The first release of the Gephi’s Python Console plugin is finally available for download. Through this plugin, you can execute queries and manipulate the graph structure by typing commands on a scripting console, making it a very powerful and concise tool to work with.
This console started as a joint proposal with the GUESS project which aimed at porting the Gython language as a console plugin for Gephi during the Google Summer of Code 2011 program. This project was mentored by Eytan Adar, from the GUESS project, and co-mentored by Mathieu Bastian, from Gephi.
After installation, the plugin can be accessed through the left slide on Gephi’s UI or through the Window > Console.
Among the features available through the console scripting language are:
Inspired by the Gython language from the GUESS project (i.e. additional operators for manipulating graphs).
Based on Jython 2.5.2, which implements the Python 2.5 specification.
Graph structure and attributes manipulation.
Filtering support.
Support for running layouts.
Export API support (i.e. generate PDF/GEXF/PNG exports from within the console).
Batch scripts support for automating tasks.
Loads third-party Python libraries.
For example, if you would like to filter the male persons from your social graph and make the result visible, you could simply type the following command:
visible = g.filter(gender == "male")
If you want set this subgraph nodes’ color to blue, you could just type:
g.filter(gender == "male").nodes.color = blue
Or, even better, if you want to color both the nodes and edges of this same subgraph, just type:
(gender == "male").color = blue
Implementing batch scripts for automating tasks is very easy. Just save the script as a file with the py extension and load it with the execfile function. For instance, a batch script for creating a random graph with 50 nodes would look like this:
And to run the script, you would call the following command on the console:
The Scripting Plugin can be installed through the Gephi’s Tools/Plug-ins menu:
Go to the Tools > Plug-ins menu on Gephi’s user interface.
Open the Available Plugins tab.
Click the “Reload Catalog” button, to make sure you have an up-to-date catalog.
Select the “Scripting Plugin” on the list and click the Install button.
After installation, the plugin can be accessed through the left slide on Gephi’s UI (as shown in the image below) or through the Window > Console menu.
Documentation
The console’s documentation at the wiki has instructions for downloading and installing the plugin.
Feedback and Contributing
This plugin has been developed by Luiz Ribeiro since the Google Summer of Code 2011 program and we’re really looking forward to see what you’ll be able to do with this new tool.
The plugin’s source code is hosted on GitHub and is open to your contributions. If you find any bugs or have requests or feature ideas make sure to open a new ticket on the Issues Tracker.
Martin Škurla, developer of the Neo4j connector in Gephi and former Google Summer of Code student in 2010, gave a complete talk about his plug-in at the last FOSDEM conference in the workshop on Graph Processing. His talk covers the installation and showcase of visualization capabilities of Neo4j graph database in Gephi, as long as the exploration of general useful features of Gephi applying them on imported Neo4j database. Watch the video below, and comment it to ask additional questions!
The Neo4j plugin of Gephi is now officially supported by Neo Technology, Inc. If you have a software project involving Gephi, contact us at consortium@gephi.org to see how we can help you.
Neo4j is a powerful, award-wining graph database written in Java. It can store billions of nodes and relationships and allows very fast query/traversal. We release today a new version of the Neo4j Plugin supporting the latest 1.5 version of Neo4j. In Gephi, go to Tools > Plugins to install the plug-in.
The plugin let you visualize a graph stored in a Neo4j database and play with it. Features include full import, traversal, filter, export and lazy loading.
The new version of the build-in layout ForceAtlas is now released. It is scaled for small to medium-size graphs, and is adapted to qualitative interpretation of graphs. The equations are the same as ForceAtlas 1, but there are more options and innovative optimizations that make it a very fast layout algorithm.
It is good enough to deal with very small graphs (10 nodes) and fast enough to spatialize 10,000 nodes graphs in few minutes, with the same quality. If you have time, it can deal with even bigger graphs.
Update Gephi (Help > Check for Updates) to get this new layout.
Force Atlas 2:
Is a continuous algorithm, that allows you to manipulate the graph while it is rendering (a classic force-vector, like Fruchterman Rheingold, and unlike OpenOrd)
Has a linear-linear model (attraction and repulsion proportional to distance between nodes). The shape of the graph is between Früchterman & Rheingold’s layout and Noack’s LinLog.
Features a unique adaptive convergence speed that allows most graphs to converge more efficiently
Proposes summarized settings, focused on what impact the shape of the graph (scaling, gravity…). Default speed should be the good one.
Now features a Barnes Hut optimization (performance drops less with big graphs)
Force Atlas 2 features these settings:
Scaling: How much repulsion you want. More makes a more sparse graph.
Gravity: Attracts nodes to the center. Prevents islands from drifting away.
Dissuade Hubs: Distributes attraction along outbound edges. Hubs attract less and thus are pushed to the borders.
LinLog mode: Switch ForceAtlas’ model from lin-lin to lin-log (tribute to Andreas Noack). Makes clusters more tight.
Prevent Overlap: Use only when spatialized. Should not be used with “Approximate Repulsion”
Tolerance (speed): How much swinging you allow. Above 1 discouraged. Lower gives less speed and more precision.
Approximate Repulsion: Barnes Hut optimization: n² complexity to n.ln(n) ; allows larger graphs.
Approximation: Theta of the Barnes Hut optimization.
Edge Weight Influence: How much influence you give to the edges weight. 0 is “no influence” and 1 is “normal”.
Force Atlas 2 was created by Mathieu Jacomy at the Sciences Po Médialab (Paris), founding member of the Gephi Consortium.
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 Neo4j plugin of Gephi is now officially supported by 
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