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− | == Feature requests for geWorkbench ==
| + | {{BJNav}} |
− | === General Features ===
| + | [[NCBC2008|NCBC Meeting, Aug 2008]] |
− | * Mantis 0000114: Persisting configuration settings designated through the visual builder
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− | At present, changes to the start up configuration effected during the
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− | application execution (through the Visual Builder) do not get persisted: when
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− | the application is launched the original start up configuration is used again.
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− | It is desirable that changes introduced by the Visual Builder be persisted in
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− | the application's configuration file so that they can be "remembered" at the
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− | next launch.
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− | * Mantis 0000115: Choosing among available application "flavors"
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− | During application launch, a start up window (which the user can opt to hide
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− | for subsequent application invocations) should prompt the user to select one
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− | among the available application configuration "flavors". This functionality
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− | should be available not only at start up but also from within the application,
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− | through a "Preferences" type of menu option.
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− | * Mantis 0000077: Context sensitive online help
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− | We need to make online help available in a context sensitive manner: from
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− | within a component, a user should be able (using F1 or by pressing a Help
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− | button) get access to the online help associated with the component.
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− | * Mantis 0000156: Extension of event exchange model <br> 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:
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− | ** Making it a rule that event data are always interfaces.
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− | ** Removing the need to specify within the throwEvent() method the listener interface and the method to invoke in that interface.
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− | ** 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.
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− | * Mantis 0000157: Extend framework to bring to focus components that receive appropriate events
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− | An issue with the GUI is that one needs to know which components respond to
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− | which events in order to inspect the results of some action. E.g., when
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− | executing the hierarchical clustering analysis and in order to review the
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− | results one needs to explicitly select the Dendrogram tab.
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− | The framework needs to be extended so that components can gain the focus as
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− | appropriate when they receive certain events.
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− | | |
− | === Menu ===
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− | * Mantis 0000166: main menubar controls for Project Folders Area are confusing.
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− | The problem is caused by the differences in type and semantics between workspace
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− | folder and project folders. For example, The "File" submenu offers "Open" and
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− | the pop-up choices are "File" or "Workspace". Select Workspace and you are
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− | offered a dialog box. Select "File" and you are told you must first select a
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− | project node. Or if you select "New" (an adjective) from the submenu, you get a
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− | choice of "Workspace" or "Project". Select "Workspace" and the current workspace
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− | folder is cleared of its contents. Thus New Workspace actually REMOVES the
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− | Workspace folder, whereas the submenu item "Remove" does not include "workspace"
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− | as an option. Select "Project" and a new project folder is added without
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− | replacing an existing one. I think the whole thing could be made more obvious
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− | and logical by making the File submenu items "Workspace" and "Projects" and
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− | perhaps "Files". Then the choices under each could be actions (verbs) - e.g
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− | Open, Remove, Load, Delete, Save, etc. In other words, you consider the folder
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− | that you want to do something to, select it in the file menu and choose the
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− | action that you want to take. Also the other file items "Export" etc. have
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− | nothing to do with the Project Folders Area and are positioned awkwardly.
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− | ----
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− | ==== File ====
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− | ----
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− | ==== Edit ====
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− | ----
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− | ==== View ====
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− | ----
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− | ==== Commands ====
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− | ----
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− | ==== Tools ====
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− | ----
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− | ==== Help ====
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− | | |
− | ----
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− | ----
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− | === Project Folders ===
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− | ----
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− | ----
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− | === Markers ===
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− | ----
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− | ----
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− | === Arrays/Phenotypes ===
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− | ----
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− | ----
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− | === Sets ===
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− | ----
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− | ----
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− | === FASTA sequences ===
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− | ==== Promoter ====
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− | ----
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− | ==== Sequence Panel ====
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− | ----
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− | ==== Position Histogram ====
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− | ----
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− | ==== Simulation ====
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− | ----
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− | ===== Network Generator =====
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− | ----
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− | ===== Phenotype & Optimizer Options =====
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− | ----
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− | ===== Interactions Display =====
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− | ----
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− | ==== 5. Sequence alignment ====
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− | ----
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− | ===== BLAST =====
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− | ----
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− | ===== HMM =====
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− | ----
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− | ===== Other =====
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− | ----
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− | ==== Pattern discovery ====
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− | ----
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− | ==== Associations ====
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− | ----
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− | ==== caScript ====
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− | ----
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− | ==== Dataset annotations ====
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− | ----
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− | ==== data history ====
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− | ----
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− | ==== Experiment Info ====
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− | ----
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− | ----
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− | === '''Microarray data''' ===
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− | The following panels/functionalities are requested specifically for Microarray data:
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− | *
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− | ==== Simulation ====
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− | ----
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− | ==== Network browser ====
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− | ----
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− | ==== Interactions ====
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− | ----
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− | ==== Aracne ====
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− | ----
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− | ==== Tabular Microarray Viewer ====
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− | ----
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− | ==== Sequence Retriever ====
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− | ----
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− | ==== Synteny ====
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− | ----
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− | ==== Microarray viewer ====
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− | ----
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− | ==== Gene Ontology ====
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− | ----
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− | ==== GSEA ====
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− | ----
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− | ==== Reverser Engineering ====
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− | ----
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− | ==== Scatter Plot ====
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− | ----
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− | ==== caBIO pathways ====
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− | ----
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− | ==== Marker Annotations ====
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− | ----
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− | ==== Color Mosaic Expression Profiles ====
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− | ----
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− | ==== Expression Value Distribution ====
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− | ----
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− | ==== Experiment Info ====
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− | ----
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− | ==== Synteny Parameters ====
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− | ----
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− | ===== Program =====
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− | ----
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− | ====== MUMmer ======
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− | ----
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− | ====== Dots ======
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− | ----
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− | ====== Synteny map ======
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− | ----
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− | ===== Genome selections =====
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− | ----
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− | ===== Annotations =====
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− | ----
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− | ==== Normalization ====
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− | ----
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− | ===== Housekeeping Genes Normalizer =====
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− | ----
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− | ===== Log2 Transformation =====
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− | ----
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− | ===== Marker-based centering =====
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− | ----
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− | ===== Mean-variance normalizer =====
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− | ----
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− | ===== Array-based centering =====
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− | ----
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− | ===== Missing value computations =====
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− | ----
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− | ===== Threshold Normalizer =====
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− | ----
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− | ===== Quantile Normalization =====
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− | ----
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− | ==== T-Profiler ====
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− | ----
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− | ==== Analysis ====
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− | The following analysis functions are requested:
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− | * ANOVA
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− | ----
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− | ===== Fast Hierarchical clustering =====
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− | ----
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− | ===== Matrix reduce =====
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− | ----
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− | ===== Svm classifier =====
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− | ----
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− | ===== Slmr classifier =====
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− | ----
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− | ===== SOM =====
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− | ----
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− | ===== T-test =====
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− | ----
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− | ===== Multi T-test =====
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− | ----
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− | ==== Associations ====
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− | ----
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− | ==== caScript ====
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− | ----
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− | ==== Dataset Annotations ====
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− | ----
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− | ==== Filtering ====
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− | ----
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− | ===== Deviation filter =====
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− | ----
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− | ===== Affy detection call filter =====
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− | ----
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− | ===== Expression threshold filter =====
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− | ----
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− | ===== Genepix flags filter =====
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− | ----
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− | ===== Missing value filter =====
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− | ----
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− | ===== 2 channel threshold filter =====
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− | ----
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− | ==== Dataset History ====
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− | * Mantis: 0000300: need array info
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− | We should be able to display information about a microarray - the chip type, the
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− | number of markers in the dataset vs in the chip definition.
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− | ----
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