|
Research Brief outline of some of my research interests. |
|
Meetings Some meetings of interest. |
|
Institutions Various institutions doing relevant work. |
|
Other Resources includes some general literature, numerical and computational resources including complete software packages, computational libraries and data sets, websites with references and discussion of these, visualisation examples, blogs, etc. |
|
Old Meetings These have already happened. |
|
Networks and Archaeology Page on my work applying network ideas to archaeology. |
visone
pajek
The problem I found is that there is no immediate visualisation here. You seem to have to install other packages to link through to Graphviz drawing programmes or matlab graph drawing.
I have tried this on Windows and found that most, but not all aspects are not very Windows friendly. Most major packages come with a Windows installer - just make sure you pick the one for the correct version of Python (its obvious from the file names). The main Python package worked fine and I have a version 2.7 with the IDLE GUI interface. Just make sure that c:\Python27 is on the PATH environment variable.
The main problem came installing packages. The easy way is to use the easy_install command mentioned on many web pages but they fail to tell you this is part of another package that you have to install first. So first try to install setuptools from the Python package index. This worked easily enough. Note that you download a script for a python programme so you need python installed to run it (either double click on the file ez_setup.py or run it via a command window python ez_setup.py). Before you use easy_install you may have to import setuptools inside the python.
I found that there were easy Windows executables for the Windows versions of NumPy and SciPy. Watch the order you add them, one may depend on the other. I would probably now use the easy_install route.
The NetworkX I installed by downloading the source code, following instructions on the web site. The easy_install suggested on the web site would be easier and better.
I wanted to use the links to Graphviz (for the dot file conversion for instance) but I never got the pygraphviz package to install. One tip I found and tried is that a lot of these pythons things want some Microsoft C libraries which come with the Visual Studio Express 2008 which is free to download. The 2008 is critical here, versions from other years don't work. In the end I foudn the pydot package did what I wanted and installed without a problem using easy_install.
0 1 1 1 0 1 1 1 0
1 2 2 3 3 1
*Vertices 3 1 "AAA" 2 "Vertex 2" *Edges 2 1 2 1.0 3 1 *Arcs 1 2 3 1.5Here are some issues I have encountered:-
.graphml files) is an XML based format, seems widely used
e.g. read only in JUNG, read and write in igraph, used by visone
yED and yfiles. However the core format only covers basic graph topology so other features (e.g. edge colour or style)
are additions that must be defined in the relevant packages.
According to the Gephi notes,
NodeXL, Sonivis, GUESS, NetworkX and Gephi can handle this format to some extent.
.net files) uses a simple format and is produced or read by many other systems.
.gv and DOT
files are often read or written by other systems. I found the description of .dot files extremely confusing. However a few simple examples shows it is basically very simple. I used the python packages of NetworkX and pydot to find out what was going on. Here are some simple examples, one undirected, one directed.
strict graph G {
0;
1;
2;
3;
0 -- 1;
0 -- 2;
0 -- 3;
1 -- 2;
1 -- 3;
2 -- 3;
}
|
digraph G {
0
1
2
3
1 -> 3;
1 -> 2;
0 -> 1;
0 -> 3;
0 -> 2;
2 -> 3;
}
|
.gml files) seems like an old format born in 1995. According to the Gephi notes, Pajek (my version doesn't seem to) , yEd, LEDA, NetworkX and Gephi can handle this format.
Used for instance for the various network data sets of Mark Newman.
This is quite different from GraphML.
This can be related to some network analysis.