Samuel Thiriot

Monday 14 November 2016
English français

How, where to save graphs and networks ?
The classical solution is to store graphs into files using formats as interoperable as possible; yet more and more databases are proposed to store and explore networks.

File formats for storing networks

see many formats described in the gephi website.

Pajek

First case without weights for a mixed network

Second case without weights for a mixed network

Thrid case with weights for a mixed network

Source: https://gephi.org/users/supported-g...

Compact

The graph6 and sparse6 file formats (http://cs.anu.edu.au/~bdm/data/form...), proposed by Brendan McKay, are very efficient for large networks (dense resp. sparse). The result is not human-readable, and requires a tool to "unflat" the network (see showg from the nauty package above).

Databases

Neo4j

Neo4j was specially designed for storing networks: http://neo4j.org/
a NoSQL database, Java,
* Wikipedia page: http://en.wikipedia.org/wiki/Neo4j
see: http://en.wikipedia.org/wiki/Graph_database

Neo4j databases can be viewed with Gephi, or online (http://linkurio.us/)

less famous

  • Bigdata
  • CloudGraph
  • Cytoscape
  • DEX
  • Filament
  • GraphBase
  • Graphd
  • Horton
  • HyperGraphDB
  • InfiniteGraph
  • InfoGrid
  • OrientDB
  • OQGRAPH
  • sones GraphDB
  • VertexDB
  • Virtuoso Universal Server
  • R2DF
  • GiraffeDB
Bookmarks
All the bookmarks shared in this website.
Networks: public data
Network data is sometimes freely available online. Here are some examples. Real networks and data many sources in the KONECT site web map as a graph DOMES (...)
Networks: software
Software for networks analysis The igraph package (http://igraph.sourceforge.net/) is a must-have. It includes basic network generators, efficient and (...)
Networks: manipulate them in Java
How to generate, analyze, manipulate networks in Java ? Here is a panorama (not exhustive) of the existing libraries. JUNG The JUNG framework (...)
YANG - plausible networks generation
YANG (Yet Another Network Generator) is a laboratory devoted to the reconstruction of plausible networks from local rules. It was applied to the (...)
Simple Interconnected Islands network generator
Overview The Simple Interconnect Islands (SII) network generator creates networks made of nb.islands islands. Each island is made of a random network of (...)
Growing Interconnected Islands network generator
Overview In this variation of Simple Interconnected Islands, each island is made of a growing network instead of a random network. Leads to a skewed (...)

(c) Samuel Thiriot 2012-2016
This is a personal website. The views, research interests or opinions expressed here represent my own and not necessarily those of my employer.