Diff for "IdekerLabProgress"

March 2010 Sprint

• Bugs 0002127: When opening more than one network, windows are not refreshed when moving - Same as bug 2199
• Bug: Investigate why Janusz Session is slow at mouse selection and rendering functions.

• Bug: UniProt Gene Association file is not readable in ontology import. Also, need to check association file locations are up to date

• Measure how long it takes to render networks of various size, measure how long it takes to render a static image snapshot of a network, compare and contrast.
• Create a common visual style for Module finding algorithm results. The visual style should use pre-defined attribute names for specific visual properties. The module finding algorithm will then simply set the attributes for the overview network. Edge thickness should be a function of the number of shared nodes between nested networks.

• Create a benchmark plugin that can run a specified "action" and then print out time and memory statistics. Basically, this will be a plugin that simply executes a number of pre-specified CytoscapeActions and measures the duration of each.

• Create a suite of benchmark tests (for the benchmark plugin) that exercise different variants of the "render 100,000 objects" scenario. For example, render 1 network with 100,000 nodes, 100,000 networks with 1 node each, 10,001 networks with 10 nodes each with one nesting overview network, etc..

• Get the complete human interaction network from IntAct and run MCODE (make this part of the Benchmark plugin?)

• Work with grad students to update ModFind to roughly reproduce Sourav's results.

• Make module finding UI consistent across JActiveModules, MCODE, ModFind.

• A way to search for plugins from within the plugin manager.
• Search dialog for plugin website using existing metadata.

• Implement equation attributes (http://cytoscape.wodaklab.org/wiki/Cytoscape_2.8/EquationAttributes) RFC 65

• Custom Graphics as a Visual Property (CustomNodeGraphicsVisualProperty).

• Write Simplified 3.0 plan.

February 2010 Sprint

• Execute Test Plan for 2.7
• Update Test Plan for 2.7
• Update Cytoscape manual for Nested Networks
• Generate release beta release and final release files (this includes generating a new manual)
• Create an easy way to allocate memory in Cytoscape (mantis 2070)
• Remove "install web services pack" and make all of those web services part of the core.

• Optimize nested network rendering. Instead of storing BufferedImages for nested networks, store PNG (or some other compressed image format) images.

• Optimize nested network rendering. Allow user to specify resolution of nested network image.
• Verify that custom graphics still work sensibly.
• Add threshold cytoscape property to create views for modules. Set threshold to 0 by default. Creates the N top most modules where "top most" is algorithm specific.
• A new network icon for "add nested network" in the editor. Beautify. Center icons within borders.
• Change the name of the NODE_NESTED_NETWORK_VISIBLE visual property. (e.g. NODE_SHOW_NESTED_NETWORK)
• In a branch add network icon image to the Network Panel. Add a checkbox to turn this feature on/off.
• Configure cytoscape so that it remembers its window size each time it starts.
• Bug 1843: Properly handle exceptions during plugin loading
• Bug 2126: Cytoscape main window should remember its previous location
• Bug 2107: Visual Style Changes Do Not Survive Saving And Loading to/from an .XGMML File
• Bug 2132: Menu item "Plugins/Update Plugins" is broken
• Set column size width for Attribute Browser isn't 100% consistent. We seem to notice automatic resizing when switching column order and when setting column widths to small sizes. Just play with this a lot to reproduce.
• Bug 2066: Popping up a browser on Ubuntu linux doesn't work. Refactor so that we try a list of possible browsers and popup and error dialog if we can't find one we like.
• Bug 1735: The install wizard suggest an older directory for the installation
• Bugs 2111: Exception during import Vizmap property file
• Bug 2026: The error message when incorrectly guessing attribute type fails isn't very helpful.
• Bug 2113: Need suggested file name and extension when export network as GML format
• Bug 2112: Suggest file type when export network
• Bug 2110: File type in the session saving dialog should be restricted to "cys"

• Bug: Encode persistence in order and width of columns in CyAttributesBrowser SESSION

• Self-referential nested networks cause rendering weirdness when moving nodes around.

• Bug 2050: The key bindings for New->Network->From... clash with Mouse Drag Selects -> Nodes Only

• Write an RFC describing integrating custom graphics into the VizMapper and CyAttributes.

• RFC for updating plugin website.
• Update Denovo plugin to force two different attributes to be chosen for the search. Choose sensible defaults.
• Denovo plugin should only start if proper attributes exist. Determine what the criteria are and if they don't exist display an error dialog explaining the problem.
• Add error checking to Denovo to make sure that start button is enabled only after proper (two different) attributes have been selected,
• Organize (unify) menu options for module finding plugins.
• Bug 2024: The url regular expression used for loading files matches things other than regular expressions.
• Bug 2102: Network Merge Difference Operation is Incorrect for at Least Some Networks
• Bug 1936: Strange attribute names get converted into non-existent files
• Update the equation RFC by specifically addressing performance. (Questions: Do we evaluate when we get the attr or set the attr - explain problems with each. Will attributes that aren't equations be affected? Do we precompile equations? etc.)
• Bug 2084: it's hard to hide the tool panel - it behaves differently than the other cytopanels
• Filters: create default filter
• Bug 2022: jActiveModules error message isn't helpful
• Add progress bars to module finding algorithms.
• Tweak module finding GUI code so that components fit nicely and resize nicely (scroll bars pop up, etc)
• Create a common visual style for Module finding algorithm results. The visual style should use pre-defined attribute names for specific visual properties. The module finding algorithm will then simply set the attributes for the overview network. Edge thickness should be a function of the number of shared nodes between nested networks.
• Unify button names and placement for Module Finding
• Unify network selection for Module Finding (combo box at top)
• Run network rendering benchmarks on 2.5.x, 2.6.x, and 2.7.x versions of Cytoscape.
• Make all menu titles in Cytoscape consistent - like Firefox, Word, Excel, etc., captialize all words except "and", "a", "for", etc.
• Bug 1835: The calculation of the default edge handle for multiple edges between nodes is flawed.
• Bug 1827: render.stateful.renderGraph() Is Using the Wrong Variables For Custom Graphics
• Bug 2169: Error while importing attributes from Biomart

• Bug 2175: Programmatically generated Visual Style does not recognized by VizMapper GUI

• Bug 1873: VisMapper gets confused

• Bug 2181: Make BioMart client query from selected nodes

• Bug 2182: Attributes are missing for genes in original query (NCBI Clinet)

• Bug 2119: EditorDisplayer for Node Line Style is broken

• Bug 1961: import of Annotations is always case sensitive even when you uncheck Case Sensitive box
• Bug 2190: table Import does not support xlsx format file
• Bug 2019: Table Import order of operations error after clicking "Show all entries" radio button
• Bug 2174: Unable to edit network name on 'Edit bookmark' window
• Cytoscape plugin website: the admin page should use the text field to display conmpatible Cytoscape versions instead of radio buttons
• Bug 2192. When using the Nimbus UI style, the editor pane has size problems.
• Bug 2197 When failing to import a file, pop up a confirmation dialog informing the user of the problem.
• Bug 2147 Add an entry to the node/edge menu for hiding a node/edge.
• Bug 2195: Proxy port number windows is too small.
• Bug 2196: When the control panel is not being displayed, the "View/Show Tool Panel" does not show the tool panel. (Hide or grey out the menu entry when it is inapplicable.)

January 2010 Sprint

• Port MCode - Edges in overview graph can be used to indicate that nodes in nested networks exist in both nested networks.
• Port JActiveModules - Edges in overview graph can be used to indicate that nodes in nested networks exist in both nested networks.

• Implement Rohith/Greg/Sourav/PLoS CompBio 2008 code

• Write a demonstration plugin that provides the ability to visualize the edges that exist between nodes that are in nested networks (providing a DualLayout type of visualization).

• Apply visual style to multiple networks (selected in NetworkPanel)

• Make Network Panel pop-up commands consistent (allow user to apply commands to selected networks)

• Allow ArrowHead color to inherit from Edge Color. Provide an option for coupling and decoupling this feature.

• RFC for feature to allow functions in AttributeBrowser cells.

• A visual property that will determine whether to display the nested network or not and add VizMap GUI support for boolean properties.

• Fix looping problems with NNF formats (2123, 2122)
• Write a mini-review of Cytoscape in English and translate it into Chinese.

• Prepare for BioHackathon 2010. Make RDFScape work with the trunk code (2.7.0).

• Encode width of columns persistence in order and in CyAttributesBrowser (code is in coreplugins/browser).

• Attribute browser code to allow editing list attributes.
• Bug 0002109: Apply Visual style on wrong view when import XGMML file.
• Filters Bug: Colons in filter string breaks filter restoration.
• Old Filters: save defined filters (properties) to session.

• QuickFind bug: Null pointer exception when many subnetworks are created.

December 2009 Sprint

• Allow Nested Network Model by adding getNetwork/setNetwork methods to CyNode

• Network Browser - Network attr indicating its parents, node attr indicating its children
• File I/O support for nested networks (NNF Reader, XGMML Reader/Writer, and refactoring for session reader/writer)
• Network Editing - Add an icon in editor that allows a network to dropped on a node or on the canvas (where a node would be created)
• Network Editing - Add a right-click option to the node menu allowing a network to be added/removed
• Right click on a node menu option to jump to nested network
• Rendering - recursive rendering (a nested network will be rendered within the bounds of a node by a recursively defined renderer.) Assuming rendering only, NO user interaction

• Label Wrap - add an option to LabelPosition that allows a node/edge label width to be specified and automatically wraps lines when the text is longer than the width

• GenomeSpace analysis task requirements (due in Jan)

• Add new edge types to Cytoscape (dotted [circles, not dashes], dot-dash, ////, sine wave, parallel lines, ->->->->, parallel lines with single sided arrows)

• Editor - update editor instructions
• Editor - add check box that allows node id to be specified when node is dropped (mantis 2087)

• BioMart plugin maintenance

• A PSIQUIC client release (This works with 2.7)
• Maintenance release for Scripting plugins
• Select all nodes/edges is very slow
• Bug - Fiddling with default visual style and node label position broke all of the control panel.
• Add newlines in the attr browser by either adding \n manually or by typing alt-enter, some combination. Do whatever excel does. (mantis 2088) toggling between large networks can be slow (mantis 2068)

• Bug: In PluginManager Dialog, "Released by" field is missing for some installed plugins

• Bug: In Pluginmanager dialog, some plugins are labeled "out-of-date" incorrectly