Gephi 0.9.2 : a new CSV importer

A new version of Gephi has been released! Thanks to Eduardo’s relentless issue fixing, Gephi’s overall stability has been improved. Eduardo is the author of the Data Laboratory, and at this occasion he revamped its CSV importer for a more flexible and straightforward user experience.

The new CSV/spreadsheet importer

Did you know that Gephi can export and import just the table of nodes or the table of edges? This feature is useful in many situations, for instance to produce charts in Excel or to clean data in Open Refine. Below we will showcase the new features and more generally explain how to import a spreadsheet as a list of nodes.

To import a spreadsheet you have to reach the Data Laboratory and click on Import Spreadsheet. In the example below a network is already loaded: we will decide later whether the imported nodes will be merged into the existing ones or not.

Tuto01

Gephi is now able to recognize the type of file you upload, and the support of Excel files has been added. Choosing the right separator is crucial since improperly separated columns would compromise the data. In the example below Gephi recognized that the separator is the Comma (as in a properly formatted CSV file).

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The encoding of the file is a common issue, notably with languages using accents and special characters. Gephi can guess the encoding and you can manually edit it if necessary. In the example below Gephi correctly guessed the UTF-8 encoding.

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Selecting a different encoding would produce errors. Fortunately the Preview table allows you to see them and fix the encoding. In the screenshot below, see how the wrong encoding produces exotic characters in the data.

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When you validate these settings, Gephi now opens the exact same panel as when you open a new network. I personally love this addition since it brings more consistency to the user experience. It allows Gephi to provide a number of useful informations like the number of nodes detected or the issues found during the import process.

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Do not miss an important feature here: in this panel you decide either to create a new workspace with the imported data or to merge the new nodes with the old ones. This very useful feature was already present at the opening of a new network, but many users still ignore it exists. Mind to select the Append option if you intend to merge the nodes. In that case when an imported node has the same Id than an already present one, the new node data will override the old one.

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More info

Take a look at the full list of improvements there:
https://github.com/gephi/gephi/releases/tag/v0.9.2

How do I get this release?

  • If you have a recent Gephi, the update will be automatically proposed to you
  • If you have an older version (0.8 or before) you have to download and install manually
  • This update can be downloaded from http://gephi.org

Gephi updates with 0.9.1 version

splash091A new Gephi version has been released and can be downloaded from gephi.org. This version is an update from the 0.9.0 version released last December and mostly addresses issues discovered since.

One notable improvement is a new localization: German! Gephi is now localized in nine languages (English, French, Spanish, Japanese, Brazilian Portuguese, Russian, Chinese, Czech and German) and we hope to continue the momentum on this effort in the future.

new_german_l10n

Other notable improvements include a better support for parallel edges, appending to existing workspaces and how filters are saved in .gephi files. More than 60 bugs were fixed with a majority of them reported by the community. Thanks to all users who took the time to help! The complete list of bugfixes and improvements can be found in the changelog on GitHub.

In the next few weeks we would like to focus on documentation as there’s still many features brought in the 0.9.0 version without up-to-date documentation. This is especially important for more complex features such as dynamic graphs, which got a major upgrade.

As usual, please share your experience/feedback on our Facebook group or on Twitter.

Gephi 0.9 released: Play with network data again

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We’re proud to announce the release of the next major version of Gephi! This 0.9.0 version has been more than three years in the making but today brings an exciting new life to this project, and the graph/network analytics community at large. You can download it here for Windows, Mac OS X and Linux.

Gephi is the leading graph visualization software – known as the “Photoshop for networks” and is open-source and free. It has been downloaded more than a million times and is used by many scholars and data scientists around the world. This new release brings new features in the area of dynamic networks (i.e. network over time) and major compatibility and performance improvements.

Since the last release in 2013, users were facing compatibility issues with Java, which have been resolved with this release. Development had slow down three years ago but had never stopped. In fact, in March 2013 the time had come to think about what Gephi 1.0 would look like and realize it needed a new core. This was by far the most complex project the team had to overcome but developers had a long-term vision and know that future developments will now rely on a robust and extensible core, with world-class performances.

The world is increasingly complex and interconnected. Gephi’s purpose is to unfold this complex relational data in a way anyone can understand them. It allows you to visualize graph data as a map and create the visualizations to support your narratives. State-of-the-art algorithms make readable layouts, highlighting communities or influential nodes. Visual tools tweak colors and shapes to reveal hidden patterns in the data, helping solving complex problems. More and more network-maps are pictured in online, offline press and other communication media. They spread from science to business, art and activism. People are increasingly exposed to them and learn how to read them. Gephi aims to accelerate this commoditization process by providing free and easy-to-use tools.

What’s new in Gephi 0.9?

The list is too long! The complete changelog for this version can be found on GitHub’s release page.

Next steps

There are a few immediate next steps coming up right after this release. Following-up on the recent plugin development announcement we’ll get in touch with plugin developers and start migrating plugins to this version. There’s more than 80 plugins to update!

Then, we’ll identify and resolve new issues that appeared with this version. A future Gephi 0.9.1 release will come next year to address those.

A Gephi Toolkit release will also be made very soon so developers can update their application built on top of Gephi’s modules. In the meantime, we’re interested in users’ feedback and want to hear from you on Twitter or Facebook. Issues can directly be reported on GitHub as well, where the developers are.

Finally, thanks to all contributors and the community for supporting this project!

Announcing Gephi 0.9 release date

Gephi 0.9

Gephi has an amazing community of passionate users and developers. In the past few years, they have been very dedicated creating tutorials, developing new plugins or helping out on GitHub. They also have been patiently waiting for a new Gephi release! Today we’re happy to share with you that the wait will come to an end December 20th with the release of Gephi 0.9 for Windows, MacOS X and Linux.

We’re very excited about this upcoming release and developers are hard at work to deliver its roadmap before the end of 2015. This release will resolve a serie of compatibility issues as well as improve features and performance.

Our vision for Gephi remains focused on a few fundamentals, which were already outlined in our Manifesto back in 2009. Gephi should be a software for everyone, powerful yet easy to learn. In many ways, we still have the impression that we’ve only scratched the surface and want to continue to focus on making each module of Gephi better. As part of this release, we’ve undertaken one of the most difficult project we’ve worked on and completely rewrote the core of Gephi. Although not very visible for the end-user, this brings new capabilities, better performance and a level of code quality we can be proud of. This ensure a very solid foundation for the future of this software and paves the way for a future 1.0 version.

Below is an overview of the new features and improvements the 0.9 version will bring.

Java and MacOS compatibility

This release will restore Gephi’s compatibility with the latest Java versions on all platforms. This will resolve issues our users encounter with Java 7 and 8. Compatibility issues with Mac OS will also be resolved and full support for Retina display screens added.

New redeveloped core

This release will improve performance and reliability by a large margin. The graph structure at Gephi’s core has been redeveloped from scratch and will bring multiple new features, better performance and lower memory consumption. On benchmarks, simple operations such as reading nodes or setting attributes see performance improvements ranging from 2X to 100X. This new core will make many operations in Gephi faster and push the envelope even further in large graphs exploration. Reducing memory usage has also been an area of focus and we have measured a 2X reduction compared to Gephi 0.8.2 on a medium-size graph.

New Appearance module

We’re introducing a new user module named Appearance designed to combine and replace Ranking and Partition modules. Appearance will group in one place all controls acting on the node or edge appearance. The partition capabilities will also greatly improve as part of this new module and a new palette selector is being added. In addition of the default palettes, we’re also adding a cool palette generator designed to find the optimal colors (i.e. partitions can be differentiated from each other). Moreover, it will be possible to “Auto-apply” partitions as well, which is a feature that was only available for Ranking so far.

Appearance Partition Palette selector Palette Generator

Timestamp support

This 0.9 release adds a new way to represent networks over time: timestamps. So far, users could only represent time using intervals and that was cumbersome when the underlying network data was collected at fixed time intervals (e.g. one network per day). Starting with this release, Gephi will support both intervals and timestamps to represent evolving network topology and/or evolving attribute values.

GEXF 1.3 support

The GEXF format is also evolving to its 1.3 version. This version improves the support for graphs over time and introduces the ability to represent time using timestamps rather than intervals. In addition, it’s now possible to set a timestamp or an interval for the entire graph, allowing building collections of GEXF files where each represents a “slice”. This is a common request from the community and we hope this will greatly facilitate the exploration of longitudinal networks.

Multiple files import

With the 0.9 version users will be able to import multiple files in Gephi at the same time. Once the files have been read, two choices are offered, either to import each file into a separate workspace or merge them into the same workspace. The latter is a powerful option when used with dynamic graphs. Indeed, a collection of GEXF files representing the same network over time will be imported in Gephi in a single step.

Import Report Multiple Graphs

Multi-graph support

Multi-graph exampleThis release will bring support for multi-graphs, where multiple edges can exist between two nodes each with a different relationship. Users will be able to import, filter and run algorithms on these graphs but the support for visualizing these graphs will come in a further release.

New workspace selection UI

We’ve heard users’ feedback and the workspace selection user interface will be improved. The new interface will be a “tab-style” interface where each workspace is a tab and switching from one workspace to another only requires a single click. Tabs will be located at the top just under the perspective selection. The previous interface is located at the bottom right corner and will be entirely removed.Workspace Tabs

Gephi Toolkit release

A new release of the Gephi Toolkit, based on the 0.9 version will be made soon after December 20th.

Bug fixes

We’ve done a serious bug squash and already addressed many difficult issues, more to come until the release date.

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Follow us on Twitter or join the Facebook group to get the latest news. If you want to know more about this upcoming release, or want to help out please send us a note.

0.8.2 beta released

The latest version of Gephi has been released, download it for Windows, Mac OS and Linux platforms. This release captitalizes the bugfixes and stability improvements we have done over the last few months. It also greatly improves the Mac OS X compatibility with the Gatekeeper and Retina Display support. Gephi should now starts right away when double-clicking on the App with a Gatekeeper-enabled computer. However if you have an older version of Gephi on your computer, you should uninstall it and remove the user directory, see the installation instructions.

This release is the first one based on our new Continuous Integration environment. This new system makes it easy for developers to create a new release and for beta-testers to test an early version. Users eventually get a software which has been tested much more heavily and by a larger population compared to previous releases.

Plugins need to be checked for compatibility. They will reappear on the Plugin Center in the coming days, as they are verified. Thanks for your patience.

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

New and Noteworthy

* Data Laboratory’s time interval merge strategy now supports custom date format
* Improved parser for dynamic types. Literal strings are now supported.
* Add Retina Display support to the Mac OS X version

Bug fixes

* Filters ‘Duplicate’ does not work (Issue 176)
* Exporting SVG File throws DomException due to invalid stroke-widths (Issue 697)
* File name entered is lost when changing folder (Issue 463)
* Datalab: can’t export all columns (Issue 628)
* NullPointerException when importing from database (Issue 691)
* Filter on column created with regex causes crash (Issue 663)
* “Long cannot be cast to a String” when either exporting a graph or saving a gephi file (Issue 679)
* Mapping of Escape Keyboard Shortcut for “Save changes before closing?” dialog box (Issue 686)
* DataLab: filling edge weight column doesn’t work when dynamic (Issue 619)
* Spreadsheet import of dynamic data: support of “infinity” (Issue 631)
* Missing license headers (Issue 664)
* Spreadsheet import and self-loops (Issue 683)
* Timelime interval set in infinite loop (Issue 712)
* OutDegreeRange broken (Issue 651)
* Shortest path on filtered graphs fails (Issue 650)
* Weighted degree computation fails (all values 0) when a filter is applied (Issue 636)
* Dot parser fixes (Issue 621)
* Filtering leads to Null Pointer exception when saving (Issue 617)
* Partition percentages incorrectly composed across filters (Issue 637)
* Start/end attributes are always imported using DATETIME format (Issue 649)
* HeatMap / Shortest Path on undirected Graph wrongly paints / calculates (Issue 630)
* Typo fix connetion to connection (Issue 642)
* Timeline sparkline bug (Issue 615)
* Fixes calculation of clustering coefficient on graph (Issue 625)
* Unix timestamp support (Issue 612)
* GML loading cannot accept scientific notation for float-type edge property (Issue 300)
* GML export does not respect specs (Issue 604)
* GEXF export outputs incorrect files (Issue 570)
* Problems with export of PNG files (Issue 601)
* Edge pencil: unable to set edge directedness (Issue 549)
* Presets of “Preview settings” are incorrectly / not saved (Issue 575)
* Option “Time intervals as dates” in Timeline (Issue 613)
* 8.1 and 8.0 both freeze at start-up when on network (Issue 592)
* Data laboratory max columns unintuitive (Issue 590)
* Modularity with Edge Weight Causes Array Out-of-Bounds (Issue 577)

Do Gephi technologies matter for your research or business? You can support us by donating to the Gephi Consortium, or becoming a member to have an impact on our roadmap.

The next version will be a new serie (0.9) and will bring a strengthen core and new features. Stay tuned for that.

Feel free to reach to us if you are willing to organize events (meetups, workshops, hackathon, etc.), we will support them.

Beta Tester program starts

Hi all, today we are announcing a new program and it’s all about testing the latest versions of Gephi. Anyone can join the program and test the development version, send feedback and discuss features. We want to build a team of beta-testers who the developers can work with to detect issues before the software reaches the standard users.

So far, testing has been done by a small group of developers and users but we would like to extend it to a larger audience. There are many different versions of Windows, Mac OS X and Linux Gephi supports. Testers will help to detect compatibility issues specific on a single platform and overall participate in testing new features.

To make this effort successful, we’re making it super easy to test the latest development version without requiring to know about programming or how Gephi is built. We’re introducing a nightly build package which gets updated automatically every night with the latest version of the code. Once downloaded and installed, this version of Gephi will ask you to update itself every time a new version is available so you don’t have to download and install Gephi over and over again. If you’re already familiar with Gephi’s auto update capability, this is using the same system.

How to get started?

    1. Join the gephi-tests@lists.gephi.org mailing list

Developers and testers will discuss on this list.

    1. Fill this questionnaire online.

Cuple of questions on your hardware and software configurations.

Questions? Feel free to stop by on this forum thread.

0.8.1 beta released

The latest version of Gephi has been released, download it for Windows, Mac OS and Linux platforms. This release delivers a complete new timeline component with many awaited features. The timeline is at the heart of our dynamic network analysis (longitudinal networks) effort at Gephi and this feature is the result of last year’s Google Summer of Code. It gives the ability to explore a network over time in a very powerful way.

timeline_sparkline
New Timeline with embedded sparkline. Example with a Twitter user network.

The timeline new features include animation (play button), custom bounds and embedded sparkline. In the previous Gephi version we added the ability to run metrics over time. For instance, one can calculate the average degree over time or simply the number of nodes (like in the example above). With the new timeline it’s possible to display a dynamic attribute directly in the component. For example if you’re looking at a Twitter network you can plot the total number of tweets as a sparkline.

This release also ships with three new languages: Czech, Chinese and Russian. Special Thanks to our awesome localization team.

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We just started the Google Summer of Code with exciting projects! We’re looking for talented students this summer (apply here). The team will also work on the next major release of Gephi (0.9). If you have ideas or suggestions, please don’t hesitate to express then on our forum or through GitHub issues. Our roadmap is open and most ideas comes from users’ experience.

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

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

New features

tineline_thumb New Timeline

Exciting new timeline with animation, custom bounds settings and embedded spakline. The timeline interval and bounds can now be set manually by the user. By hitting the play button the interval moves automatically. All parameters can be configured. The timeline date support has been completely rewritten, now showing dates and periods in a readable way.

local_scale_thumb Local/Global Ranking

Compare networks over time or with different filters is now easier as Ranking lets you decide whether the scale should be local or global. In local scale, sizes and colors depend on the visible sub-graph. In global scale (set by default) they depend on the whole graph, thus allowing comparisons over time.

Screen-shot-2012-03-25-at-3.39.56-PM Weighted community-detection

Louvain Modularity (Community detection) adds edge weight support and resolution setting.

New and Noteworthy

* Better Preview performance when hidden edges (good for large graphs)
* Self-loop filter. Remove self loops in the graph.

New localization (Go to Tools > Languages)

* Russian
* Chinese (China)
* Czech

Bug fixes

* Exception when deserializing a preview preset (Issue 554)
* ClassCastException when saving a gephi file after PDF export (Issue 552)
* Cannot Preserve Z-Coordinate in GEXF exporter (Issue 547)
* Gephi won’t start on Mac OS X Lion because of a missing JAWT library (Issue 542)
* Add a local/global scale button to Ranking (Issue 541)
* Spreadsheet import: edge weight not imported (Issue 540)
* NOT operator wrong with topology filters (Issue 539)
* Multiple partition filters not named: cannot tell them apart (Issue 537)
* AttributeContollerImpl should be renamed to AttributeControllerImpl (Issue 530)
* Timeline – Set Custom Bounds does not support DATETIME (Issue 529)
* Data Laboratory – Dynamic Attributes Edit function resets values (Issue 528)
* DL exporter fix (Issue 525)
* Validator of MySQL’s “host” field (Issue 521)
* Edge/Node attributes don’t support datetime format (Issue 518)
* Directed Graph cluster coefficient provides incorrect values in certain situations (Issue 517)
* NullPointer in GUI when defining range Filters (Issue 516)
* datalab: empty column fails edge csv import (Issue 515)
* updateDimensions in PreviewController does not take into account node size (Issue 514)
* Overview’s graph area does not redraw edges automatically (Issue 513)
* c+p correction: HITS hub chart was repeated twice in output. (Issue 510)
* database import from Postgres does not handle node color attribute (Issue 506)
* Incorrect Teradata JDBC url (Issue 505)
* [Datalab] Duplicated nodes on import spreadsheet (Issue 498)
* [Datalab] Failing silently to load attribute values on import spreadsheet (Issue 497)
* Attribute Columns Property editors don’t support dynamic numbers (Issue 494)
* Arrows not hidden when edges hidden on Preview (Issue 493)
* Some text appears garbled when loaded from a project file (Issue 488)
* Exception when adding a new Perspective plugin development (Issue 486)
* NullPointer Exception with Edge Labels (Issue 478)
* Filter range does not filter if min == max (Issue 477)
* Heatmap Tool Sometimes Doesn’t Work (Issue 472)
* deleting a field in data lab yields an error (Issue 468)
* Email imports can’t be cancelled (Issue 466)
* Invalid XML character error when loading a gephi file (Issue 465)
* Range Slider writes N/A if the min and max values are the same (Issue 464)
* datalab: exception on hiding a column used to sort the table (Issue 454)
* Can’t build without Netbeans installed (Issue 452)
* Auto-refresh not updated after changing the spline (Issue 448)
* AttributeRangeFilter returns main graph when nothing matches filter (Issue 435)
* Timeline need more precision when dealing with dates (Issue 202)
* Degree Filter Not Filtering as Subfilter in Tookit (Issue 69)
* UnsatisfiedLinkError on startup on Mac OS X (Issue 44)

Plugins development

Last november we migrated our source code from Launchpad to GitHub and have seen an increase of activity in plugin development. We also simplified the environment and wrote more documentation how to get started. We created a dedicated repository on GitHub and compiled a list of more than 20 different code examples on the Gephi Plugins Bootcamp.

Do Gephi technologies matter for your research or business? You can support us by donating to the Gephi Consortium, or becoming a member to have an impact on our roadmap.

Feel free to reach to us if you are willing to organize events (meetups, workshops, hackathon, etc.), we will support them.