|
|
| (256 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| − | == Feature requests for geWorkbench ==
| + | {{BJNav}} |
| − | === General Features ===
| + | [[NCBC2008|NCBC Meeting, Aug 2008]] |
| − | * 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 <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:
| |
| − | ** 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.
| |
| − | | |
| − | === 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 ====
| |
| − | * 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.
| |
| − | | |
| − | | |
| − | | |
| − | ----
| |
| − | | |
| − | ==== 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 ====
| |
| − | * only related to (closed) Mantis 0000225: Microarray panel details
| |
| − | It would be nice to have the values (min, max) displayed next to the color legend
| |
| − | | |
| − | | |
| − | ----
| |
| − | | |
| − | ==== 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.
| |
| − | | |
| − | ----
| |
