Gephi donation campaign ended

Thank you for your support!

During the last 9 months you donated over €700 to the Gephi NGO. This helped us to pay the Web server. Now this campaign is over, but you can still continue to help! The Gephi NGO has been transformed to the Gephi Consortium, and you can support our activity.

While all of the administrative effort is currently through unpaid volunteers, our expenses include:

  • Server costs
  • Legal and Accounting
  • Normal office expenses
  • Marketing and PR.

Your sponsorship will allow the Gephi Consortium to meet these expenses as well as expand our capability to maintain our leadership in the developer and Open Source communities. Funding will allow us to enhance our community outreach, set up development programs, student challenges and user groups, and perform non-code related improvements to projects such as better documentation and more comprehensive websites.

We regularly participate in conferences and events: JavaOne, IEEE Eurovis, INSNA Sunbelt, International Design Biennale…but also help teaching (social) network analysis at the university. This year, the Gephi Consortium and our sponsor INIST-CNRS spent jointly more than €8,000 in registration fees and travel reimbursements. Gephi was presented that way to different communities and we met very interesting people. Contact us to organize a Gephi workshop in your company or university!

If you think that our actions are useful, consider also to make a donation.

 

Click here to lend your support to: Support Gephi Consortium and make a donation at www.pledgie.com !

Gephi maps exhibited at the International Design Biennale

affiche_last2-187x300 The Saint Étienne International Design Biennial, holding from 20 November to 5 December, is a unique event in the domain of design, due to the exhibitions shown as well as the diversity of its attendees. The Biennial democratizes design and makes it accessible to all kinds of audiences, proving that this creative discipline can take many forms, and is often driven by human aspects, including its uses by humans.

The theme of the 2010 biennial is around teleportation. It intends to explore paths of discoveries that will tend in their extreme expression to lead to a possible teleportation as the dematerialization of movement which appears to be an incredibly revealing notion of our era.

Sebastien Heymann will exhibit maps of designers’ conceptual world, placed at the center of the “Prédiction” exhibition. Made in collaboration with Benjamin Loyauté, curator of the event, these inscriptions are a proposal to reveal the state of knowledge sharing in Design today.

Useful information on how to come here.

 

You may contact Sebastien by email to appoint a meeting during the first weekend.

Ten free tickets will be given to the first comments of this post!

EDIT: photos are available on the Facebook page of Gephi.

OpenOrd: New layout plugin, the fastest algorithm so far

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A new force-directed layout algorithm plugin named OpenOrd has just been released. It is one of the few force-directed layout algorithms that can scale to over 1 million nodes, making it ideal for large graphs.

Features:

  • Very fast, scales to millions nodes
  • Can be run in parallel, run it on multicore processors
  • Aims to highlight clusters

Install it directly from Gephi (Tools > Plugins > Available Plugins) or download it from the Plugin Center. Longer description and source code can be found directly on the plug-in page.

Below is a small demo of how fast this algorithm is layouting a 10K nodes network, and only using one processor.

OpenOrd Layout Demo in Gephi from gephi on Vimeo.

The algorithm original design and implementation can be found at this address. Kudos to the authors!

Gephi has a Student Program

mini-300x260 The Gephi project now has a Student Program. The idea is simple: propose various tasks adapted to computer science students and help them to create Gephi plug-ins. Inspired by the Google Summer of Code and our own experience as students, the program offers original ideas and a real open-source experience.

Computer science students are usually asked to complete many small projects during their studies, often by group. We want to propose original projects, which the result can easily be packaged as a plug-in and shared. Graphs and networks are at the heart in variety of problems, including Graph Theory, Sociology, Data Mining, Statistics or HCI (Human-Computer Interaction). The ability to visualize and manipulate graph structures in a simple way is central to understand these problems. Moreover, what a best way to learn graph theory than code on of its algorithm?

The wiki page will maintain an (open) list of ideas and projects. For each student interested, we will provide some help to get things done and promote his project. We are also thinking about free tee-shirts for all students.

A Google Map for the Gephi Community

Gephi is now an international community, and thanks to the Internet we can exchange at distance through the forum, mailing-lists and live chat.

However IRL meetings are still very important, as great collaborations can start with a beer! It’s the secret part of the Gephi history

So we set up a Google Map for the Gephi community to claim our locations and therefore help organizing local meetings. Internet makes communication easy but it’s always better to have real meetings to help each other and exchange our experiences in data analysis with Gephi face-to-face! Discover if a Gephi supporter lives in San Francisco, Warszawa or Tōkyō.

Please contribute and add the information you want: this map is publicly editable for your own use.

How to organize a meeting?

  1. Put a marker on the map to set the place of meeting and detailed information.
  2. Contact the local members you find on the map.
  3. Inform us on the forum by giving details on the event location and date.
  4. We advertise your event through the Gephi official blog and social media: Facebook, LinkedIn, and Twitter.

 

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

Gephi at JavaOne 2010

Gephi is one of the Duke’s Choice Award winners this year and has therefore be kindly invited to attend the JavaOne conference in San Francisco.

The project has been featured in the Mason Street tent during the five days of the conference. Moreover, Mathieu Bastian (Gephi’s Software Architect) presented Gephi during the Java Frontier Keynote as a brilliant example of Java innovation. Mathieu provided a short demo using a longitudinal Java dependency graph, the classes in the Java package from Java 1.2 to Java 6. The keynote was introduced by Ray Kurzweil, who insisted on the vast amount of data, the “Petabyte Age” and the need to process, analyze and extract value from it.

You can watch the video of the Gephi presentation online (go to topic 36). EDIT: now on Vimeo in HD!

Mathieu Bastian presenting a live demo of Java packages evolutions at JavaOne 2010 conference.

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The project has been also mentioned in the following articles:

Announcing the Gephi Consortium

The Gephi Team is proud to announce a major shift for Gephi:

The former Gephi NGO is ready to launch the Gephi Consortium, a legal entity created to ensure future developments of Gephi by collecting funds and in-kind contributions to the members. It is a not-for-profit corporation governed by the French law of July 1st, 1901, equivalent of the United States 501(c)(3) organization. It aims to join the efforts of industrials, laboratories and civil society to pursue the goals fixed on the Gephi Manifesto. We plan to officially launch it on October 1st, 2010.

Gephi Software key figures

  • Launched in 2008
  • Development cost evaluated at 2M$ with COCOMO
  • 150,000 lines of code
  • 20 contributors in 8 different countries, translated in English, French and Spanish
  • 33,000 software downloads
  • 600,000 pages viewed/year on gephi.org (estimation 2010)

Why a Consortium?

What have research laboratories, big data companies and human societies in common? The recurrent need to map and understand complex phenomenons, revealing patterns and trends in relational data. The knowledge discovery process faces now with the “data deluge” problem provocatively emphasized by Chris Anderson on Wired Magazine… and everyone is becoming concerned by mining data/information from the flow.

Most of the data can be expressed as networks: transportations routes, power grids, emails, food webs, interlocking directorates or the relations between scientific papers are just a part of their applications.

The Gephi project aims to tackle this underlying complexity by giving the power to visualize, filter and manipulate every kind of networks in real time. A generic infrastructure and long-term vision are the keys to overcome these challenges.

Since we started in 2008 in France, many individuals, students and companies already downloaded and tried Gephi. Sign of good health, we federate engineers and reseach scientists from many different countries.

But the project needs fundings and leadership to comply with these plans. This is the purpose of the Gephi Consortium.

A long-term mission

The Consortium makes an R&D effort to build generic and reusable parts of Gephi, improve a competitive technology at low cost, and create standards to ensure interoperability.

It provides core services to the Gephi community, support the development of the Gephi Open Source framework, and help other projects like the GEXF universe (format specifications, libraries and Flex applications) and a soon-to-be graph-stream format. Real-life meetings and retreats are also on the list.

We act as a central point to coordinate the worldwide distributed development, promote it and legally protect it.

These goals are only reachable with the financial and in-kind support of the community. The founding members include INIST-CNRS, Linkfluence SAS and WebAtlas NGO. They have been selected for their past investments to support Gephi at the early stages. Other organizations are already eager to join like SciencePo Paris and the TIC-Migrations research program, and more currently in discussion. A rapid growth is expected as the consortium is a structural solution to the community’s need ( see for instance this comment on Christian Tominski’s review ).

The ecosystem we set up is made for the benefit of the whole community. The governance is held by a Board of Directors electing the Management Office every three years. The consortium can only receive funding from grants, donations and membership fees to ensure the respect of antitrust laws. Contracts are then held by members on their sole commitment, out of the consortium’s responsibility scope.

We expect this way to generate opportunities for companies to build by-products and services, Gephi developers to get hired for their recognized skills, analysts to improve their insights as long as our technology evolves, and academics to use a robust infrastructure for visualization and network science research for free.

About the legals, Gephi is distributed under the GNU AGPL license. The obligation for the contributors to sign a Contributor License Agreements (CLA) certifies the ability for the Consortium to protect the ecosystem.

So why joining us?

Academics: We provide an infrastructure for Visualization and Network Science research. Use our technology as a platform for implementing new research ideas in a very short time, focus on your novelty, and get feedback from the community.

Corporates: We propose legal solutions to integrate Gephi in your value chain. Use it as a module in final products or in R&D departments. If you can’t use an Open Source software for any reason, you may get a dual license on demand to use Gephi like any proprietary software.

Individuals: We organize the community in a transparent manner, provide online tools and build a knowledge base for the benefit of everyone.

In a nutshell, key benefits are:

  • Leadership and strategic directions taken according to the members’ common needs
  • Personalized business made possible
  • Address book, connection with skilled developers and talented researchers, open innovation
  • Distributed assistance on Gephi technology, i.e. understand how to extend or reuse Gephi to get things done
  • Advices in software engineering and graph visualization in general
  • Legal guidance in Open Source / Free Software licensing

 

We focus on the specifications and development of the Gephi Open Source core. This R&D effort to build generic and reusable parts is only made possible by the collaboration of multiple companies, research laboratories and organizations.

 

 

Learn more about the Gephi Consortium at http://consortium.gephi.org.
Get the executive summary in PDF here.
Get the nutshell presentation in PDF here.

Gephi wins Duke’s Choice Award 2010

The Duke’s Choice Awards recognize and honor extreme innovation in the world of Java technology, and are granted to the most innovative uses of the Java platform. Because the primary judging criteria is innovation, the awards put even small developer shops on an equal footing with multinational giants. The winners are selected by Oracle’s Java technology leadership team.

Congratulations to all Gephi contributors! Thank you to the Oracle’s Java Team to make Gephi a Duke’s Choice and the technology that have enabled us to build Gephi and Gephi Toolkit.

The winners will be featured at the JavaOne Conference in San Francisco, September 19-23rd. Gephi’s Software Architect, Mathieu Bastian will be present there to receive the award, and attend the conference!

Java provides all the components and development tools to develop large data-intensive open-source applications. Gephi is built on top of the Netbeans Platform, and profit from its module and window systems. The platform allows us to propose solutions to reuse and extend features, in terms of plug-ins, and let developers create new data wrappers, algorithms or filters easily. The rendering engine is built with JOGL (Java OpenGL) and gives responsiveness and interactivity, thanks to hardware acceleration. We use a large number of Java libraries. I would like to use the occasion to offer thanks to all contributors of these projects.

A new video that features Gephi in five minutes:

Introducing Gephi at JavaOne from gephi on Vimeo.