Difference between revisions of "User:Bjagla"

 
Line 1: Line 1:
−
Here come my comments about geWorkbench
+
== 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.
 +
 
 +
----

Revision as of 14:20, 19 September 2006

Contents

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.

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