Talk:Home
Contents
- 1 Feature requests for geWorkbench
- 1.1 General Features
- 1.2 Menu
- 1.3 Project Folders
- 1.4 Markers
- 1.5 Arrays/Phenotypes
- 1.6 Sets
- 1.7 FASTA sequences
- 1.8 Microarray data
- 1.8.1 Simulation
- 1.8.2 Network browser
- 1.8.3 Interactions
- 1.8.4 Aracne
- 1.8.5 Tabular Microarray Viewer
- 1.8.6 Sequence Retriever
- 1.8.7 Synteny
- 1.8.8 Microarray viewer
- 1.8.9 Gene Ontology
- 1.8.10 GSEA
- 1.8.11 Reverser Engineering
- 1.8.12 Scatter Plot
- 1.8.13 caBIO pathways
- 1.8.14 Marker Annotations
- 1.8.15 Color Mosaic Expression Profiles
- 1.8.16 Expression Value Distribution
- 1.8.17 Experiment Info
- 1.8.18 Synteny Parameters
- 1.8.19 Normalization
- 1.8.20 T-Profiler
- 1.8.21 Analysis
- 1.8.22 Associations
- 1.8.23 caScript
- 1.8.24 Dataset Annotations
- 1.8.25 Filtering
- 1.8.26 Dataset History
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
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.
