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Feature requests for geWorkbench

General Features

  • 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.

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.


File


Edit


View


Commands


Tools


Help



Project Folders



Markers



Arrays/Phenotypes



Sets



FASTA sequences

Promoter


Sequence Panel


Position Histogram


Simulation


Network Generator

Phenotype & Optimizer Options

Interactions Display

5. Sequence alignment


BLAST

HMM

Other

Pattern discovery


Associations


caScript


Dataset annotations


data history


Experiment Info



Microarray data

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

Simulation


Network browser


Interactions


Aracne


Tabular Microarray Viewer


Sequence Retriever


Synteny


Microarray viewer


Gene Ontology


GSEA


Reverser Engineering


Scatter Plot


caBIO pathways


Marker Annotations


Color Mosaic Expression Profiles


Expression Value Distribution


Experiment Info


Synteny Parameters


Program

MUMmer

Dots

Synteny map

Genome selections

Annotations

Normalization


Housekeeping Genes Normalizer

Log2 Transformation

Marker-based centering

Mean-variance normalizer

Array-based centering

Missing value computations

Threshold Normalizer

Quantile Normalization

T-Profiler


Analysis

The following analysis functions are requested:

  • ANOVA

Fast Hierarchical clustering

Matrix reduce

Svm classifier

Slmr classifier

SOM

T-test

Multi T-test

Associations


caScript


Dataset Annotations


Filtering


Deviation filter

Affy detection call filter

Expression threshold filter

Genepix flags filter

Missing value filter

2 channel threshold filter

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.