Functionality Plugins ~ 0.8 Generator plugin science
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.
Community Website ~ book programming science visualization
Gephi has now its own book store!
It’s a great place for those who want to discover the key theories beyond networks. It has also an “Information Visualization” and “Programming” section for those who want to master the subject and join the Gephi team. All these books give valuable information for understanding what is guiding the people who are developing Gephi and how concepts were put in practice.
The Network Science section refers to the science beyond networks. It describes where networks are in nature, society or organizations and helps understand their properties and patterns. Newcomers can starts with Linked by Albert-Laslo Barabasi, the major reference, from 2001. You can also directly jump to Bursts, Barabasi’s new book released few days ago.
Social network theory views a network as actors who are connected by a set of relationships and is referenced as Social Network Analysis (SNA). As people increasingly use social networking websites (e.g. Facebook, YouTube, LinkedIn etc.), Social Network Analysis brings tools to study patterns of communication and communities. Social Network Analysis by Wasserman & Faust is a major reference.
These books are for all audience, so researchers would find a clear state of the art of the domain with The Structure and Dynamics of Networks or Dynamical Processes of on Complex Networks.
Data Visualization and Human Computer interaction (HCI) are at the base of Gephi. Learn about how visualization and interaction enhance understanding and knowledge discovery of complex data. Information Visualization or Visual Analytics make reference to this domain as well.
One can easily find the roots of the Visual Analytics in the book Readings in Information Visualization: Using Vision to Think by Stuart Card, Jock Mackinlayis and Ben Shneiderman. Exploratory Data Analysis started with John Tukey, and has recently been extended by Andrienko.
The last stone is added with the knowledge of efficient programming, in particular how to design a modular software based on services with Practical API Design: Confessions of a Java Framework Architect. And as the human factor is central, take a look at The Mythical Man-Month: Essays on Software Engineering. Mathieu is a great fan 
Also we foster you to go beyond with more references at the Reader’s circle and of course send us book suggestion.
Community ~ conference internet science
The European Science Foundation (ESF), in partnership with COST is organising the following conference:
Future Internet and Society: A Complex Systems Perspective
Hotel Villa del Mare, Acquafredda di Maratea, Italy
2-7 October 2010
Chair: Romualdo Pastor-Satorras – Departament de Física i Enginyeria Nuclear (FIB), Universitat Politècnica de Catalunya, ES
Co-Chair: Claudio Castellano – CNR-ISC (Istituto dei Sistemi Complessi) and Dipartimento di Fisica, Sapienza Universitá di Roma, IT
The digital revolution and the advent of the Internet are transforming the way we work, how we spend our free time. These phenomena are also changing how we communicate with each other and the way in which we establish and maintain our social relations. The relationship between Internet and society is complex and bidirectional, leading to a co-evolution of the two systems. In fact, the Internet exists because humans need networking and the Internet evolution is ultimately driven by our ever-increasing use of it.
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Community ~ Community Design gexf graphic engine interactive exploration science
Today I have the honnor to interview a special member of Gephi Team: Mathieu Jacomy.
Mathieu is an engineer, a founder of the WebAtlas NGO, teacher in Sciences Po Paris, and leads R&D in the TIC Migrations program in the Fondation Maison des Sciences de l’Homme and Telecom ParisTech school.
He is the main developer of the “Navicrawler” software. He also created the first Gephi prototype.
Sebastien Heymann: Hi Mathieu Jacomy, you are the creator of Graphiltre, the first Gephi prototype that you developed in 2006. What was the purpose of making a yet-another-graph-software?
Mathieu Jacomy: Hi ! I’m glad to answer your questions, and I hope our readers will be pleased to know more about Gephi.
At this time I was analyzing a lot of graphs and I wasn’t satisfied by the existing free tools. That’s why I started to build my own tools.
I had no money to use professional tools, and I needed to understand precisely what the software was doing : the open source, free softwares perfectly fit these constrains.
I was using the amazing software Guess proposed by Eytan Adar, that himself built for his own needs. I was doing quite the same thing as him, and I couldn’t start to explore graphs without this tool.
But I wasn’t satisfied because the software didn’t allow so much manipulations. I couldn’t look at the substructures as easily as I wanted, and it was difficult to make nice cartographies.
I was dreaming of a “graph-dedicated Photoshop“, a visualization-oriented software rather than a script-oriented tool.
A good way to figure out what I mean is to look at the spatialization process. In famous softwares such as Pajek or Guess, you have algorithms called “layout”, “force-vectors” or “energy model”. These algorithms give its shape to the graph, and it is probably the most critical part of the process to build a clear visualization. Because the substructures or “patterns” that one may see in the image strongly depend on the algorithm and the settings chosen. But in the same time, most of users also want to quickly look at the global shape of the graph, and may not be aware that it’s important to search for the best algorithm to use depending on the time you have, the quality you want, the size of the graph, its degree distribution, the substructure that you expect to recognize… I was careful with these algorithms but even if I understood their principles and specificities, I couldn’t figure out how they were transforming the graph, and I couldn’t evaluate their differences.
Why? Because in these softwares you can’t :
- Manipulate the graph while the algorithm is running
- Modify the settings while the algorithm is running
- And sometimes, you can’t event see the graph while the algorithm is running
How can you just understand what’s happening there? Of course I started to work on a software that allowed this. But the same kind of problems appears again in other parts of the process, like filtering, image exporting… Pajek is clearly built in a mathematical perspective. Guess is more user-friendly, but not enough. I didn’t want a tool for mathematics experts, but a tool for people that actually have to explore and understand graphs. A professional tool for a job that didn’t exist at this time.
This was the starting point of “Graphiltre“. Building a graph exploration system so that you can understand what you are doing by looking at what happens on the screen, and do anything (including filtering) without typing a single script line.
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Exhibition Networks ~ complex network diseasome science
Gephi team presents today a science-mapping project: Diseasome. Asked by Magali Roux, Senior Scientist at CNRS, to create a website to come with the publication of her book, Biology – The digital era, we worked on the “Human Disease Network” dataset and built a network exploration platform.
“On a unique place, one can find information about the book, the dataset related to the writings, an online data exploration framework and the file to manipulate these data with Gephi.”
The HDN (Human Disease Network) and the GDN (Gene Disease Network) were extracted from the original dataset and treated with Gephi. From the results, an interactive map has been created with the help of RTGI/Linkfluence tools. A poster is also available, with the full network and some useful statistics.
Although this work is experimental, we hope it can help scientists to explore and search in this complexity. The Diseasome is above all an innovative way to present a scientific work. The importance of complex data in science and particularly network graphs brings a lot of challenges. As well as computational issues, many things can be done with graphic design and interaction.
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