Gephi 0.7beta released

1 October 2010

Major milestone for Gephi today. The 0.7 beta version is ready for download for Windows, Mac OS and Linux platforms. It brings many awaited features and more than 80 bug fixes!. Stability and productivity improvements are the main objectives of this release. A complete support for longitudinal network is part of this release, it is now more easy and flexible to import and explore dynamic networks. Consult this new tutorial to see how input longitudinal networks in Gephi. We support three different methods, to cover all use cases.

Because it’s a major release, changes are not deployed through the AutoUpdate, you need to download and install the new version if you had the alpha. Plug-ins also need to be checked for compatibility. They will reappear on the Plugin Center in the coming days, as they are verified.

Consult the release notes and the new Javadoc for more informations.

An announcement for modules developed this summer by the Google Summer of Code students, in particular Neo4j and Social Network import. They may be fully integrated in Gephi for its 0.8 version, in the meantime they will be released as plug-ins through our Plugin Center. Stay tuned, it will be fast.

A new version of the Gephi Toolkit will be released in a few days, based on the beta codebase.

Features highlight

New Data Laboratory

The Data Laboratory receives tons of new features, developed this summer by Eduardo Ramos. It now proposes to manipulate and edit data in a broader and more productive way. A detailed list of features is available on the Introducing Data Laboratory post. The laboratory is also now auto-refreshing when filters are manipulated. Another essential point is that the laboratory is easily extensible with plug-ins.

Longitudinal networks

They are now fully supported in Gephi. Explore how the network topology change over time by using the Timeline component, which now appears automatically. The major improvement is the dynamic attributes support. The edge weight or any attribute value can evolve over time as well, and the visualization shows the value in the right range. Enable the timeline with a single button. See tutorial.

Edit

Simple edit by selecting one or several nodes or edges in the Data Laboratory. Keep Control key on the table to select several rows and change values of several elements in one action. Edit also manually visualization variables like color, size or position. The Edit window is available by right-clicking on rows. Many other features are now available through the context menu, and more can be added with plug-ins.

Search/Replace

General Data Laboratory actions like Add node/edge, Search/Replace or Import CSV. The Search/Replace feature shows an advanced UI to search and replace values in the table cells. It can do a normal search or a regular expression based search, among other useful options. It is implemented in a separate controller that is part of the Data Laboratory API.

Columns merge

Manipulate columns and do basic calculations. On numerical columns one can get sum, average, median, … from several other columns. New columns can be created from a regular expression based on a existing column. Among other merge strategies, a Time Interval column can be get from a simple numerical column. Get a longitudinal network from a simple ‘year’ column in your data.

Label visibility

Decide whether a label should be visible or not from the filter result. Nodes and edges not in the filtered graph will have their labels hidden. Can be reset by the ‘Reset Visible’ action (left of graph window).

Copy and Move to a workspace

New option when right-clicking on the graph. You can copy or move the selection to a new or existing workspace.

Import ‘Missing Nodes’ option

New option in the import panel to import nodes which were not properly defined in the file. Use this option to create nodes only from their reference in edges.

Import Time Frame

Their are different way to import longitudinal network in Gephi. One of them is to import multiple ’static’ files, where each is a particular snaphsot in time (one file per day or per month). There is a new option for that in the import report. See this tutorial section to use it.

Time Frame settings

Decides whether the time format is a date or a real number. The processor will look for existing elements in the workspace and append the time frame to nodes and edges. The network becomes longitudinal, each node, edge and attribute is defined with time intervals.

Preview Presets

The Preview settings has now default presets: Default Curved, Highlight Mutual Edges, Small Labels and more.

Rescale weight in Preview

New option in preview to have edge weight look the same as Overview. Meta-edges have also now a separate scale slider in Visualization settings. This scale value is used in Preview to respect dimensions.

Original color option

When edges color are imported from a file or set by Partition, they have a custom color. This color mode can now be rendered by Preview by setting ‘Original’ in the color dialog.

Localization

Localization is now possible in Gephi, French and Spanish versions will be available soon. Please consider helping us, show up on the Translations forum section.

New And Noteworthy

* NOT Operator (Filters)
* MASK Operator (Filters) – keep edges according to source/target/both/any – can easily obtain neighbors of a set of nodes
* Display edge weight as labels on visualization
* New StAX GEXF importer and exporter, with hierarchy and dynamic support
* New List/Arrays attribute types. Can only be imported from GEXF for now.
* Flatten Filter – Flatten a hierarchical graph to the visible view, transform meta-edges into normal edges
* New Giant Component Filter
* Set size for the ‘Reset Size’ action, by right-clicking on the reset size button
* Get degree column from Undirected graphs
* Statistics reports now saved in Gephi projects
* When parallel edges are found during import, it now increases the weight of the edge by default
* Option in Ego Filter to include the parent node or not
* Meta-edges have now a separate scale slider in Visualization settings, change how thick they are compared to normal edges
* Ranking and Partition list of attributes are now sorted
* Ranking now updates itself with filtered graphs. Clicking on Apply will refresh bounds and the transformation (color, size)
* It’s now possible to drag a filter sub query to become a main query
* With dynamic attributes, Ranking, Partition, Visualization and Filters will use the current Timeline range to find values
* Edge weight can be dynamic, type DYNAMIC_FLOAT. Force Atlas layout will use the current Timeline range
* Filters are refreshed when the graph is modified, the current filter is reexecuted

Bug fixes

* Nodes not unselected after turning off Selection on Filter Panel bug 649920
* PDF Export only with default font bug 651273
* Ego Filter doesn’t include the node itself bug 649908
* Exception on opening project file bug 648617
* Partition filter automatically filters null value bug 648600
* Edges weight not merged with parallel edges bug 648600
* Negative edges not rendered in Preview bug 628223
* Edge weight scale is different between Graph and Preview bug 569329
* Edges native color are not displayed in Preview bug 586237
* Text not displayed in Preview bug 627567
* Errors at PDF export when labels have font size zero bug 626865
* Filtering not refreshed when sub-queries set or removed bug 594511
* Wrong stroke weight when SVG imported in Illustrator bug 626378
* Generating a graph on a previously loaded undirected graph bug 624671
* Wrong folder selected in the Export Panel when changing file type bug 620337
* Node Degree not in Label Text settings bug 598170
* Ranking and Partition parameters list not ordered bug 594520
* Read positions from dot files bug 594793
* Wrong node size when Ranking has same min and max size bug 631689
* SVG files not listed in Export dialog bug 626394
* Export to pdf background is always white bug 583386
* Selected filter query not properly refreshed in UI bug 626483
* Wrong node positions when setting X or Y to zero bug 615844
* z-coordinate not exported in GraphML bug 614606
* Partitions don’t refresh when opening project not from Overview bug 612902
* duplicate label in filter window bug 604003
* Visualization size limitation bug 602470
* Can’t close project when generating a graph bug 631341
* csv file export problem bug 598767
* Can’t import the same file twice in Welcome window bug 598157
* “CommandLineParsing null” message when error on opening file from command line or desktop bug 594630
* Default selection of Nodes in Data Laboratory necessary bug 594515
* Preview ratio not available at first time bug 594176
* Impossible to cancel the Average Path Length Statistic calculation bug 590226
* Auto-scale flips the graph bug 577843
* “Node must be in the graph” error when importing a hierarchical graph with height greater than 1 bug 577180
* FileNotFoundException during saving of PDF file bug 572876
* dynamic graph unrecognized if everlasting nodes bug 555637
* Edit window not hidden on tabs bug 552494
* ‘Format’ not recognized on DL import bug 619069
* Visualization selection color inversion between ‘out’ and ‘both’ color bug 618726
* Workspace Selection failed to refresh after closing workspace bug 616814
* NullPointerException when selecting “–Choose a Layout” in the Layout ComboBox bug 606964
* In/Out degree metric doesn’t work with undirected graphs bug 606305
* Right click on workspace after deleting a node throws “node can’t be null” bug 605947
* Import transform to Undirected don’t merge weight bug 603478
* Can’t display edge weight as text bug 603134
* Can’t select Postgresql driver in database import settings bug 595223
* Error when opening Plugin Center bug 616829
* Node invisible (too small) when created with the node pencil bug 574807
* Ranking not refreshed when graph filtered bug 632459
* Ranking parameters re-initialized at each new ranking bug 594231
* Can’t drag a filter sub-query to become a root query bug 626495
* NullPointerException when switching between workspaces while a layout is running bug 597458
* NullPointerException when executing the “Eigenvector Centrality” Statistic bug 589731
* Memory Leak in Graph Distance bug 587450
* ForceAtlas and Fruchterman Reingold not layouting with meta-edges bug 584286
* Cannot save / saves as when opening a Gephi by doubleclick a graph in Windows bug 583397
* GraphML importer doesn’t import node labels data bug 581629
* Exception on clicking on ‘Hierarchy’ while running multilevel layout bug 631663
* Opening Archived ZIP files is broken bug 578876
* Partition Settings in Filter not saved on switching workspaces bug 616052
* Filtered graph not exported with “Select” pressed bug 573685
* Partition “All Blacks” feature randomizes colors bug 601066
* ’start’ and ‘end’ attributes are missing when exporting dynamic GEXF bug 521848
* EdgeList Database Configuration is not saved bug 571263
* Slowness on picking a partition entry bug 519549
* Unable to cancel a project opening bug 616415
* Progress is not shown when opening/saving project bug 594644
* Incorrect mutual edge weight on Preview bug 610469
* Memory Leak in GEXF/GraphML Parser bug 596872
* Node Size Mode and Filter Paramaters don’t save in project bug 596430
* Errors with Yifan Hu MultiLevel Layout on a filtered graph bug 594643
* Preview is not displaying meta-edges bug 584289
* Meta-edges are not displayed bug 584283
* gtk+ slider problem bug 529913
* NullPointerException on importing dynamic graph bug 581872
* NullPointerException when filtering undirected graphs bug 571153
* Filtering with convex hulls displayed bug 541819
* Wrong edge removed from Edge Weight filter bug 603469

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