Gephi - The Open Graph Viz Platform | Hacker News Reader

Gephi - The Open Graph Viz Platform

gephi.org

74 pointsash35 comments

Naive question: is "graph viz" a term of art that happens to be easily confusable with "GraphViz", the graph rendering software?

It appears to be, as this doesn't seem to import any GraphViz file formats natively (sadly). From the user manual, it does sound like there's a plugin to handle them, though it's a bit ambiguous, so it may just be as an example of a possible plugin.

I'm Gephi main dev. Supporting DOT file format is in our roadmap and will be done very soon.

Have you thought about bundling some canonical example graphs and using it as a teaching tool for graph theory?

(I'm already working on a similar project. Feel free to shoot me an email at the address in my profile if you want to talk about it.)

If you guys go into that, I'd suggest leaving a path open for TikZ (text to embed pics in TeX, see here http://news.ycombinator.com/item?id=1204172 , about use in a graph theory book).

Makes neat print-style pictures - for example this chart: http://www.texample.net/tikz/examples/gajski-kuhn-y-chart/ , which is not a graph; but the ones in the book looked good.

P.S. http://www.texample.net/tikz/examples/prims-algorithm/ illustrates the graph algorithm with overlays.

for what it is worth, i managed to check out your great work by using tulip's dot import to get tulip's tlp file format, which you support just fine. i like where the tool is going!

Done! The DOT format support is finished, update Gephi to profit from this feature. http://gephi.org/2010/new-graphviz-dot-csv-and-ucinet-format...

graph viz = graph visualization

I immediately assumed GraphViz too, but I think the "viz" generally refers to "visualization."

That looks awesome. Hard to believe it's open source & free. I'm definitely hanging onto this site, thanks for the link!

edit: trying it on my Mac now, it runs quite well on some sample data (a couple thousand nodes). The UI and a couple things reek of open-source-projectitis, but overall it's quite good, with a couple display / coloring bugs. Could use some more built-in displaying tools, as it's a little meagre at first attempts, but that'll probably come with time.

I have an interest in force-directed algorithms, and was going to ask about the "Force Atlas algorithm" mentioned in the paper (PDF at http://www.aaai.org/ocs/index.php/ICWSM/09/paper/view/154/10... ), but a cursory search found this recent explanation by the author: http://gephi.org/forum/topic.php?id=5403

Neat looking site, congratulations and thanks to the authors. I'd suggest not going too heavy on the slangy abbreviations (Viz, hi-quality). For me, adding 'Interactive' and removing 'Platform' would improve the headline.

_Related question_: Anyone know of a software to display points in 3D space on screen and allow the display to be rotated left, right, up, down, etc. (in real-time using mouse or keyboard)? I need it to run on Windows or Linux Ubuntu. Gephi looks awesome, but my data points are just 3D points, not a network.

There used to be a program called MacSpin which was perfect for my needs, but is no longer available (and I don't have a Mac).

Bonus if I can add values to change the size and color of the points, and/or label them. Extra bonus if the software is Free and/or Open Source.

If you can borrow a mac, Grapher is waiting for you. It's free with OSX, it's current, and it easily handles a set of 3d coords. I highly recommend it.

I'll be ... yes, Grapher is tucked away in the Utilities folder under Applications. Time to clean the dock of iChats and suchlike ...

(I've use of a Mac again for three months now, after a hiatus of many moons, and had not noticed. Thanks.)

Hmm, that sounds pretty specific. The best I can think of is a thin shell over Ogre3D? http://www.orgre3d.org

I've used gnuplot to display and rotate 3D graphs, but I don't know if single points could be added as well. Have you tried it?

Try VRML.

Transform your nodes to generate the VRML (XML). Create a containing HTML which links to the VRML resource (like an image, flash) and the VRML client will render it. Most of the VRML clients allow you to 'fly' around the model.

You'll almost certainly need a VRML plugin for your browser. I used the Cosmo player back in the day (1997!!!)

I last did this process circa 2000, so I did a quick google for contemporary resources:

http://cic.nist.gov/vrml/vbdetect.html

http://www.web3d.org/x3d/vrml/tools/viewers_and_browsers/

It seems VRML --> X3D in the intervening 10 years.

An intersting program which would seem to fit your need would be http://en.wikipedia.org/wiki/Flux_%28software%29

Never used it myself...

tulip might be what you want; I'm not sure if the viz. is built-in or just something others have done with it though. But well worth knowing about, for all interesting in graph viz.

  http://tulip.labri.fr/TulipDrupal/

Ubigraph seems to do something like what you want.

http://ubietylab.net/ubigraph/

This seems like it would be a very cool front-end to Neo4j -- a graph-oriented DB.

http://neo4j.org/

You bet! The projects are just starting to collaborate, see: http://wiki.neo4j.org/content/Google_Summer_of_Code_for_Neo4...

Built with the Netbeans Java IDE.

http://netbeans.org

I belive it is using NetBeans platform itself.

http://en.wikipedia.org/wiki/NetBeans#NetBeans_Platform

This looks like excellent work.

Any chance on supporting other formats like spreadsheets, csv, or generic XML schemas s.t. I can just specify a couple of xpaths as the node end points and have it figure out how to draw the graph?

Gephi supports CSV imput already and has some plans to make assistant plugins to import data from other sources like Excel files, RDF or XML.

Excellent. One of the problems I've always had with graph viz tools is the need to cram my data into some predefined schema to make the tool work instead of having the tool do that kind of stuff for me.

Been playing around with it for a bit. Amazing work for a beta release. The "generate random network" option is fantastic. Some GUI bugs, like drag doesn't seem to want to turn back on, but really great stuff.

Yes there is a bug with drag. I just filled a bug report https://bugs.launchpad.net/gephi/+bug/546986

Support for weka's file format would be great as well

One open source graph visualisation program I really like is Cytoscape which is also Open Source and written in Java.

ok, I've searched for a minute how to add a node and didn't found a way. So I closed the app. Maybe in a future version, it will be possible to easily add a node in an Open Graph Viz Platform.

I'm gephi main dev. That will be fixed with better documentation asap. You can add nodes and edges by using "Node Pencil" and "Edge Pencil" tools in the toolbar.

Quick suggestion: Instead of better documentation, I suggest you remove less-used elements from the main screen and put more emphasis on the important ones. For such an important feature (add a node), it should be trivially easy to see how to do it.

Also, it could be great to have a project open by default when you first open the application.. instead of the: file new project.

Oh, and everyone can down me, I don't care, I use a smurf account. Constructive critism = down vote, while saying wow good job, is +5 karma. So, I have 2 accounts: one to say wow, and one to say real important critismes.

Guess what, one is always around 0 karma while the other is high ranked.. what a shame :)

My guess is that your tone grated. This may help:

Moving parts in rubbing contact require lubrication to avoid excessive wear. Honorifics and formal politeness provide lubrication where people rub together. Often the very young, the untraveled, the naive, the unsophisticated deplore these formalities as “empty,” “meaningless,” or “dishonest,” and scorn to use them. No matter how “pure” their motives, they thereby throw sand into machinery that does not work too well at best.

(Heinlein, filched here: http://www.angelfire.com/or/sociologyshop/lazlong.html)

I don't think your tone is bad at all, like ableal thinks. I also think the same way as you, I've almost given up on commenting here.

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