Gephi Toolkit released, based on 0.7beta

toolkitarticleexample1-300x211 The 0.7beta version of Gephi has been released last week. It is today the Gephi Toolkit release, based on the latest codebase. Download the latest package, including Javadoc and demos by clicking on the link below.

It includes all features and bugfixes the 0.7beta version has. Therefore it is possible to use dynamic networks and new Data Laboratory features from the Gephi Toolkit.

Two new demos are available from the Toolkit Portal:

  • Import Dynamic – How to import several static files and transform them into longitudinal network
  • Dynamic Metric – How to execute a metric (ex: Average Degree) for each slice of a dynamic network

Links you may be interested:

Since it’s launch in July, the Gephi Toolkit has been used in various use cases for graph visualization. Recently, the Indiana University launched Truthy, a system to analyze and visualize the diffusion of information on Twitter. Truthy uses the Gephi Toolkit for layout.

Gephi 0.7beta released

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

Scientist Christian Tominski about Gephi

Guest blog post from Dr. Tominski who accepted to review Gephi 0.7alpha4 for us.

Christian Tominski received his diploma (MCS) from the University of Rostock in 2002. In 2006 he received doctoral degree (Dr.-Ing.) from the same university. Currently, Christian is working as a lecturer and researcher at the Institute for Computer Science at the University of Rostock. Christian has authored and co-authored several articles in the field of information visualization. His main interests concern visualization of multivariate data in time and space, visualization of graph structures, and visualization on mobile devices. In his research, a special focus is set on interactivity, including novel interaction methods and implications for software engineering.

Recently, I stumbled upon the Gephi Project – an open source graph visualization system. As I’ve done some research in the area of interactive graph visualization, I was eager to see how Gephi works and if it brings some new concepts or if it’s yet another graph visualization system. I’ll share my thoughts on Gephi from three perspectives. The first one is the user perspective. I’ll take the role of a user who is interested in getting a visual depiction of some graphs. Secondly, I’ll take the role of a developer and shed some light on the aspect of software engineering. And finally, I’ll be a scientist and try to foresee if and in which regard Gephi might have some impact on visualization research.

The User’s Perspective

Gephi has been designed with the users and their needs in mind. The system welcomes its users with a familiar look and feel. It is quite easy to load graph data into the system. Many of the known file formats for graphs are supported, as for instance, DOT, GML, GraphML, or Tulip’s file format TLP. A nice thing about the data import is that an import report provides essential information about the import process (e.g., number of nodes and edges, edge-directedness, potential problems, etc.). Once imported, the graph is shown as nodes and links in a main view, and several complementary views provide additional information.

The main view is the core for visual graph exploration. It allows users to zoom in, to select nodes, to adjust node size and color, to find shortest paths, and to access attributes of nodes and edges. In addition to letting users set sizes and colors manually, the system can also set these automatically based on attributes associated with nodes and edges. What is called “Partition” in Gephi is used to assign unique colors to nodes and edges based on qualitative data attributes (e.g., class affiliation). Quantitative data values can be mapped to size and color of nodes, edges, and labels using the “Ranking” tool. All these tools are customizable. It is worth mentioning, that Gephi provides some nice user controls to parameterize the color coding.

Gephi also supports graph editing, i.e., insertion and deletion of nodes and edges as well as manipulation of attribute values. What is missing in terms of editing the data is the possibility to add (and delete) attributes, for instance to generate some derived data values using simple formula.

A key aspect in graph exploration is the layout of node and edges. As it is usually unclear what will be the best layout for a given graph, Gephi offers various layout algorithms to choose from. While a layout is being computed, the main view constantly updates itself to provide feedback of the progress made. A big plus is that users can interrupt the layout algorithm once they deem the result to be ok or if they find that it might be more suitable to use the current result as the initial setup for another algorithm. This way users can easily tune the layout to fit the graph and the particular needs. Users may put the finishing touches to the layout by moving nodes manually in the main view.

Once a suitable visual representation has been created, the final step is to export nice pictures of the graph. To this end, Gephi follows the philosophy of providing a dedicated export interface with many options to create high quality printouts.
People that have been working with larger graphs might know that some computations on graphs (including layout computation) are quite complex and take some time. While other systems are blocked during computation and in the best case provide a progress bar, Gephi is different. Long running calculations are concurrent to the main application. From my point of view, this is one of the strongest points of Gephi, the system does not block during costly computations. The benefit for the users is that they can always interact, for instance to initiate some other computations or to cancel running ones when they recognize that a re-parameterization would yield better results.

Concurrency is Gephi’s solution to offering computations of statistics about the graph. Currently, Gephi supports a variety of classic graph statistics including degree distribution, number of connected components, and others. Based on data attributes and computed statistics, the graph can be filtered to reduce nodes and edges to those that fulfill the filter criteria. In a dynamic filtering UI, several filters can be combined using drag’n’drop and thresholds can be manipulated easily, for instance via sliders. Besides using filtering for data reduction, Gephi also provides basic support for graph clustering. However, the currently implemented MCL algorithm is still experimental. But there is the possibility to manually group nodes to build a hierarchical structure on top of the visualized graph. Yet, this is quite cumbersome for larger graphs. Additional tools are needed to support the user in creating a navigable hierarchy on top of a graph. Configurable clustering pipelines that combine several strategies for clustering (e.g., based on attributes or based on bi-connected components) in addition to a clustering wizard user interface would be helpful.

In summary, I see a much potential in Gephi, the overall shape of the system impressed me – me as a user. I personally felt it easy to work with Gephi and explore some of my own data sets and some provided at Gephi’s website. Given the fact that the version I’ve worked with is 0.7 alpha, there is also much space for improvements. In the first place I would like to mention the navigation of the graph. The main view provides just basic zoom and pan navigation, which is even imprecise in some situations. Navigation tools like those provided in Google Earth and navigation based on paths through a graph would be really helpful. Moreover, I was missing the concept of linking between views. Selecting an element (node or edge) in one view should highlight that element in all other views. Right now this is not really an issue as the number of views seen in parallel is quite low. But once additional views are needed, for instance to focus on data attributes in a Parallel Coordinates Plot or to visualize the cluster hierarchy in a dedicated view, or when one and the same graph is shown in parallel in two or more main views for comparing different analytic results, linking will be crucial for user experience. But these things are not too complex and should be easy to integrate in future versions of Gephi. Another aspect regards highlighting in the main view: instead of marking the selected node, all non-selected nodes faded out to focus on the selected node. This implies rather big visual changes because all but one nodes change their appearance when a single node gets selected and deselected.

Pros: Cons:
  • Easy graph import and export
  • Many options for visual encoding
  • Various layout algorithms to choose from
  • Support for dynamic filtering
  • Computation of graph statistics
  • Basic support for graph clustering
  • System does not block during long running computations
  • Graph navigation can be improved
  • No linking among views
  • Few visual glitches
  • Still an alpha version with bugs here and there

The Developer’s Perspective

Now let me switch to the developer’s view. Gephi is open source software so that everybody can participate in improving the system or can adapt the system to personal or business needs. Gephi seems to be very well designed on the back-end. The project is based on the Netbeans platform and the Java language. It is subdivided into a number of modules that define several APIs and SPIs and that provide implementations of these interfaces. Thanks to the modular structure, Gephi can be extended quite easily. The best way to do so is to implement plugins. Plugins can be used, for instance, to add further layout or clustering algorithms, statistical computations, filter components, or export methods. The modular structure also allows for using only specific parts of the Gephi project in one’s own projects. The Gephi Toolkit is a good example. It is not an end-user desktop application, but a class library that provides all the functionality of Gephi to those who want to reuse Gephi’s functionality and data structures in different ways.

As I’ve mentioned in the user perspective, the way how Gephi deals with long running computations is a big plus. Given the fact that aspects of multi-threading are inherent in the system from the very beginning and are manifested at the systems core, I sincerely hope – no, I’m quite sure that Gephi will not run into all the problems that are likely to occur when multithreading is integrated into an existing single-threaded system, as I have experienced it myself. Also I conjecture that others will find it much easier to implement concurrent non-blocking extensions of the system simply by following the way how existing code handles things in Gephi.

As Gephi is split up into many different modules, it took me a while to get accustomed to the system and to learn which functionality can be found in which module. But I have to add that I had no prior experience in Netbeans platform development and the module concept that is used there. I also found that the code documentation could be improved in several parts of Gephi’s sources. On the other hand, the Gephi website provides informative wiki pages with various examples and tutorials.

My view from the developer’s perspective can be summarized as the following pros and cons:

Pros: Cons:
  • Open source
  • Modular structure
  • Well defined interfaces
  • Extensible via plugins
  • Inherently multithreaded
  • In-code documentation can be improved

The Scientist’s Perspective

As a scientist I’m not so much interested in developing fully-fledge end-user software, but in developing solutions to scientific questions and in publishing the results. A difficulty in interactive visualization is that usually one needs a broad basis of fundamental functionality to be able to develop such solutions. Previous attempts of establishing a common infrastructure for interactive data exploration made notable progress, but eventually did not fully succeed or are no longer actively maintained. This is due to the fact that a single researcher usually simply does not have the time to do decent research and at the same time to maintain a larger software project.

I personally feel that Gephi can become such a fundamental infrastructure. Maintained by an active community, the system allows researchers to focus on solutions in form of plugins, while they can utilize the functionality that the system provides. Visualization researchers will be happy if they can simply plug in new visualization techniques as additional views, test new layout algorithms, and experiment with new clustering methods. Moreover, new solutions can be easily disseminated to real users in the community. This might prove beneficial when it comes to acquiring early user feedback or when more formal user evaluation is needed prior to publishing new techniques and concepts.

A big issue in visualization research is visual analytics, that is, the combination of analytical, interactive, and visual means to facilitate making sense of large volumes of data. In terms of analytic means, a goal is to break analytic black boxes and make analysis algorithms interactively steerable. With the architecture of Gephi, where parameterizable algorithms run concurrently and provide feedback in form of intermediate results, I believe this goal can be reach in the future. A thing that I’m curious about is if it is also possible to come up with concepts that allow for plugging in new interaction techniques. As interaction is usually quite tightly bound to a view, I wonder if interaction could be implemented as independent plugins as well, and if novel interaction concepts will be supported in the future (e.g., touch interaction)? Furthermore, aspects of interactive collaboration of multiple users working to solve a common analysis problem could be of interest. A question related to the visual side is whether it is possible to use Gephi with different displays and display environments such as tabletop displays, display walls, smart phones, or multi-display environments?

A facet of graph visualization that I did not mention in the user’s perspective as I felt it more suited to be mentioned here is dealing with dynamically changing graphs. Visualization of time-varying graphs is a hot research topic and Gephi is about to face this challenge. There is preliminary support for exploring time-dependent graphs via a time slider. But there is more to this that just browsing in time. Concepts have to be integrated to support easy comparison of multiple snapshots of a graph and to highlight significant changes in the development of a graphs history.

Let me try to put my thoughts into a pros and cons list:

Pros: Cons:
  • Potential infrastructure for visualization research
  • Researchers can focus on solutions in form of plugins
  • Potential to use community for user feedback and evaluation
  • Partial results for current research questions (graph clustering, steerable algorithms, dynamic graphs)
  • Nice playground for experimentation and testing new ideas
  • Unclear if new and alternative technologies will be supported

Summary

Since I’ve put hands on Gephi I’m infected. Maybe I’m dazzled by the beautiful demo video or the nice pictures that have been generated using Gephi, but in my opinion Gephi has the potential to become a big player in interactive visual graph exploration and analysis. From all perspectives that I’ve taken I see many positive things – and plenty of room for improvements or additional features. I do hope that the people behind Gephi will continue their work to the benefit of all users, developers, and researchers.

Related Stuff

There are many other systems and frameworks out there that do a great job in interactive graph visualization or in supporting it as a toolkit. I would like to give credit to these systems, because they can be the source of many ideas and much inspiration:

To go further about Gephi design, see also this article about semiotics.

Making up after the 100-Day Plan

After more than four months of intense activity, and after the end of the 100-Day Plan it’s time to sum up what was achieved since the release of the 0.7 version. Most of the objectives have been carried out and Gephi has been downloaded more than 17K times since February. The future looks bright and more and more people are interested using and developing the software. Networks are gaining a lot of momentum in the research community and in the industry, by being a generic and extensible platform we position Gephi as a reference tool. If you’re interested funding us, please let us know.

To beta version

Four versions have been released and a lot of bugs have been fixed during this period. The current version is 0.7 alpha 4, released last month. New features were also developed, with the help of the developer community and were quickly deployed, for instance PDF Export and new Metrics. Not later than yesterday, new bug-fixes were deployed and available through Gephi updates.

The milestone date is also fixed for the 0.7 beta: August 14, 2010. The aim is to fix remaining bugs until this date. If you notice one, please consider reporting it.

Documentation

A Quick Start Guide and a Visualization Tutorial have been written. The community made great tutorials also, which made a huge difference. Kudos to them. The forum has also showed great ability to connect with users and provide quick support. Many efforts are still needed in that way and hope to get more support writing tutorials.

Manifesto

We completed the Gephi Manifesto, to understand the project’s goals and aims.

Communication

The video Introducing Gephi 0.7 had a huge success, viewed more than 12K times. It was done to promote the release of the 0.7 version and succeeded in this job. Gephi has now its place among graph visualization software and is already recognized for its easiness and efficiency. But above all, the audience see great potential in Gephi and many people are thinking how they could use or reuse Gephi for achieving bigger tasks. That is very positive and we are cheering developers to code plug-ins.

Follow the #madewithgephi hashtag on Twitter to see recent comments. The Gephi team also attended the IEEE EuroVis conference in June and will provide software demonstration at Sunbelt XXX next week, on Friday July 2.

Development

Thought the 0.7 beta is still in preparation, the new developments still continue and are now in a very active period. Indeed, six Google Summer of Code students are working hard and are preparing outstanding improvements. The whole code is also profiting from the toolkit project, where essential modules are built together in a single JAR in order to be reused as a Java library. Good progress is made on this project. It is very important for many developers who wants to reuse Gephi features in other Java applications. So stay tuned about GSoC updates and gephi-toolkit!

The roadmap and blueprints page also got a lifting.

We would like also to reinforce interoperability with other tools and develop connectors to new file formats.

Developers tutorials

New help pages for developers were created: Checkout Code, Configuring NetBeans and Plugin Quick Start. HowTo for extending Gephi features have been written also, including layout, metric and import and were already used by third-parties developers to create new plugins.

The next tutorial will concentrate on the gephi-toolkit project and how to reuse Gephi as a Java library.

Many other tasks are on the way, notably translating Gephi in French and Spanish and preparing Gephi Student Program. We are very interested involving CS students and propose to them challenging tasks for a semester or a quartile. We hope to interest professors about that.

One more thing, after discussing with the community members we decided to move to AGPL licence for the beta version. The GNU Affero General Public License is a modified version of the ordinary GNU GPL version 3. It has one added requirement: if you run the program on a server and let other users communicate with it there, your server must also allow them to download the source code corresponding to the program that it’s running. If what’s running there is your modified version of the program, the server’s users must get the source code as you modified it. It is specifically designed to protect the Gephi Toolkit.

Bug fixes and new metrics deployment

We invite you to update your Gephi installation to profit from latest fixes and new metrics features. To do so, please go to Help > Check for Updates in Gephi.

Patrick McSweeney has been working to bring new network metrics to Gephi:

That are really useful and widely used metrics, if you want to propose new ideas, a forum topic is dedicated for New Metrics. Please join the discussion.

In addition to other small improvements in the statistics package, he also fixed graph distance memory issues. Average Path Length and Diameter metrics are now working fine.

In the meantime we are working on the toolkit project, which will be announced soon.

New Tutorial: Visualization in Gephi

A new tutorial is available about Visualization in Gephi. It will guide you to the basic and advanced visualization settings in Gephi and introduce selection, interaction and tools.

Gephi has a powerful and customizable visualization engine but sometimes capabilities are not obvious and the richness of some features remains hidden. For instance text drawing is essential for visualization efficiency and needs to me controlled in the best way, in particular for large graphs.

This tutorial explains also in details some of the important tools, including:

  • Shortest Path
  • Heatmap
  • Edit

Gephi 0.7 alpha4 released

The alpha4 version has just been released, check out Download page or Check for Updates in your Gephi. This release comes with new features, including PDF export and bugfixes. Thank you to all members that reported bugs on the forum or through the Crash reporter, that helps a lot, more than you think!

Many bugs have been fixed, including the Menubar problem on Mac OS X and some annoying filters issues.

Let’s have a look on what’s new, and read the complete release notes.

PDF Export

The built-in PDF Exporter is now fully working. It exports the network exactly how it’s displayed in the “Preview” window. We have been impressed how fast it’s processing and exporting. One can configure the page size and margins, in addition to the orientation. Thus you can directly export your network and embed or print it anywhere. Note that texts in PDF are searchable, very useful. Special thanks to Jeremy Subtil who worked on his free time on this feature.

GraphML Export

Files in GraphML format can now be exported from Gephi. Interoperability is very important and the GraphML format is well known and supported in other tools such NodeXL, igraph or NetworkX. We hope that we reach interoperability with these tools and that we use GraphML in the same way. If not, please let us know.

Ego Network

A new filter has been created, it let’s you filter the graph from a node at depth 1, 2, 3 or Max. Enter a node label and the depth and it shows the network around this node.

Other new features in this release

  • CSV export – Export adjacency list and matrix
  • New LabelAdjust algorithm, faster and better quality. Thanks to Mathieu Jacomy.
  • Watts-Strogatz Small World Generator

Interested by being a Gephi official tester? Please consider joining the community.