Another Word For It Patrick Durusau on Topic Maps and Semantic Diversity

March 30, 2011

Playing with Gephi, Bio4j and Go

Filed under: Biomedical,Gephi,Visualization — Patrick Durusau @ 12:36 pm

Playing with Gephi, Bio4j and Go

From the blog:

It had already been some time without having some fun with Gephi so today I told myself: why not trying visualizing the whole Gene Ontology and seeing what happens?

First of all I had to generate the corresponding file in gexf format containing all the terms and relationships belonging to the ontology.

For that I did a small program (GenerateGexfGo.java) which uses Bio4j for terms/relationships info retrieval and a couple of XML Gexf wrapper classes from the github project Era7BioinfoXML.

This looks like fun!

And a good way to look at an important data set, that could benefit from a topic map.

March 5, 2011

Gephi Workshop

Filed under: Gephi,Graphs,Visualization — Patrick Durusau @ 2:14 pm

Gephi Workshop 23 March 2011

Its events like this that make me wish I were on the West Coast.

Even so, there are a number of resources listed for those of us who cannot attend.

From the website:

The next Gephi Workshop will be on Wednesday, March 23rd at 1PM at the IC classroom in Green Library.

I’ll occasionally be able to provide two-hour workshops on the basics of using Gephi, the network analysis package with which I’ve made the images and videos below. The workshops will focus on:

  • getting graph data into Gephi using .gexf, .csv and database connections
  • running Filters, Analytics and Layouts on the data
  • optimization of Gephi for large datasets
  • overview of layout algorithms and strategies for their use
  • creating dynamic (time-enabled) networks
  • general Q&A

February 17, 2011

Visualising Twitter Dynamics in Gephi, Part 1 – Post

Filed under: Gephi,Visualization — Patrick Durusau @ 6:39 am

Visualising Twitter Dynamics in Gephi, Part 1

From the post:

In the following posts I’m finally keeping my promise to explore in earnest the use of Gephi’s dynamic timeline feature for visualising Twitter-based discussions as they unfolded in real time. A few months ago, Jean posted a first glimpse of our then still very experimental data on Twitter dynamics, with a string of caveats attached – and I followed up on this a little while later with some background on the Gawk scripts we’re using to generate timeline data in GEXF format from our trusty Twapperkeeper archives (note that I’ve updated one of the scripts in that post, to make the process case-insensitive). Building on those posts, here I’ll outline the entire process and show some practical results (disclaimer: actual dynamic animations will follow in part two, tomorrow – first we’re focussing on laying the groundwork).

This article was mentioned in Dynamic Twitter graphs with R and Gephi (clip and code) as an interesting example of “aging” edges.

While there is an obvious time component to tweets, is there an implied relevancy based on time for other information as well?

Tactical information should be displayed to ground level commanders and be sans longer term planning data, while for command headquarters, tactical information is just clutter on the display.

Looks like a fruitful area for exploration.

February 5, 2011

Mapping Wikileaks’ Cablegate topics using Python, MongoDB, Neo4j and Gephi

Filed under: Gephi,MongoDB,Neo4j — Patrick Durusau @ 7:55 am

Mapping Wikileaks’ Cablegate topics using Python, MongoDB, Neo4j and Gephi

Data and slides and movies while the conference is ongoing! Oh My!

This is the sort of effort that topic maps needs to step up to and compete against.

I have some thoughts on what that would take with the Afghan war diaries that I will be posting later today.

February 2, 2011

Mapping Wikileaks’ Cablegate using Python, mongoDB and Gephi – Saturday, 5 Feburary 2011

Filed under: Gephi,MongoDB,Natural Language Processing — Patrick Durusau @ 10:34 am

Mapping Wikileaks’ Cablegate using Python, mongoDB and Gephi

From the website:

Text analysis and graph visualization on the Wikileaks Cablegate dataset.

We propose to present a complete work-flow of textual data analysis, from acquisition to visual exploration of a complex network. Through the presentation of a simple software specifically developed for this talk, we will cover a set of productive and widely used softwares and libraries in text analysis, then introduce some features of Gephi, an open-source network visualization & analysis software, using the data collected and transformed with cablegate-semnet.

See: cablegate-semnet

If you are in (or can be) Brussels, Belgium this coming Saturday and Sunday, don’t miss this presentation!

There will be many others worthy of your attention as well.

January 26, 2011

GSoC 2010 mid-term: Graph Streaming API – Post

Filed under: Data Mining,Gephi,Graphs,Visualization — Patrick Durusau @ 6:08 am

GSoC 2010 mid-term: Graph Streaming API by André Panisson.

From the blog:

The purpose of the Graph Streaming API project, run by André Panisson, is to build a unified framework for streaming graph objects. Gephi’s data structure and visualization engine has been built with the idea that a graph is not static and might change continuously. By connecting Gephi with external data-sources, we leverage its power to visualize and monitor complex systems or enterprise data in real-time. Moreover, the idea of streaming graph data goes beyond Gephi, and a unified and standardized API could bring interoperability with other available tools for graph and network analysis, as they could start to interoperate with other tools in a distributed and cooperative fashion.

There are times when no comment seems adequate. This is one of those times.

Read the post, play with the code, follow the work (and support it!).

August 8, 2010

Gephi – The Open Graph Viz Platform

Filed under: Gephi,Graphs,Information Retrieval,Interface Research/Design,Maps,Software — Patrick Durusau @ 3:51 pm

Gephi is an “interactive visualization and exploration platform” for graphs.

From the site:

  • Exploratory Data Analysis: intuition-oriented analysis by networks manipulations in real time.
  • Link Analysis: revealing the underlying structures of associations between objects, in particular in scale-free networks.
  • Social Network Analysis: easy creation of social data connectors to map community organizations and small-world networks.
  • Biological Network analysis: representing patterns of biological data.
  • Poster creation: scientific work promotion with hi-quality printable maps.

I find the notion of interaction with a graph, or in our case a topic map represented as a graph quite fascinating.

Imagine selecting or even adding properties as the basis for merging and then examining those results in an interactive rather than batch process.

Can “drag-n-drop” topic map authoring be that far away?

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