Announcement Events ~

This is an announcement for the first Gephi Plugins Developers Workshop October 6, 2011 in Mountain View, California. Come and learn how to write your first Gephi plugin and ask questions. The workshop is organized by Mathieu Bastian, Gephi Architect and will be gratefully hosted by IMVU.

Gephi is a modular software and can be extended with plug-ins. Plug-ins can add new features like layout, filters, metrics, data sources, etc. or modify existing features. Gephi is written in Java so anything that can be used in Java can be packaged as a Gephi plug-in! Visit the Plugins Portal on the wiki and follow the tutorials to get started.

The workshop will start with a presentation of Gephi’s architecture and the different types of plugins that can be written with examples. Details about Gephi’s APIs, code examples and best practices will be presented in an interactive “live coding” way. The Gephi Toolkit will also be covered in details. The second part of the workshop will be dedicated to help individuals with their projects and answer questions.

Some of the best projects using or extending Gephi are developed in the Silicon Valley and we are looking forward helping the developer community. Please don’t hesitate to send us your ideas to maximize efficiency.

RSVP here

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Functionality Plugins ~


Cezary Bartosiak and Rafał Kasprzyk just released the Complex Generators plugin, introducing many awaited scientific generators. These generators are extremely useful for scientists, as they help to simulate various real networks. They can test their models and algorithms on well-studied graph examples. For instance, the Watts-Strogatz generator creates networks as described by Duncan Watts in his Six Degrees book.

The plugin contains the following generators:

  • Balanced Tree
  • Barabasi Albert
  • Barabasi Albert Generalized
  • Barabasi Albert Simplified A
  • Barabasi Albert Simplified B
  • Erdos Renyi Gnm
  • Erdos Renyi Gnp
  • Kleinberg
  • Watts Strogatz Alpha
  • Watts Strogatz Beta

The plug-in can be installed directly from Gephi 0.8, from the Plugins menu.

The source code is available on Launchpad.

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Plugins ~

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!

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Announcement Plugins ~

The project takes another big step forward and bring dynamic graph exploration on the web in one click from Gephi with the Seadragon Web Export plugin.

Mathieu Bastian and Julian Bilcke worked on a Seadragon export plugin. Directly export large graph pictures and put it on the web. Seadragon is pure Javascript and works on all modern browsers. As it uses images tiles (like Google Maps), there is no graph size limit.

Go to your Gephi installation and then to the Plugin Center (Tools > Plugin) to install the plugin. You can also download manually the plugin archive or get the source code.

Sample with Diseasome Network dataset directly exported from Gephi

Communication about (large) graphs is currently limited because it’s not easy to put them on the web. Graph visualization has very much same aims as other types of visualization and need powerful web support. It’s a long time we are thinking about the best way to do this and found that there is no perfect solution. We need in the same time efficiency, interactivity and portability. The simpleness of making and hacking the system is also important, as we want developers to be able to improve it easily.

By comparing technologies we found that Seadragon is the best short-term solution, with minimum efforts and maximum results. It has however still a serious limitation: interactivity. No search and no click on nodes are possible for the moment. But as it is JS, I don’t see hurdles to add these features in the future, help needed.

The table below see our conclusions on technologies we are considering. We are very much eager to discuss it on the forum. As performance is the most important demand, WebGL is a serious candidate but development would require time and resources. We plan to start a WebGL visualization engine prototype next summer, for Google Summer of Code 2011, but we would like to discuss specifications with anyone interested and make this together.

Portability Efficiency Effort Interactivity
Flash
Java2D/Processing
Canvas (Processing.js/RaphaelJS)
WebGL
Seadragon
Figure: Comparing technologies able to display networks on the web.

How to use the plugin?

Install the plugin from Gephi, “Tools > Plugin” and find Seadragon Web Export. After restarting Gephi, the plugin is installed in the export menu. Load a sample network and try the plugin. Go to the Preview tab to configure the rendering settings like colors, labels and edges.

Export directly from Gephi Export menu

The settings asks for a valid directory where to export the files and the size of the canvas. Bigger is the canvas, more you can zoom in, but it takes longer time to generate and to load.

Export settings, configure the size of the image

Note that result on the local hard-drive can’t be viewed with Chrome, due to a bug. Run Chrome with “–allow-file-access-from-files” option to make it work.

Kudos to Microsoft Live Labs for this great library, released in Ms-PL open source license. Thank you to Franck Cuny for the CPAN Explorer project that inspired this plugin. Other interesting projects are GEXF Explorer, a Flash-based dynamic widget and gexf4js, load GEXF files into Protovis.

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Plugins ~

Yi Du

During this summer, six students are working on Gephi with the Google Summer of Code. They contribute to Gephi by developing new features that will be integrated in the 0.8 version, released later this year.

Yi Du is adding the module Direct Social Networks Import during this summer, which provides several kinds of importers like Emails, Twitter or Facebook. The goal of this article is to briefly introduce some of the importers, as well as several samples provided.

The ability to import any kind of structured data and build network from it is essential for users. This step is often missing and requires time and scripting abilities, although tools and libraries able to read and parse all type of data already exist. Moreover it has never been so easy to quickly access meaningful datasets online.

Email importer

Email is a simple and widely used tool in communication among people, yet many people have no knowledge of its mechanism. To some extent, our work on analyzing emails can help people better know their relationship with others. In our email importer module, each email address is represented as a node. If there are two email addresses with the same display name, an option will be provided to allow the user to determine whether to regard them as a node or two different nodes. Afterwards, if there is an email from A to B, an edge will be built, along with an option permitting the user to determine whether Cc or Bcc will be viewed as an edge.

We provide two ways to import emails: on the one hand, the emails are obtained from the email server (POP3 or IMAP), in a one-by-one manner. On the other hand, we get the emails from local files or folder. This importer will arise a problem, that is, different email clients may have different file format. Fortunately, our importer has an easy-to-extend API, as well as a default implementation (EML files). EML is standard and can be obtained from Thunderbird, Outlook and Gmail with tools like Gmail Backup.

This is a sample to illustrate how email importer outputs the data (2000 emails with EGO filter, 700 nodes, 1300 edges).
fig1a_The_EGO_graph fig1b_Graph_whose_indegrees_bigger_than_0
fig1c_Modularize_the_graph fig1d_Subgraph_who_has_the_max_number_of_Modularity_count
fig1e_The_hottest_group

Twitter importers

Twitter is a very popular social network. People can send and receive short messages, which we usually call tweets, using Twitter. We can follow person we are interest in and topics we like. Twitter networks has been popularized by NodeXL which has a similar feature. See this nice gallery.

We provide two kinds of networks: “Twitter Search Network” and “Twitter User Network”.

We support Twitter search network to analyze people who search or mention similar keywords. We present one Twitter user as a node and define three kinds of edge construction:

  • Replies-to relationship: If A reply to B in a searched tweet, an edge from A to B will be added.
  • Mentions relationship: If A mentions B in a searched tweet, an edge from A to B will be added.
  • Followers relationship: If A follows B in constructed graph, an edge from A to B will be added.

The second network we provide is “twitter user network”. We analyze people who follow each other to show the relationships between twitter users. We add an edge from A to B if A follows B in the whole graph by default. We provide three options for vertex construction:

  • Person followed by the user: If searched user A follows B, B will be added as a vertex.
  • Person following the user: If A follows searched user B, A will be added as a vertex.
  • Both: Both the above two options.

The interface of the two importers are shown as below.
fig2a_User_network_importer_ui fig2b_Search_network_importer_ui

New-York Times importer

The New York Times is an American daily newspaper founded and continuously published in New York City. It has a series of APIs for developers on news and social networks. There are several APIs of NYT, such as Article Search API, Best Seller API, etc.

We provide two kinds of social network importers in Gephi: “Article Network” and “TimesPeople Network”. We use article network to analyze articles with specific filters (date, facets, etc). User can choose which option constructs the edge. For example, user can choose date as the edge. If two articles have the same date attribute, an edge between them will be built. TimesPeople is a social network for Times readers, it’s similar to Facebook, we can analyze the relationship between them.

Interface of NYT article network import and TimesPeople network are shown below:
fig3a_NYT_article_network_importer_ui fig3b_NYT_timespeople_network_importer_ui

Display of TimesPeople network:
Display of TimesPeople network Display of TimesPeople network
Display of TimesPeople network

Conclusion and future work

In this article, we introduced several importers: Email, Twitter and NYT. By using these importers, users can import data they want and analyze them. They can find the hottest group, the relationship of their friends, the most related author of a facet and other import information by analyzing them.
Until the end of the GSoC, we will have four major importers: Email, Twitter, NYT and Facebook. Among these four importers, Twitter will have “Twitter User Network” and “Twitter Search Network”. NYT will have “NYT article search network” and “NYT TimesPeople Network”. Facebook will have “Facebook Friends Network” and “Facebook Group Network”. Besides adding Facebook importer, we will also optimizing the UI of the importers, and make them more user friendly.

Yi Du

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