color legend

• Mantis 0000326: absolute visualization needs viewing controls

If a set of unnormalized Affy data is read in, for example the cardiogenomics dataset, with the tools->preferences->visualization mode set to absolute, the dynamic range of the data is so large that only a few data points appear. Some options to deal with this would be: 1. a control labeled "Display as log transform" 2. an intensity control such as in the color mosaic panel.

• Mantis 0000431: Table View does not sort properly

Sorting by most columns not work properly (does not order numerically or alphabetically) and attempting to sort by pValue appears to do nothing. => also true for any table

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Color Mosaic

• Mantis 0000477: Missing right click actions

CM should have the right click actions consistent with Expression Profiles, EVD,Scatter Plot which supports zoom in/out,save as & print.

=> least have a mouse-over function that displays the chip and value for the spot

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Analysis

The following analysis functions are requested:

• ANOVA

• mantis 0000307: Analysis should write to dataset history

When any type of analysis is done, basic facts should be written to the Dataset History log, such as whether all markers were used or an activated panel; the number of markers/arrays in the activated panel, and the array type, and a timestamp.

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Fast Hierarchical clustering

• Mantis 0000148: Euclidean distance shoud use normalized vectors

Data should be transiently normalized

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Dataset History

• Mantis: 0000300: need array info

We should be able to display information about a microarray - the chip type, the number of markers in the dataset vs in the chip definition.

• Mantis 0000476: Data set annotation missing

Issue: Users analyze data, use activated sets, limit arrays included and none of these steps are captured in the annotation. The system should capture these steps for the user in a log so the researcher is clear on what the results include and how to reproduce.

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