http://gephi.org/forum/ Community support en Wed, 10 Mar 2010 16:02:48 +0000 http://gephi.org/forum/topic.php?id=5408#post-5525 Wed, 10 Feb 2010 19:22:48 +0000 esudo 5525@http://gephi.org/forum/ <p>I was wondering how I could add texts to nodes or edges. That is either inside the nodes or beside the nodes, or even words on the edges for the graph. I am using graphml for my text input. </p> http://gephi.org/forum/topic.php?id=5403#post-5522 Sat, 06 Feb 2010 11:55:43 +0000 jacomyma 5522@http://gephi.org/forum/ <p>Hi,</p> <p>As many force vectors, ForceAtlas has speed, cooling (those are almost redundant), inertia, attraction, repulsion, and gravity (that centers the graph and prevent disconnected nodes from going anywhere).</p> <p>ForceAtlas works almost like Früchterman Rheingold, with a difference: the repulsion between two nodes is (almost) proportional to degree(n1)*degree(n2). For example this makes nodes of degree=1 closer to their neighbor. The graph is more compact, nicer.</p> <p>When I created this algorithm I had an empirical approach, and the layout isn't mathematically consistent. That's why there is a convergence issue that I fixed by implementing an auto-stabilization.</p> <p>Later I implemented another useful function: distributed attraction. This makes the attraction divided by the outdegree: hubs attract less that authorities, thus hubs tend to be more peripheral and authorities more central. This helps to make maps more relevant since authority is more important.</p> <p>My empirical approach made this layout efficient, but some very clever guy named Andreas Noack made a far better job than me to solve the same issues. Its layout is called LinLog and will be implemented soon. ForceAtlas works almost like LinLog: makes compact graphs and has something that looks like Noack's "edge repulsion".</p> <p>The Size Adjust (that may need a new implementation in gephi 0.7) prevents nodes from superposing each other.</p> <p>Hope that this will help you... </p> http://gephi.org/forum/topic.php?id=5405#post-5521 Sat, 06 Feb 2010 11:45:17 +0000 Sébastien Heymann 5521@http://gephi.org/forum/ <p>Hi,</p> <p><em>- how do you create input files for the software for the different formats? DO you need a different software package to create the input files?</em></p> <p>All these input file formats are common to other graph softwares. You need to create them "by hand" or with a library of your choice. In Gephi 0.7, you'll be able to make your own connector to a database, or implement your own import/export plugin for the file format you use.</p> <p><em>- Are the algorithms to run the data written in Java/OpenGl?</em><br /> They are only in Java. Behind that, Gephi handles the mechanism to interact with OpenGL.</p> <p><em>How do we add a new algorithm to the system library?</em><br /> In Gephi 0.7, we will provide a high-level API for accessing topology and associated data. You will be able to implement your own algorithms and distribute them as NetBeans packages (NBM) in 10 minutes (it's like creating a JAR). We will also provide a community repository for plugins, making them available to all users in the software update center.</p> <p>I hope I have answered with sufficient details :-) </p> http://gephi.org/forum/topic.php?id=5405#post-5520 Fri, 05 Feb 2010 15:39:27 +0000 esudo 5520@http://gephi.org/forum/ <p>I have a few questions about the software which i need to clarify<br /> first question<br /> - how do you create input files for the software for the different formats? DO you need a different software package to create the input files? </p> <p>Second question<br /> - Are the algorithms to run the data written in Java/OpenGl?</p> <p>Third question<br /> How do we add a new algorithm to the system library? </p> http://gephi.org/forum/topic.php?id=5403#post-5518 Tue, 02 Feb 2010 21:14:49 +0000 martinf 5518@http://gephi.org/forum/ <p>Hi</p> <p>I'm looking for a short description of Force Atlas algorithm. How it works with nodes that have lots of relation? Cluster, etc.</p> <p>Thank you</p> <p>Martin F </p> http://gephi.org/forum/topic.php?id=5393#post-5508 Thu, 07 Jan 2010 10:51:26 +0000 Sébastien Heymann 5508@http://gephi.org/forum/ <p>Hi,</p> <p>Supported graph formats are described here: <a href="http://gephi.org/support/supported-graph-formats/" rel="nofollow">http://gephi.org/support/supported-graph-formats/</a></p> <p>Dynamic Datasource was an experiment. I advise you to wait for a future release to try it. </p> http://gephi.org/forum/topic.php?id=5393#post-5507 Wed, 06 Jan 2010 13:59:52 +0000 TomBrooklyn 5507@http://gephi.org/forum/ <p>What data sources can be used to create gephi charts? </p> http://gephi.org/forum/topic.php?id=5383#post-5497 Mon, 07 Dec 2009 09:20:32 +0000 Mathieu Bastian 5497@http://gephi.org/forum/ <p>Hi, please use the bug tracker system to report this bug. However we're not fixing 0.6 bugs anymore, due to the close 0.7 release.</p> <p>see <a href="https://bugs.launchpad.net/gephi/+bug/493498" rel="nofollow">https://bugs.launchpad.net/gephi/+bug/493498</a> </p> http://gephi.org/forum/topic.php?id=5383#post-5496 Fri, 04 Dec 2009 10:03:38 +0000 gexin 5496@http://gephi.org/forum/ <p>Gephi gives error information when I tried to load new project.</p> <p>Error</p> <p>Message:<br /> java.lang.NullPointerException<br /> Level:<br /> SEVERE<br /> Stack Trace:<br /> null<br /> gephi.controller.desktop.DesktopProjectController$2.run(DesktopProjectController.java:213)<br /> java.lang.Thread.run(Unknown Source) </p> http://gephi.org/forum/topic.php?id=5375#post-5488 Fri, 27 Nov 2009 22:15:48 +0000 seinecle 5488@http://gephi.org/forum/ <p>Thanks for the tip. I was asking because I'd like to find a graph format common to GUESS, SoNIA, GEPHI... so that I could easily switch from one to another. From my quick inspection, DyNetML seemed to be the richest, but as it turns out it is not supported by many softwares.</p> <p>So I change my strategy and just put my data on Excel, and use basic macro language to turn in into a text file formatted either in GEXF, SON, or GDF... It is really basic, but it fits my very limited programming skills. And it works!</p> <p>Thanks again for the multiple answers, I let you work now! </p> http://gephi.org/forum/topic.php?id=5375#post-5487 Fri, 27 Nov 2009 21:21:47 +0000 Sébastien Heymann 5487@http://gephi.org/forum/ <p>No, but we may help you creating the import and export classes, the API is really simple :) </p> http://gephi.org/forum/topic.php?id=5375#post-5486 Fri, 27 Nov 2009 20:11:09 +0000 seinecle 5486@http://gephi.org/forum/ <p>Hi again,</p> <p>Will DyNetML be supported as an import format in GEPHI 0.7, or in a later version?</p> <p>Thx!</p> <p>Clement </p> http://gephi.org/forum/topic.php?id=5373#post-5485 Fri, 27 Nov 2009 19:56:45 +0000 Sébastien Heymann 5485@http://gephi.org/forum/ <p>Hi,</p> <p>You can drag and move by keeping pressed the right-click button.</p> <p>And yes, an improved version of potatoes will be available on Gephi 0.7 with clustering :) </p> http://gephi.org/forum/topic.php?id=5370#post-5484 Fri, 27 Nov 2009 19:54:10 +0000 Sébastien Heymann 5484@http://gephi.org/forum/ <p>Hi, this synthax is effectively used in 1.1 only, and is a slightly improvement in semantics. </p> http://gephi.org/forum/topic.php?id=5373#post-5482 Thu, 26 Nov 2009 22:59:24 +0000 seinecle 5482@http://gephi.org/forum/ <p>Hi,</p> <p>Another user comment: after spending some time playing with a graph, I really miss a tool to drag and move through the graph with the mouse (like in GUESS, for instance). The map on the bottom left of the screen is not that useful to me.</p> <p>Clement<br /> PS: I've seen the "potato" tool on vimeo. Looks great! Will it be on Gephi 0.7? </p> http://gephi.org/forum/topic.php?id=5370#post-5479 Thu, 26 Nov 2009 15:00:11 +0000 seinecle 5479@http://gephi.org/forum/ <p>Hi,</p> <p>The GEXF 1.1 draft Primer states on p. 7, line 22 of the example of block of code:</p> <p> &lt;attvalue for="0" value="http://gephi.org"/&gt;</p> <p>It bugged and I had to change it to:</p> <p> &lt;attvalue id="0" value="http://gephi.org"/&gt;</p> <p>Is it a typo in the primer, or is the "for=" a new syntax to be implemented not before 1.1?</p> <p>Thx!</p> <p>Clement </p> http://gephi.org/forum/topic.php?id=5367#post-5478 Thu, 26 Nov 2009 14:49:35 +0000 seinecle 5478@http://gephi.org/forum/ <p>Hi,</p> <p>Ok thanks. It clarifies my question. Simply, with the move to 0.7, and GEXL 1.1, I was not sure what was already supported in 0.6 and 1.0 Now I know! </p> http://gephi.org/forum/topic.php?id=5367#post-5475 Wed, 25 Nov 2009 22:34:56 +0000 Sébastien Heymann 5475@http://gephi.org/forum/ <p>Hi,</p> <p>I don't understand...the viz data are already working. See this viz !:</p> <p><img src="http://gephi.org/wp-content/gallery/screenshots/eurosis-seb.png"><br /> You may also look at these datasets: <a href="http://gephi.org/2008/demo-data-set/" rel="nofollow">http://gephi.org/2008/demo-data-set/</a></p> <p>But perhaps your question do not occur on this. Could you be more precise, please?</p> <p>Note that the viz namespace specs do not change from GEXF 1.0 to GEXF 1.1, so you data are safe :)<br /> GEXF 1.0 is read by Gephi 0.6 and 0.7. GEXF 1.1 is only used by Gephi 0.7.<br /> You may also be interested in transforming your data with libgexf, which is the official C++ toolkit library for the GEXF file format: <a href="http://gexf.net/lib/" rel="nofollow">http://gexf.net/lib/</a></p> <p>cheers </p> http://gephi.org/forum/topic.php?id=5367#post-5474 Wed, 25 Nov 2009 18:08:00 +0000 seinecle 5474@http://gephi.org/forum/ <p>Hi,</p> <p>Well, all is in the title. I am working on a GEXF file and would like to include viz attributes, but before that I would like to be sure that they are actually useful!</p> <p>Best,</p> <p>Clement.<br /> PS: thanks for the previous replies I received. </p> http://gephi.org/forum/topic.php?id=5365#post-5472 Tue, 24 Nov 2009 18:36:03 +0000 Sébastien Heymann 5472@http://gephi.org/forum/ <p>Hi,</p> <p>You'll find an example in the video tutorial : <a href="http://gephi.org/support/tutorials/video-tutorial1-getting-started/" rel="nofollow">http://gephi.org/support/tutorials/video-tutorial1-getting-started/</a></p> <p>In a few words, you need to choose a cylinder as a selection area. If you want a precise selection, please use filters like in this video: <a href="http://gephi.org/2009/gephi-features-tour/" rel="nofollow">http://gephi.org/2009/gephi-features-tour/</a> (02:45 and 04:10)</p> <p>cheers!<br /> Seb </p> http://gephi.org/forum/topic.php?id=5364#post-5471 Tue, 24 Nov 2009 18:22:58 +0000 julian 5471@http://gephi.org/forum/ <p>Hi,</p> <p>Dynamic graph is fairly new in Gephi, and it's support is limited to file import in the current official release of Gephi (0.6).</p> <p>However a more complete dynamic graph support will be available in the next release of Gephi (0.7).<br /> This version will include playback of dynamic graph animation, and navigation in dynamic graphs using a special scrollbar.</p> <p>Gephi 0.7 should arrive at the end of this year, so I recommand you to stay tuned and subscribe to the Gephi RSS feed in order to be informed of updates.</p> <p>The RSS feed is located at this address: <a href="http://launchpad.net/gephi/+announcements" rel="nofollow">http://launchpad.net/gephi/+announcements</a></p> <p>We will be very interested of hearing about your uses of Gephi!</p> <p>regards, </p> <p>Julian </p> http://gephi.org/forum/topic.php?id=5365#post-5470 Tue, 24 Nov 2009 18:11:23 +0000 seinecle 5470@http://gephi.org/forum/ <p>Hi again,</p> <p>Sorry for such a basic question, but I can't figure out how to use the selection tool. I supposed that I just had to left-click and keep pressed while tracing a selection area encompassing the nodes I want to select, but nothing seems to happen. How does it work?</p> <p>Thanks!</p> <p>Clement </p> http://gephi.org/forum/topic.php?id=5364#post-5469 Tue, 24 Nov 2009 16:03:33 +0000 seinecle 5469@http://gephi.org/forum/ <p>Hi,</p> <p>I could not find where are the commands to display the animation of a dynamic file? That is, I have a gexf file with nodes and attributes in dynamic mode, and I can't find in GEPHI where to run the display of the file "through time" (just like in the demo videos!)</p> <p>I looked into the "dynamic data" menu but it seems there is no useful command there... so any help?</p> <p>Thanks,</p> <p>Clement </p> http://gephi.org/forum/topic.php?id=5348#post-5456 Sun, 15 Nov 2009 10:06:39 +0000 Sébastien Heymann 5456@http://gephi.org/forum/ <p>Hi, this feature is mainly a proof-of-concept we didn't release. It was very buggy at the time of MediaLab openning, and we were crazy enough to make a live demo ^^. So this datasource isn't present in Gephi 0.6 beta3, but you may download the <a href="https://code.launchpad.net/~gephi.team/gephi/0.6">source code</a> and compile the project :) (follow <a href="http://gephi.org/community/developer-handbook/howto-get-gephi/">this</a> tutorial and <a href="http://gephi.org/community/developer-handbook/howto-build-gephi/">this</a> one)</p> <p>But I think you may just wait for a future Gephi release, which include this feature properly and easily! </p> http://gephi.org/forum/topic.php?id=5348#post-5452 Sat, 14 Nov 2009 12:04:43 +0000 sebastienbillard 5452@http://gephi.org/forum/ <p>I saw your videos showing mapping in real time using 3 computers. Though I don't see how to use Gephi and Navicrawler to do the same thing (with one computer). Navicrawler says "Ouvrez Géphi et ouvrez la source de données Navicrawler avant d'activer. Le graphe sera alors communiqué en temps réel dans Géphi". I open Gephi, create a new project, click on "dynamic data" / "data sources" but cannot see any navicrawler source, only the exemple source ?</p> <p>Any tutorial or documentation ? (am not an engineer) </p> http://gephi.org/forum/topic.php?id=5320#post-5424 Thu, 01 Oct 2009 07:26:56 +0000 Sébastien Heymann 5424@http://gephi.org/forum/ <p>A special issue of Science is dedicated to Network Science : <a href="http://www.sciencemag.org/content/vol325/issue5939/index.dtl" rel="nofollow">http://www.sciencemag.org/content/vol325/issue5939/index.dtl</a></p> <p>This article is written by Barabasi : <a href="http://www.barabasilab.com/pubs/CCNR-ALB_Publications/200907-24_Science-Decade/200907-24_Science-Decade.pdf" rel="nofollow">http://www.barabasilab.com/pubs/CCNR-ALB_Publications/200907-24_Science-Decade/200907-24_Science-Decade.pdf</a></p> <p>And this one is about career opportunities in Network Science : <a href="http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2009_07_24/caredit.a0900091" rel="nofollow">http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2009_07_24/caredit.a0900091</a> </p> http://gephi.org/forum/topic.php?id=5315#post-5422 Sat, 26 Sep 2009 08:54:14 +0000 Mathieu Bastian 5422@http://gephi.org/forum/ <p>Yeah, GSOC 2010? We will of course want to participate, do you have some subject to propose ?<br /> I see that you like algorithms, are you familiar with graph theory algorithms ? </p> http://gephi.org/forum/topic.php?id=5317#post-5420 Thu, 24 Sep 2009 17:13:08 +0000 Mathieu Bastian 5420@http://gephi.org/forum/ <p>The release is late, of course like always, but not so much :-) It is planned now for November.</p> <p>Working a lot on GUI right now. </p> http://gephi.org/forum/topic.php?id=5317#post-5419 Thu, 24 Sep 2009 15:36:16 +0000 Delux 5419@http://gephi.org/forum/ <p>Any updates on when we might see a 0.7 alpha? I am looking for a new toolkit to play with. :) </p> http://gephi.org/forum/topic.php?id=5312#post-5417 Wed, 23 Sep 2009 22:09:01 +0000 Mathieu Bastian 5417@http://gephi.org/forum/ <p>Although I'm deeply interested in applications of Gephi and especially Network Science, I'm currently developing the 0.7 version of Gephi and don't have time for anything else. </p> <p>However I encourage you to get knowledge about complex networks, to see in what way you could turn your data in it. Do you have a database about the connections you're talking about ? </p> http://gephi.org/forum/topic.php?id=5312#post-5416 Wed, 23 Sep 2009 19:47:55 +0000 Ribeiro 5416@http://gephi.org/forum/ <p>Ok, Mathieu. It is so complicated to me. I am a doctor and all my kownloge is about human´s body and behavior, so computer´s languague is absolutelly new for me. </p> <p>Well, I am from Brazil... so farway...But I am realy interested in this softaware, can we devolp a project together? I think about the conections between body´s molecules and enviroment´s molecules. It means the network of lifestyle and health. What do you think about it?</p> <p>Thanks for your attention. </p> http://gephi.org/forum/topic.php?id=5315#post-5415 Mon, 21 Sep 2009 12:02:37 +0000 arunkrishnamurthy 5415@http://gephi.org/forum/ <p>hi iam arun krishnamurthy,a student from india ,chennai intrested in working with gephi for gsoc 2010<br /> iam good @ c++ reference <a href="http://www.spoj.pl/users/arunkcec" rel="nofollow">www.spoj.pl/users/arunkcec</a> and a fast learner ,could anybody guide or help me with the basics of applying for gephi,iam ready to work on it from now </p> http://gephi.org/forum/topic.php?id=5314#post-5414 Mon, 21 Sep 2009 10:43:13 +0000 Sébastien Heymann 5414@http://gephi.org/forum/ <p>Hi,</p> <p>As edge labels is a late addition in gexf format, this functionality is currently not available in Gephi 0.6 series, but will be added for the next 0.7 release. </p> http://gephi.org/forum/topic.php?id=5314#post-5413 Mon, 21 Sep 2009 09:59:36 +0000 Claude Moulin 5413@http://gephi.org/forum/ <p>Gexf allows for defining edge label.<br /> Does gephi support the display of edge labels ?<br /> Thank You </p> http://gephi.org/forum/topic.php?id=5312#post-5412 Mon, 21 Sep 2009 07:34:52 +0000 Mathieu Bastian 5412@http://gephi.org/forum/ <p>Hi, to use Gephi you have to load a compatible graph file format, listed on this <a href="http://gephi.org/support/supported-graph-formats/">page</a>. For instance, if you have your data in Excel you can easylee export a CSV file and transform it into a GDF. </p>