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The SAGE Graph Theory Project aims to implement Graph objects and algorithms in [SAGE] [[TableOfContents]]
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The following is a survey of existing Graph Theory software.
{{{
  <ul>
    <li>Software included with SAGE</li>
      <ol>
        <li>GAP</li>
        <li>Maxima</li>
        <li>Singular</li>
        <li>PARI, MWRANK, NTL</li>
        <li>Matplotlib</li>
        <li>GSL, Numeric</li>
      </ol>
    <li>Software SAGE interfaces with (but does not include)</li>
      <ol>
        <li>Gnuplot</li>
        <li>KASH</li>
        <li><a href="http://magma.maths.usyd.edu.au/magma/htmlhelp/text1452.htm">Magma</a></li>
          <ul>
            <li><b>Representation</b></li>Sparse support; function computes memory requirement for graph with n verts and m edges; consists of graph itself, vertex set, and edge set
            <li><b>Storage/Pipes</b></li>one function opens either file or stream, files stored in <a href="http://cs.anu.edu.au/~bdm/data/formats.html">Graph6 and Sparse6 format</a>
            <li><b>Construction</b></li>From matrix; from edge tuples; from vertex neighbors; from edges of other graphs; subgraphs; quotient graphs; incremental construction; complement; contraction; breaking edges; line graph; switch nbrs for non-nbrs of a vertex; disjoint unions, edge unions; complete unions; cartesian, lexicographic and tensor products; n-th power (same vert set, incident iff dist <= n); graph <-> digraph; Cayley graph constructor; Schreier graph constructor; Orbital graph constructor; Closure graph constructor (given G, add edges to make G invariant under a given permutation group); Paley graphs and tournaments; graphs from incidence structures; converse(reverse digraph); n-th odd graph; n-th triangular graph; n-th square lattice graph; Clebsch, Shrikhande, Gewirtz and Chang graphs;
            <li><b>Decorations (Coloring, Weight, Flow, etc.)</b></li>Vertices have labels only; Edges have labels, capacity(non-negative integers, loops=0) and weights(totally ordered ring);
            <li><b>Invariants</b></li>#verts, #edges; characteristic polynomial; spectrum
            <li><b>Predicates</b></li>2 verts incident, 2 edges incident, 1 vertex and 1 edge incident, subgraph, bipartite, complete, Eulerian, tree, forest, empty, null, path, polygon, regular
            <li><b>Subgraphs and Subsets</b></li>has k-clique, clique number, all cliques, maximum clique (<a href="http://magma.maths.usyd.edu.au/magma/htmlhelp/text1473.htm">"When comparing both algorithms in the situation where the problem is to find a maximum clique one observes that in general BranchAndBound does better. However Dynamic outperforms BranchAndBound when the graphs under consideration are large (more then 400 vertices) random graphs with high density (larger than 0.5%). So far, it can only be said that the comparative behaviour of both algorithms is highly dependent on the structure of the graphs."</a>), independent sets and number,
            <li><b>Adjacency, etc.</b></li>(in- & out-) degree, degree vector, valence (if regular), vertex nbrs, edge nbrs, bipartition, dominating sets
            <li><b>Connectivity</b></li>(strongly) connected, components, separable, 2-connected, 2-components, triconnectivity (<a href="http://magma.maths.usyd.edu.au/magma/htmlhelp/text1466.htm">"The linear-time triconnectivity algorithm by Hopcroft and Tarjan [HT73] has been implemented with corrections of our own and from C. Gutwenger and P. Mutzel [GM01]. This algorithm requires that the graph has a sparse representation."</a>), k-vertex connectivity, vertex separator, k-edge connectivity, edge separator
            <li><b>Paths, etc.</b></li>distance and geodesic, diameter and corr. path, ball and sphere, distance partition, equitable partition, girth and corr. cycle
            <li><b>Trees, etc.</b></li>spanning tree, breadth first and depth first searches, rooted, root, parent, vertex paths
            <li><b>Colorings</b>(see also Decorations)</li>chromatic number and index, optimal vertex and edge colorings, chromatic polynomial
            <li><b>Optimization</b></li>Max flow min cut (2 algorithms: <a href="http://magma.maths.usyd.edu.au/magma/htmlhelp/text1499.htm#15274">Dinic & push-relabel</a>), maximum matching for bipartite,
            <li><b>Embedding</b> (Planar graphs, etc.)</li>planarity, Kuratowski subgraphs, faces of a planar graph, embedding info as orientation of edges from a vertex
            <li><b>Algebra</b></li>adjacency matrix, distance matrix, incidence matrix, intersection matrix
            <li><b>Morphisms/Group Actions</b></li>interfaces <i>nauty</i>
            <li><b>Symmetry</b></li>vertex, edge and distance transitivity; orbit partitions; primitivity; symmetric; distance regularity and intersection array
            <li><b>Geometry</b></li>Go back and forth between incidence and coset geometries and their graphs; finite planes;
            <li><b>Generation/Random Graphs</b></li>interfaces <i>nauty</i>
            <li><b>Database</b></li>database interface, strongly regular graph DB, random graph from DB, slick implementation of for loops ("for G in D do ... end for;")
          </ul>
        <li>Maple</li>
        <li>Mathematica</li>
        <li>mwrank</li>
        <li>Octave</li>
        <li>Tachyon Ray Tracer</li>
      </ol>
    <li>Software that SAGE can now include as is</li>
    <li>Software that SAGE should include (or maybe interface with), pending stuff (e.g. licensing)</li>
    <li>Software that is incompatible with SAGE but still useful</li>
  </ul>		 == Introduction ==
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  <p>Functionality categories:
          <ol>
            <li><b>Representation</b></li>
            <li><b>Storage/Pipes</b></li>
            <li><b>Construction</b></li>
            <li><b>Decorations (Coloring, Weight, Flow, etc.)</b></li>
            <li><b>Invariants</b></li>
            <li><b>Predicates</b></li>
            <li><b>Subgraphs and Subsets</b></li>
            <li><b>Adjacency, etc.</b></li>
            <li><b>Connectivity</b></li>
            <li><b>Paths, etc.</b></li>
            <li><b>Trees, etc.</b></li>
            <li><b>Colorings</b>
            <li><b>Optimization</b></li>
            <li><b>Embedding</b> (Planar graphs, etc.)</li>
            <li><b>Algebra</b></li>
            <li><b>Morphisms/Group Actions</b></li>
            <li><b>Geometry</b></li>
            <li><b>Topology</b></li> Homology groups
            <li><b>Generation/Random Graphs</b></li>
            <li><b>Database</b></li>
            <li><b>Visualization</b></li>
          </ol>		 We are implementing graph objects and algorithms in ["SAGE"]. The main people working on this project are Emily Kirkman and Robert Miller.
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}}} == Current Status ==

 * NetworkX base classes have been interfaced, and all functions are soon to follow (SAGE Days 3 project).
 * Graph plotting has been implemented:
 * We are currently seeking possible additions to our [http://sage.math.washington.edu:9001/graph_survey survey] of existing graph theory software.
 * The initial [http://sage.math.washington.edu:9001/graph_benchmark benchmarking] has proven that ["NetworkX"] is the solution for SAGE.
 * On Friday, October 20th, Robert Miller gave a [http://sage.math.washington.edu/home/rlmill/talk_2001-10-20/2006-10-20SAGE.pdf talk] about the state of affairs for existing software which shared a few benchmarks and discussed some implementation ideas.
 * Emily Kirkman (and soon Jason Grout (Brigham Young)) is working on a database of well-known graphs.
 * Robert Miller has wrapped the basic functionality of NetworkX into SAGE's Graph class, and implemented plotting of graphs.
 * Jim Morrow has expressed interest in using SAGE for his summer REU on graphs. Robert Miller is currently working on implementing some of the algorithms of this group.
 * Chris Godsil (Waterloo) has expressed interest in helping design a more general discrete math package in SAGE, including perhaps an open source version of nauty.

== Wiki Pages ==

=== Survey of Existing Software ===
 * [http://sage.math.washington.edu:9001/graph_survey Link]
 * We have attempted to make a complete list of existing graph theory software. We posted functionality lists and some algorithm/construction summaries. We are very interested in feedback!
=== Benchmarks ===
 * [http://sage.math.washington.edu:9001/graph_benchmark Link]
 * Our initial tests are designed to compare the constructions and very basic functionality found in our survey of existing software. At this stage in the game, we are testing to find the best way to represent graph objects in SAGE.
 * We will post results on the wiki as we get them. And as always, we love feedback!
=== Plotting ===
 * [http://sage.math.washington.edu:9001/graph_plotting Link]
 * So far: NetworkX graphics primitive
=== Database ===
 * [http://sage.math.washington.edu:9001/graph_database Link]
 * So far: Basic graph structures with intuitive graphics
 * Plan: Extensive educational docstrings and many, many more graph constructors
=== Survey of Existing Database Software ===
 * [http://sage.math.washington.edu:9001/graph_db_survey Link]
 * I've found some resources, but please recommend...

TableOfContents

Introduction

We are implementing graph objects and algorithms in ["SAGE"]. The main people working on this project are Emily Kirkman and Robert Miller.

Current Status

  • NetworkX base classes have been interfaced, and all functions are soon to follow (SAGE Days 3 project).
  • Graph plotting has been implemented:

  • We are currently seeking possible additions to our [http://sage.math.washington.edu:9001/graph_survey survey] of existing graph theory software.

  • The initial [http://sage.math.washington.edu:9001/graph_benchmark benchmarking] has proven that ["NetworkX"] is the solution for SAGE.

  • On Friday, October 20th, Robert Miller gave a [http://sage.math.washington.edu/home/rlmill/talk_2001-10-20/2006-10-20SAGE.pdf talk] about the state of affairs for existing software which shared a few benchmarks and discussed some implementation ideas.

  • Emily Kirkman (and soon Jason Grout (Brigham Young)) is working on a database of well-known graphs.
  • Robert Miller has wrapped the basic functionality of NetworkX into SAGE's Graph class, and implemented plotting of graphs.
  • Jim Morrow has expressed interest in using SAGE for his summer REU on graphs. Robert Miller is currently working on implementing some of the algorithms of this group.
  • Chris Godsil (Waterloo) has expressed interest in helping design a more general discrete math package in SAGE, including perhaps an open source version of nauty.

Wiki Pages

Survey of Existing Software

Benchmarks

  • [http://sage.math.washington.edu:9001/graph_benchmark Link]

  • Our initial tests are designed to compare the constructions and very basic functionality found in our survey of existing software. At this stage in the game, we are testing to find the best way to represent graph objects in SAGE.
  • We will post results on the wiki as we get them. And as always, we love feedback!

Plotting

Database

Survey of Existing Database Software

graph (last edited 2009-11-29 06:48:46 by newacct)