graph-tool is a Python module for manipulation and statistical analysis of graphs (AKA networks). The core data structures and algorithms of graph-tool are implemented in C++, making extensive use of metaprogramming, based heavily on the Boost Graph Library. Many algorithms are implemented in parallel using OpenMP, which provides increased performance on multi-core architectures.
Features
- Creation and manipulation of directed or undirected graphs.
- Association of arbitrary information to the vertices, edges or even the graph itself, by means of property maps.
- Filter vertices and/or edges "on the fly", such that they appear to have been removed.
- Support for dot, Graph Modelling Language and GraphML formats.
- Convenient and powerful graph drawing based on cairo or Graphviz.
- Support for typical statistical measurements: degree/property histogram, combined degree/property histogram, vertex-vertex correlations, assortativity, average vertex-vertex shortest path, etc.
- Support for several graph-theoretical algorithms: such as graph isomorphism, subgraph isomorphism, minimum spanning tree, connected components, dominator tree, maximum flow, etc.
- Support for several centrality measures.
- Support for clustering coefficients, as well as network motif statistics and community structure detection.
- Generation of random graphs, with arbitrary degree distribution and correlations.
- Support for well-established network models: Price, Barabási-Albert, Geometric Networks, Multidimensional lattice graph, etc.
Suitability
Graph-tool can be used to work with very large graphs in a variety of contexts, including simulation of cellular tissue,2 data mining,34 analysis of social networks,56 analysis of P2P systems,7 large-scale modeling of agent-based systems,8 study of academic Genealogy trees,9 theoretical assessment and modeling of network clustering,10 large-scale call graph analysis,11 and analysis of the brain's Connectome.12
External links
- Free and open-source software portal
References
Graph-tool performance comparison, Graph-tool http://graph-tool.skewed.de/performance ↩
Bruno Monier et al, "Apico-basal forces exerted by apoptotic cells drive epithelium folding", Nature, 2015 [1] http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14152.html ↩
Ma, Shuai, et al. "Distributed graph pattern matching." Proceedings of the 21st international conference on World Wide Web. ACM, 2012. [2] http://dl.acm.org/citation.cfm?id=2187963 ↩
Ma, Shuai, et al. "Capturing topology in graph pattern matching." Proceedings of the VLDB Endowment 5.4 (2011): 310-321. [3] http://dl.acm.org/citation.cfm?id=2095690 ↩
Janssen, E., M. A. T. T. Hurshman, and N. A. U. Z. E. R. Kalyaniwalla. "Model selection for social networks using graphlets." Internet Mathematics (2012). [4] http://www.mathstat.dal.ca/~janssen/papers/Graphlets.pdf ↩
Asadi, Hirad Cyrus. Design and implementation of a middleware for data analysis of social networks. Diss. M Sc thesis report, KTH School of Computer Science and Communication, Stockholm, Sweden, 2007. [5] Archived 2015-01-22 at the Wayback Machine http://www.student.nada.kth.se/~hias02/xjobb-en.pdf ↩
Teresniak, Sven, et al. "Information-Retrieval in einem P2P-Netz mit Small-World-Eigenschaften Simulation und Evaluation des SemPIR-Modells."[6] Archived 2015-01-22 at the Wayback Machine http://asv.informatik.uni-leipzig.de/thesis/thesis_document/25/masterarbeit.pdf ↩
Hamacher, Kay, and Stefan Katzenbeisser. "Public security: simulations need to replace conventional wisdom." Proceedings of the 2011 workshop on New security paradigms workshop. ACM, 2011. [7] http://dl.acm.org/citation.cfm?id=2073288 ↩
Miyahara, Edson Kiyohiro, Jesus P. Mena-Chalco, and Roberto M. Cesar-Jr. "Genealogia Acadêmica Lattes." [8][permanent dead link] http://www.linux.ime.usp.br/~edsonkm/mac499/download/monografia.pdf ↩
Abdo, Alexandre H., and A. P. S. de Moura. "Clustering as a measure of the local topology of networks." arXiv preprint physics/0605235 (2006). [9] https://arxiv.org/abs/physics/0605235 ↩
Narayan, Ganesh, K. Gopinath, and V. Sridhar. "Structure and interpretation of computer programs." Theoretical Aspects of Software Engineering, 2008. TASE'08. 2nd IFIP/IEEE International Symposium on. IEEE, 2008. [10] https://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4549888 ↩
Gerhard, Stephan, et al. "The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes." Frontiers in neuroinformatics 5 (2011). [11] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112315/ ↩