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[CIShell-SVN] SF.net SVN: cishell: [556] trunk/clients/gui/org.cishell.reference.gui. brand.cishell
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From: <bh...@us...> - 2007-12-12 20:50:42
|
Revision: 556
http://cishell.svn.sourceforge.net/cishell/?rev=556&view=rev
Author: bh2
Date: 2007-12-12 12:50:23 -0800 (Wed, 12 Dec 2007)
Log Message:
-----------
Committing changes to various cishell plugins in preparation for the new releng system.
The cishell brand now contains much of the extra files that go into its release.
Modified Paths:
--------------
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/.project
Added Paths:
-----------
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/configuration/
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/configuration/config.ini
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/configuration/default_menu.xml
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-apache-commons-collections.txt
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-cishell.txt
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-colt.txt
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-jung.txt
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-knopflerfish.txt
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-prefuse.txt
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/isi/
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/isi/barabasi-vespignani-wasserman.isi
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/isi/savedrecs-barabasi.isi
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/isi/savedrecs-garfield.isi
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/isi/savedrecs-vespignani.isi
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/isi/savedrecs-wasserman.isi
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/TARL/
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/TARL/agingfunction.txt
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/TARL/iniscript.tarl
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/bio/
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/bio/FlyMINT.nwb
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/bio/TF_DNA_regulonDB.nwb
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/bio/WI5.nwb
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/bio/WormMint.nwb
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/bio/YeastMINT.nwb
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/conversionGraph.graphml.xml
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/florentine.nwb
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/friendster.graphml.xml
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/friendster.xgmml.xml
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/netsci06-conference.net
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/seiyu.graphml.xml
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/terror.graphml.xml
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/network/terror.xgmml.xml
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/icons/cishell.icns
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/icons/cishell.ico
trunk/clients/gui/org.cishell.reference.gui.brand.cishell/icons/cishell.xpm
Modified: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/.project
===================================================================
--- trunk/clients/gui/org.cishell.reference.gui.brand.cishell/.project 2007-12-11 22:54:31 UTC (rev 555)
+++ trunk/clients/gui/org.cishell.reference.gui.brand.cishell/.project 2007-12-12 20:50:23 UTC (rev 556)
@@ -20,9 +20,15 @@
<arguments>
</arguments>
</buildCommand>
+ <buildCommand>
+ <name>net.sourceforge.metrics.builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.pde.PluginNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>net.sourceforge.metrics.nature</nature>
</natures>
</projectDescription>
Added: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/configuration/config.ini
===================================================================
--- trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/configuration/config.ini (rev 0)
+++ trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/configuration/config.ini 2007-12-12 20:50:23 UTC (rev 556)
@@ -0,0 +1,6 @@
+#Product Runtime Configuration File
+
+osgi.splashPath=platform:/base/plugins/org.cishell.reference.gui.brand.cishell
+eclipse.product=org.cishell.reference.gui.brand.cishell.cishell
+osgi.bundles=org.eclipse.equinox.common@2:start,org.eclipse.update.configurator@3:start,org.eclipse.core.runtime@start,org.eclipse.equinox.ds@3:start,org.eclipse.equinox.log@3:start,org.eclipse.equinox.metatype@3:start,org.eclipse.equinox.event@3:start,org.cishell.service.autostart@4:start
+osgi.bundles.defaultStartLevel=4
Property changes on: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/configuration/config.ini
___________________________________________________________________
Name: svn:mime-type
+ text/plain
Added: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/configuration/default_menu.xml
===================================================================
--- trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/configuration/default_menu.xml (rev 0)
+++ trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/configuration/default_menu.xml 2007-12-12 20:50:23 UTC (rev 556)
@@ -0,0 +1,127 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- <?xml version="1.0" encoding="ISO-8859-1" ?> -->
+<menu_layout>
+ <top_menu name="File">
+ <menu name="Load..." pid= "org.cishell.reference.gui.persistence.load.FileLoad "/>
+ <menu name="Load CSV Files" pid= "edu.iu.nwb.preprocessing.csv.CsvAlgorithm"/>
+ <menu name="Directory Hierarchy Reader" pid= "edu.iu.nwb.preprocessing.prefuse.beta.directoryhierarchyreader.DirectoryHierarchyReaderAlgorithm"/>
+ <menu name = "Datasets" type="group">
+ <menu name="Parallel Coordinates (demo) STF Dataset" pid="org.mediavirus.parvis.sampledata/pcvis_data.txt"/>
+ </menu>
+ <menu type="break"/>
+ <menu name="Save..." pid= "org.cishell.reference.gui.persistence.save.Save"/>
+ <menu type="break"/>
+ <menu name="View..." pid= "org.cishell.reference.gui.persistence.view.FileView"/>
+ <menu name="View With..." pid= "org.cishell.reference.gui.persistence.viewwith.FileViewWith"/>
+ <menu type="break"/>
+ <menu name = "Test" type="group">
+ <menu name="Scheduler Tester" pid= "org.cishell.tests.ProgressTrackableAlgorithm.AlgorithmTest"/>
+ </menu>
+ <menu type="break"/>
+ <menu name="Exit" type="preserved"/>
+ </top_menu>
+ <top_menu name="Preprocessing">
+ <menu name="Random Node Deletion" pid="edu.iu.iv.errortolerance.ErrorToleranceAlgorithm"/>
+ <menu name="High Degree Node Deletion" pid="edu.iu.iv.attacktolerance.AttackToleranceAlgorithm"/>
+ <menu name="Pathfinder Network Scaling" pid="edu.iu.nwb.analysis.pathfindergraphnetworkscaling.PathfinderGraphAlgorithm"/>
+ <menu name="Multipartite Joining" pid="edu.iu.nwb.analysis.multipartitejoining.JoiningAlgorithm"/>
+ <menu type="break"/>
+ <menu name="Snowball Sampling (n nodes)" pid="edu.iu.nwb.analysis.sampling.snowball.SnowballAlgorithm"/>
+ <menu name="Node Sampling" pid="edu.iu.nwb.analysis.sampling.node.NodeAlgorithm"/>
+ <menu name="Edge Sampling" pid="edu.iu.nwb.analysis.sampling.edge.EdgeAlgorithm"/>
+ </top_menu>
+ <top_menu name="Modeling">
+ <menu name="Random Graph" pid="edu.iu.nwb.modeling.erdosrandomgraph"/>
+ <menu name="Watts-Strogatz Small World" pid="edu.iu.nwb.modeling.smallworld"/>
+ <menu name="Barabási-Albert Scale-Free" pid="edu.iu.nwb.modeling.barabasialbert"/>
+ <menu type="break"/>
+ <menu name="Can" pid="edu.iu.iv.modeling.p2p.can.CanAlgorithm"/>
+ <menu name="Chord" pid="edu.iu.iv.modeling.p2p.chord.ChordAlgorithm"/>
+ <menu name="Hypergrid" pid="edu.id.iv.modeling.p2p.hypergrid.Hypergrid"/>
+ <menu name="PRU" pid="edu.iu.iv.modeling.p2p.pru.PruAlgorithm"/>
+ <menu type="break"/>
+ <menu name="TARL" pid="edu.iu.iv.modeling.tarl.TarlAlgorithm"/>
+ </top_menu>
+
+ <top_menu name="Analysis">
+ <menu name = "Unweighted && Undirected" type="group">
+ <menu name="Node Degree" pid="edu.iu.nwb.analysis.totaldegreesequence"/>
+ <menu name="Degree Distribution" pid="edu.iu.nwb.analysis.totaldegreedistribution"/>
+ <menu type="break"/>
+ <menu name="k-Nearest Neighbor" pid="edu.iu.nwb.analysis.undirectedknn"/>
+ <menu name="Watts Strogatz Clustering Coefficient" pid="edu.iu.nwb.analysis.clustering"/>
+ <menu name="Watts Strogatz Clustering Coefficient Over k" pid="edu.iu.nwb.analysis.clustering_vs_k"/>
+ <menu type="break"/>
+ <menu name="Diameter" pid="edu.iu.nwb.analysis.diameter"/>
+ <menu name="Average Shortest Path" pid="edu.iu.nwb.analysis.averageshortestpath"/>
+ <menu name="Shortest Path Distribution" pid="edu.iu.nwb.analysis.shortestpathdistr"/>
+ <menu name="Node Betweenness Centrality" pid="edu.iu.nwb.analysis.sitebetweenness"/>
+ <menu type="break"/>
+ <menu name="Connected Components" pid="edu.iu.nwb.analysis.connectedcomponents"/>
+ <menu name="Weak Component Clustering" pid="edu.iu.nwb.analysis.weakcomponentclustering.ClusteringAlgorithm"/>
+ </menu>
+
+ <menu name = "Unweighted && Directed" type="group">
+ <menu name="Node Indegree" pid="edu.iu.nwb.analysis.indegreesequence"/>
+ <menu name="Node Outdegree" pid="edu.iu.nwb.analysis.outdegreesequence"/>
+ <menu name="Indegree Distribution" pid="edu.iu.nwb.analysis.indegreedistribution"/>
+ <menu name="Outdegree Distribution" pid="edu.iu.nwb.analysis.outdegreedistribution"/>
+ <menu type="break"/>
+ <menu name="k-Nearest Neighbor" pid="edu.iu.nwb.analysis.directedknn"/>
+ <menu name="Single Node In-Out Degree Correlations" pid="edu.iu.nwb.analysis.onepointcorrelations"/>
+ <menu type="break"/>
+ <menu name="Page Rank" pid="edu.iu.nwb.analysis.pagerank"/>
+ </menu>
+
+ <menu name = "Weighted and Undirected" type="group">
+ </menu>
+ <menu name = "Weighted and Directed" type="group">
+ </menu>
+ </top_menu>
+
+ <top_menu name="Search">
+ <menu name="Can" pid="edu.iu.iv.search.p2p.can.CanSearchAlgorithm"/>
+ <menu name="Chord" pid="edu.iu.iv.search.p2p.chord.ChordSearchAlgorithm"/>
+ <menu name="k Random-Walk" pid="edu.iu.iv.search.p2p.randomwalk.RandomWalkAlgorithm"/>
+ <menu name="Random Breadth First" pid="edu.iu.iv.search.p2p.bfs.BreadthFirstSearchAlgorithm"/>
+ </top_menu>
+
+ <top_menu name="Clustering">
+ <menu name="Weak Component Clustering" pid="edu.iu.nwb.analysis.weakcomponentclustering.ClusteringAlgorithm"/>
+ </top_menu>
+
+ <top_menu name="Visualization">
+ <menu name="Circular" pid="edu.iu.nwb.visualization.jungnetworklayout.JUNGCircleLayout"/>
+ <menu name="Specified" pid="edu.iu.nwb.visualization.prefuse.beta.specified.Specified"/>
+ <menu type="break"/>
+ <menu name="Radial Tree/Graph" pid="edu.iu.nwb.visualization.radialgraph.RadialGraph"/>
+ <menu name="Radial Tree/Graph with Annotation" pid="edu.iu.nwb.visualization.prefuse.beta.radialgraph.RadialGraph"/>
+ <menu name="Tree Map" pid="edu.iu.nwb.visualization.prefuse.beta.treemap.TreeMap"/>
+ <menu name="Tree View" pid="edu.iu.nwb.visualization.prefuse.beta.treeview.TreeView"/>
+ <menu type="break"/>
+ <menu name="Force Directed" pid="edu.iu.nwb.visualization.prefuse.beta.graphview.GraphView"/>
+ <menu name="Kamada-Kawai" pid="edu.iu.nwb.visualization.jungnetworklayout.JUNGKamadaKawaiLayout"/>
+ <menu name="Fruchterman-Reingold" pid="edu.iu.nwb.visualization.jungnetworklayout.JUNGFruchtermanReingoldLayout"/>
+ <menu name="Fruchterman-Reingold with Annotation" pid="edu.iu.nwb.visualization.prefuse.beta.fruchtermanreingold.FruchtermanReingold"/>
+ <menu name="Spring" pid="edu.iu.nwb.visualization.jungnetworklayout.JUNGSpringLayout"/>
+ <menu name="Small World" pid="edu.iu.nwb.visualization.prefuse.alpha.smallworld.app.SmallWorld"/>
+ <menu type="break"/>
+ <menu name="Parallel Coordinates (demo)" pid="org.mediavirus.parvis.ParallelCoordinatesAlgorithm"/>
+ </top_menu>
+
+ <top_menu name="Tools">
+ <menu name="GnuPlot" pid="edu.iu.nwb.visualization.gnuplot"/>
+ <menu name="Scheduler" pid=""/>
+ </top_menu>
+
+ <top_menu name="Help">
+ <menu name="Dataset Details" pid=""/>
+ <menu name="Algorithm Details" pid=""/>
+ <menu name="Tutorials" pid=""/>
+ <menu type="break"/>
+ <menu name="Update" pid=""/>
+ <menu name="Manage Configuration" pid=""/>
+ <menu type="break"/>
+ <menu name="About Network Workbench Tool" pid=""/>
+ </top_menu>
+</menu_layout>
Property changes on: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/configuration/default_menu.xml
___________________________________________________________________
Name: svn:mime-type
+ text/plain
Added: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-apache-commons-collections.txt
===================================================================
--- trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-apache-commons-collections.txt (rev 0)
+++ trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-apache-commons-collections.txt 2007-12-12 20:50:23 UTC (rev 556)
@@ -0,0 +1,202 @@
+
+ Apache License
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+
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Property changes on: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-apache-commons-collections.txt
___________________________________________________________________
Name: svn:mime-type
+ text/plain
Added: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-cishell.txt
===================================================================
--- trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-cishell.txt (rev 0)
+++ trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-cishell.txt 2007-12-12 20:50:23 UTC (rev 556)
@@ -0,0 +1,20 @@
+CIShell: Cyberinfrastructure Shell
+Copyright 2005 Indiana University
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+implied. See the License for the specific language governing
+permissions and limitations under the License.
+
+Project Contacts:
+Bruce Herr (bh...@bh...)
+Weixia Huang (hu...@in...)
+Shashikant Penumarthy (sp...@in...)
+Dr. Katy Borner (ka...@in...)
Property changes on: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-cishell.txt
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Added: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-colt.txt
===================================================================
--- trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-colt.txt (rev 0)
+++ trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-colt.txt 2007-12-12 20:50:23 UTC (rev 556)
@@ -0,0 +1,10 @@
+ Packages cern.colt* , cern.jet*, cern.clhep
+
+Copyright (c) 1999 CERN - European Organization for Nuclear Research.
+
+Permission to use, copy, modify, distribute and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation. CERN makes no representations about the suitability of this software for any purpose. It is provided "as is" without expressed or implied warranty.
+
+ Packages hep.aida.*
+
+Written by Pavel Binko, Dino Ferrero Merlino, Wolfgang Hoschek, Tony Johnson, Andreas Pfeiffer, and others. Check the FreeHEP home page for more info. Permission to use and/or redistribute this work is granted under the terms of the LGPL License, with the exception that any usage related to military applications is expressly forbidden. The software and documentation made available under the terms of this license are provided with no warranty.
+
Property changes on: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-colt.txt
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+ text/plain
Added: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-jung.txt
===================================================================
--- trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-jung.txt (rev 0)
+++ trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-jung.txt 2007-12-12 20:50:23 UTC (rev 556)
@@ -0,0 +1 @@
+BSD License
Property changes on: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-jung.txt
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Name: svn:mime-type
+ text/plain
Added: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-knopflerfish.txt
===================================================================
--- trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-knopflerfish.txt (rev 0)
+++ trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-knopflerfish.txt 2007-12-12 20:50:23 UTC (rev 556)
@@ -0,0 +1,35 @@
+/*
+ * Copyright (c) 2003-2006, KNOPFLERFISH project
+ * All rights reserved.
+ *
+ * http://www.knopflerfish.org/license.html
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions and the following
+ * disclaimer in the documentation and/or other materials
+ * provided with the distribution.
+ *
+ * - Neither the name of the KNOPFLERFISH project nor the names of its
+ * contributors may be used to endorse or promote products derived
+ * from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ * COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ * OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
Property changes on: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-knopflerfish.txt
___________________________________________________________________
Name: svn:mime-type
+ text/plain
Added: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-prefuse.txt
===================================================================
--- trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-prefuse.txt (rev 0)
+++ trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-prefuse.txt 2007-12-12 20:50:23 UTC (rev 556)
@@ -0,0 +1,35 @@
+
+ Copyright (c) 2004, 2005 Regents of the University of California.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+
+ 3. All advertising materials mentioning features or use of this software
+ must display the following acknowledgement:
+
+ This product includes software developed by the Group for User
+ Interface Research at the University of California at Berkeley.
+
+ 4. The name of the University may not be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
Property changes on: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/licenses/license-prefuse.txt
___________________________________________________________________
Name: svn:mime-type
+ text/plain
Added: trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/isi/barabasi-vespignani-wasserman.isi
===================================================================
--- trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/isi/barabasi-vespignani-wasserman.isi (rev 0)
+++ trunk/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/sampledata/isi/barabasi-vespignani-wasserman.isi 2007-12-12 20:50:23 UTC (rev 556)
@@ -0,0 +1,19929 @@
+FN ISI Export Format
+VR 1.0
+PT J
+AU Wuchty, S
+ Barabasi, AL
+ Ferdig, MT
+TI Stable evolutionary signal in a Yeast protein interaction network
+SO BMC EVOLUTIONARY BIOLOGY
+LA English
+DT Article
+ID SACCHAROMYCES-CEREVISIAE; FUNCTIONAL MODULES; INTERACTION MAP; CELLULAR
+ NETWORKS; COMPLEX NETWORKS; IDENTIFICATION; ORGANIZATION; ORTHOLOGS;
+ PATTERNS; DATABASE
+AB Background: The recently emerged protein interaction network paradigm
+ can provide novel and important insights into the innerworkings of a
+ cell. Yet, the heavy burden of both false positive and false negative
+ protein-protein interaction data casts doubt on the broader usefulness
+ of these interaction sets. Approaches focusing on one-protein-at-a-time
+ have been powerfully employed to demonstrate the high degree of
+ conservation of proteins participating in numerous interactions; here,
+ we expand his 'node' focused paradigm to investigate the relative
+ persistence of 'link' based evolutionary signals in a protein
+ interaction network of S. cerevisiae and point out the value of this
+ relatively untapped source of information.
+ Results: The trend for highly connected proteins to be preferably
+ conserved in evolution is stable, even in the context of tremendous
+ noise in the underlying protein interactions as well as in the
+ assignment of orthology among five higher eukaryotes. We find that
+ local clustering around interactions correlates with preferred
+ evolutionary conservation of the participating proteins; furthermore
+ the correlation between high local clustering and evolutionary
+ conservation is accompanied by a stable elevated degree of coexpression
+ of the interacting proteins. We use this conserved interaction data,
+ combined with P. falciparum /Yeast orthologs, as proof-of-principle
+ that high-order network topology can be used comparatively to deduce
+ local network structure in non-model organisms.
+ Conclusion: High local clustering is a criterion for the reliability of
+ an interaction and coincides with preferred evolutionary conservation
+ and significant coexpression. These strong and stable correlations
+ indicate that evolutionary units go beyond a single protein to include
+ the interactions among them. In particular, the stability of these
+ signals in the face of extreme noise suggests that empirical protein
+ interaction data can be integrated with orthologous clustering around
+ these protein interactions to reliably infer local network structures
+ in non-model organisms.
+C1 Northwestern Univ, NW Inst Complex, Evanston, IL 60202 USA.
+ Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+ Univ Notre Dame, Dept Biol, Notre Dame, IN 46556 USA.
+RP Wuchty, S, Northwestern Univ, NW Inst Complex, Chambers Hall,600 Foster
+ St, Evanston, IL 60202 USA.
+EM s-w...@no...
+ al...@nd...
+ mf...@nd...
+CR ALBERT R, 2000, NATURE, V406, P378
+ ALBERT R, 2002, REV MOD PHYS, V74, P47
+ BABU MM, 2004, CURR OPIN STRUC BIOL, V14, P283
+ BARABAI A, 2004, NATURE REV GEN, P101
+ BARABASI AL, 1999, SCIENCE, V286, P509
+ BORK P, 2004, CURR OPIN STRUC BIOL, V14, P292
+ BOZDECH Z, 2003, PLOS BIOL, V1, P1
+ BUTLAND G, 2005, NATURE, V433, P531
+ EISEN MB, 1998, P NATL ACAD SCI USA, V95, P14863
+ FRASER HB, 2002, SCIENCE, V296, P750
+ FRASER HB, 2003, BMC EVOL BIOL, V3
+ GAVIN AC, 2002, NATURE, V415, P141
+ GE H, 2001, NAT GENET, V29, P482
+ GIOT L, 2003, SCIENCE, V302, P1727
+ GOLDBERG DS, 2003, P NATL ACAD SCI USA, V100, P4372
+ GOLDSTEIN M, 2004, FITTING POWER LAW DI
+ HAN JDJ, 2004, NATURE, V430, P88
+ HO Y, 2002, NATURE, V415, P180
+ ITO T, 2000, P NATL ACAD SCI USA, V97, P1143
+ JEONG H, 2001, NATURE, V411, P41
+ JORDAN I, 2003, BMC EVOL BIOL, V3
+ OBRIEN KP, 2005, NUCLEIC ACIDS RES, V33, D476
+ RAIN JC, 2001, NATURE, V409, P211
+ REMM M, 2001, J MOL BIOL, V314, P1041
+ RIVES AW, 2003, P NATL ACAD SCI USA, V100, P1128
+ SCHWIKOWSKI B, 2000, NAT BIOTECHNOL, V18, P1257
+ SHARAN R, 2005, P NATL ACAD SCI USA, V102, P1974
+ SNEL B, 2002, P NATL ACAD SCI USA, V99, P5890
+ SPIRIN V, 2003, P NATL ACAD SCI USA, V100, P12123
+ UETZ P, 2000, NATURE, V403, P623
+ VAZQUEZ A, 2003, COMPLEXUS, V1, P38
+ VESPIGNANI A, 2003, NAT GENET, V35, P118
+ VIDAL M, 2005, FEBS LETT, V579, P1834
+ VONMERING C, 2002, NATURE, V417, P399
+ VONMERING C, 2003, P NATL ACAD SCI USA, V100, P15428
+ WALHOUT AJM, 2000, SCIENCE, V287, P116
+ WILLIAMS EJB, 2000, NATURE, V407, P900
+ WUCHTY S, 2002, PROTEOMICS, V2, P1715
+ WUCHTY S, 2003, NAT GENET, V35, P176
+ WUCHTY S, 2004, GENOME RES, V14, P1310
+ WUCHTY S, 2005, PROTEOMICS, V5, P444
+ XENARIOS I, 2002, NUCLEIC ACIDS RES, V30, P303
+NR 42
+TC 7
+PU BIOMED CENTRAL LTD
+PI LONDON
+PA MIDDLESEX HOUSE, 34-42 CLEVELAND ST, LONDON W1T 4LB, ENGLAND
+SN 1471-2148
+J9 BMC EVOL BIOL
+JI BMC Evol. Biol.
+PD JAN 30
+PY 2006
+VL 6
+AR 8
+DI ARTN 8
+PG 10
+SC Evolutionary Biology; Genetics & Heredity
+GA 019ZP
+UT ISI:000235877800001
+ER
+
+PT J
+AU Balazsi, G
+ Barabasi, AL
+ Oltvai, ZN
+TI Functional organization of transcriptional-regulatory networks
+SO FEBS JOURNAL
+LA English
+DT Meeting Abstract
+C1 Univ Pittsburgh, Dept Pathol, Pittsburgh, PA USA.
+ Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+EM ol...@pi...
+NR 0
+TC 0
+PU BLACKWELL PUBLISHING
+PI OXFORD
+PA 9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND
+SN 1742-464X
+J9 FEBS J
+JI FEBS J.
+PD JUL
+PY 2005
+VL 272
+SU Suppl. 1
+BP 103
+EP 103
+PG 1
+SC Biochemistry & Molecular Biology
+GA 005MG
+UT ISI:000234826100349
+ER
+
+PT J
+AU Barabasi, AL
+TI Network biology: from the metabolism to protein interactions
+SO FEBS JOURNAL
+LA English
+DT Meeting Abstract
+C1 Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+EM al...@nd...
+NR 0
+TC 0
+PU BLACKWELL PUBLISHING
+PI OXFORD
+PA 9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND
+SN 1742-464X
+J9 FEBS J
+JI FEBS J.
+PD JUL
+PY 2005
+VL 272
+SU Suppl. 1
+BP 433
+EP 433
+PG 1
+SC Biochemistry & Molecular Biology
+GA 005MG
+UT ISI:000234826102297
+ER
+
+PT J
+AU Barabasi, AL
+TI Taming complexity
+SO NATURE PHYSICS
+LA English
+DT Editorial Material
+ID SMALL-WORLD NETWORKS; COMMUNITY STRUCTURE; METABOLIC NETWORKS; INTERNET
+C1 Harvard Univ, Dana Farber Canc Inst, Ctr Canc Syst Biol, Boston, MA 02115 USA.
+ Univ Notre Dame, Ctr Complex Network Res, Notre Dame, IN 46556 USA.
+ Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+RP Barabasi, AL, Harvard Univ, Dana Farber Canc Inst, Ctr Canc Syst Biol,
+ Boston, MA 02115 USA.
+EM al...@nd...
+CR *NAT RES COUNC, 2005, NETW SCI
+ ALBERT R, 1999, NATURE, V401, P130
+ ALBERT R, 2000, NATURE, V406, P378
+ AMARAL LAN, 2000, P NATL ACAD SCI USA, V97, P11149
+ BARABASI AL, 1999, SCIENCE, V286, P509
+ BIANCONI G, 2001, PHYS REV LETT, V86, P5632
+ BOLLOBAS B, 2001, RANDOM GRAPHS
+ CALDARELLI G, 2002, PHYS REV LETT, V89
+ COHEN R, 2000, PHYS REV LETT, V85, P4626
+ DOROGOVTSEV SN, 2002, ADV PHYS, V51, P1079
+ EBEL H, 2002, PHYS REV E 2A, V66
+ ERDOS P, 1959, PUBL MATH-DEBRECEN, V6, P290
+ EUBANK S, 2004, NATURE, V429, P180
+ FALOUTSOS M, 1999, COMP COMM R, V29, P251
+ GIRVAN M, 2002, P NATL ACAD SCI USA, V99, P7821
+ JEONG H, 2000, NATURE, V407, P651
+ KRAPIVSKY PL, 2000, PHYS REV LETT, V85, P4629
+ MILO R, 2002, SCIENCE, V298, P824
+ PALLA G, 2005, NATURE, V435, P814
+ PASTORSATORRAS R, 2001, PHYS REV LETT, V86, P3200
+ WAGNER A, 2001, P ROY SOC LOND B BIO, V268, P1803
+ WATTS DJ, 1998, NATURE, V393, P440
+NR 22
+TC 2
+PU NATURE PUBLISHING GROUP
+PI LONDON
+PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND
+SN 1745-2473
+J9 NAT PHYS
+JI Nat. Phys.
+PD NOV
+PY 2005
+VL 1
+IS 2
+BP 68
+EP 70
+PG 3
+SC Physics, Multidisciplinary
+GA 006HJ
+UT ISI:000234888300002
+ER
+
+PT J
+AU Macdonald, PJ
+ Almaas, E
+ Barabasi, AL
+TI Minimum spanning trees of weighted scale-free networks
+SO EUROPHYSICS LETTERS
+LA English
+DT Article
+ID COMPLEX NETWORKS; PERCOLATION; OPTIMIZATION; INTERNET
+AB A complete characterization of real networks requires us to understand
+ the consequences of the uneven interaction strengths between a system's
+ components. Here we use minimum spanning trees (MSTs) to explore the
+ effect of correlations between link weights and network topology on
+ scale-free networks. Solely by changing the nature of the correlations
+ between weights and network topology, the structure of the MSTs can
+ change from scale-free to exponential. Additionally, for some choices
+ of weight correlations, the efficiency of the MSTs increases with
+ increasing network size, a result with potential implications for the
+ design and scalability of communication networks.
+C1 Univ Notre Dame, Ctr Network Res, Notre Dame, IN 46556 USA.
+ Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+RP Macdonald, PJ, Univ Notre Dame, Ctr Network Res, Notre Dame, IN 46556
+ USA.
+EM al...@nd...
+CR ABDELWAHAB H, 1997, INFORM SCIENCES, V101, P47
+ ALBERT R, 2000, NATURE, V406, P378
+ ALBERT R, 2002, REV MOD PHYS, V74, P47
+ ALMAAS E, 2004, NATURE, V427, P839
+ AMARAL LAN, 2004, EUR PHYS J B, V38, P143
+ BARABASI AL, 1996, PHYS REV LETT, V76, P3750
+ BARABASI AL, 1999, SCIENCE, V286, P509
+ BARRAT A, 2004, P NATL ACAD SCI USA, V101, P3747
+ BARRAT A, 2004, PHYS REV E 2, V70
+ BERLOW EL, 1999, NATURE, V398, P330
+ BRAUNSTEIN LA, 2003, PHYS REV LETT, V91
+ CALLAWAY DS, 2000, PHYS REV LETT, V85, P5468
+ CLAUSET A, 2005, PHYS REV LETT, V94
+ COHEN R, 2000, PHYS REV LETT, V85, P4626
+ DOBRIN R, 2001, PHYS REV LETT, V86, P5076
+ GOH KI, 2001, PHYS REV LETT, V87
+ GRANOVET.MS, 1973, AM J SOCIOL, V78, P1360
+ HOGG RV, 1995, INTRO MATH STAT
+ KILPATRICK AM, 2003, NATURE, V422, P65
+ KIM DH, 2004, PHYS REV E 2, V70
+ KRAPIVSKY PL, 2001, PHYS REV E 2, V63
+ NEWMAN MEJ, 2003, SIAM REV, V45, P167
+ NEWMAN MEJ, 2005, STRUCTURE GROWTH NET
+ OLIVEIRA CAS, 2005, COMPUT OPER RES, V32, P1953
+ PASTORSATORRAS R, 2001, PHYS REV LETT, V86, P3200
+ PRIM RC, 1957, BELL SYST TECH J, V36, P1389
+ SCHMITTBUHL J, 1993, J PHYS A-MATH GEN, V26, P6115
+ SREENIVASAN S, 2004, PHYS REV E 2, V70
+ STAUFFER D, 1994, INTRO PERCOLATION TH
+ STROGATZ SH, 2001, NATURE, V410, P268
+ SZABO GJ, 2003, PHYSICA A, V330, P31
+ TOROCZKAI Z, 2004, NATURE, V428, P716
+ VICSEK T, 1992, GROWTH PHENOMENA
+ WAN PJ, 2002, WIREL NETW, V8, P607
+ YOOK SH, 2001, PHYS REV LETT, V86, P5835
+NR 35
+TC 14
+PU EDP SCIENCES S A
+PI LES ULIS CEDEX A
+PA 17, AVE DU HOGGAR, PA COURTABOEUF, BP 112, F-91944 LES ULIS CEDEX A,
+ FRANCE
+SN 0295-5075
+J9 EUROPHYS LETT
+JI Europhys. Lett.
+PD OCT
+PY 2005
+VL 72
+IS 2
+BP 308
+EP 314
+PG 7
+SC Physics, Multidisciplinary
+GA 983NF
+UT ISI:000233238500024
+ER
+
+PT J
+AU Oliveira, JG
+ Barabasi, AL
+TI Human dynamics: Darwin and Einstein correspondence patterns
+SO NATURE
+LA English
+DT Editorial Material
+C1 Univ Notre Dame, Ctr Complex Network Res, Notre Dame, IN 46556 USA.
+ Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+ Univ Aveiro, Dept Fis, P-3810193 Aveiro, Portugal.
+ Harvard Univ, Dana Farber Canc Inst, Ctr Canc Syst Biol, Boston, MA 02115 USA.
+RP Oliveira, JG, Univ Notre Dame, Ctr Complex Network Res, Notre Dame, IN
+ 46556 USA.
+EM al...@nd...
+CR 1984, CORRES C DARWIN, V1
+ 1993, COLLECTED PAPERS A E, V1
+ 1993, COLLECTED PAPERS A E, V5
+ 1993, COLLECTED PAPERS A E, V8
+ 1993, COLLECTED PAPERS A E, V9
+ ABATE J, 1997, QUEUEING SYST, V25, P173
+ BARABASI AL, 2005, NATURE, V435, P207
+ BUNDE A, 2004, PHYSICA A, V342, P308
+ COBHAM A, 1954, OPER RES, V2, P70
+ KALUZA T, 1921, SITZUNGSBERICHTE PRE, V54, P966
+NR 10
+TC 15
+PU NATURE PUBLISHING GROUP
+PI LONDON
+PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND
+SN 0028-0836
+J9 NATURE
+JI Nature
+PD OCT 27
+PY 2005
+VL 437
+IS 7063
+BP 1251
+EP 1251
+PG 1
+SC Multidisciplinary Sciences
+GA 977UQ
+UT ISI:000232829100032
+ER
+
+PT J
+AU Balazsi, G
+ Barabasi, AL
+ Oltvai, ZN
+TI Topological units of environmental signal processing in the
+ transcriptional regulatory network of Escherichia coli
+SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA
+LA English
+DT Article
+DE cellular networks; regulation; transcription
+ID SINGULAR-VALUE DECOMPOSITION; COMPLEX NETWORKS; GENOME; BINDING;
+ MOTIFS; OPERON; DYNAMICS; PATTERNS; MODEL; FNR
+AB Recent evidence indicates that potential interactions within metabolic,
+ protein-protein interaction, and transcriptional regulatory networks
+ are used differentially according to the environmental conditions in
+ which a cell exists. However, the topological units underlying such
+ differential utilization are not understood. Here we use the
+ transcriptional regulatory network of Escherichia coli to identify such
+ units, called origons, representing regulatory sub-networks that
+ originate at a distinct class of sensor transcription factors. Using
+ microarray data, we find that specific environmental signals affect
+ mRNA expression levels significantly only within the origons
+ responsible for their detection and processing. We also show that small
+ regulatory interaction patterns, called subgraphs and motifs, occupy
+ distinct positions in and between origons, offering insights into their
+ dynamical role in information processing. The identified features are
+ likely to represent a general framework for environmental signal
+ processing in prokaryotes.
+C1 Northwestern Univ, Dept Pathol, Chicago, IL 60611 USA.
+ Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+ Univ Notre Dame, Ctr Complex Networks Res, Notre Dame, IN 46556 USA.
+ Univ Pittsburgh, Dept Pathol, Pittsburgh, PA 15261 USA.
+RP Oltvai, ZN, Northwestern Univ, Dept Pathol, Chicago, IL 60611 USA.
+EM ol...@pi...
+CR ALLEN TE, 2003, J BACTERIOL, V185, P6392
+ ALTER O, 2000, P NATL ACAD SCI USA, V97, P10101
+ BOLOURI H, 2002, BIOESSAYS, V24, P1118
+ BUCHLER NE, 2003, P NATL ACAD SCI USA, V100, P5136
+ CHANG DE, 2002, MOL MICROBIOL, V45, P289
+ CONANT GC, 2004, NAT GENET, V34, P264
+ CRACK J, 2004, J BIOL CHEM, V279, P9278
+ DOBRIN R, 2004, BMC BIOINFORMATICS, V5
+ GUELZIM N, 2002, NAT GENET, V31, P60
+ HARBISON CT, 2004, NATURE, V431, P99
+ HOLTER NS, 2000, P NATL ACAD SCI USA, V97, P8409
+ KALIR S, 2004, CELL, V117, P713
+ KILEY PJ, 1998, FEMS MICROBIOL REV, V22, P341
+ LIAO JC, 2003, P NATL ACAD SCI USA, V100, P15522
+ LIEB JD, 2001, NAT GENET, V28, P327
+ LUSCOMBE NM, 2004, NATURE, V431, P308
+ MA HW, 2004, BMC BIOINFORMATICS, V5
+ MANGAN S, 2003, J MOL BIOL, V334, P197
+ MANGAN S, 2003, P NATL ACAD SCI USA, V100, P11980
+ MARTINEZANTONIO A, 2003, CURR OPIN MICROBIOL, V6, P482
+ MIDDENDORF M, 2005, P NATL ACAD SCI USA, V102, P3192
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+ SETTY Y, 2003, P NATL ACAD SCI USA, V100, P7702
+ SHENORR SS, 2002, NAT GENET, V31, P64
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+ THIEFFRY D, 1998, BIOESSAYS, V20, P433
+ VAZQUEZ A, 2004, P NATL ACAD SCI USA, V101, P17940
+ YEUNG MKS, 2002, P NATL ACAD SCI USA, V99, P6163
+ ZEITLINGER J, 2003, CELL, V113, P395
+NR 37
+TC 29
+PU NATL ACAD SCIENCES
+PI WASHINGTON
+PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA
+SN 0027-8424
+J9 PROC NAT ACAD SCI USA
+JI Proc. Natl. Acad. Sci. U. S. A.
+PD MAY 31
+PY 2005
+VL 102
+IS 22
+BP 7841
+EP 7846
+PG 6
+SC Multidisciplinary Sciences
+GA 932CE
+UT ISI:000229531000013
+ER
+
+PT J
+AU Barabasi, AL
+TI The origin of bursts and heavy tails in human dynamics
+SO NATURE
+LA English
+DT Article
+ID MODEL
+AB The dynamics of many social, technological and economic phenomena are
+ driven by individual human actions, turning the quantitative
+ understanding of human behaviour into a central question of modern
+ science. Current models of human dynamics, used from risk assessment to
+ communications, assume that human actions are randomly distributed in
+ time and thus well approximated by Poisson processes(1-3). In contrast,
+ there is increasing evidence that the timing of many human activities,
+ ranging from communication to entertainment and work patterns, follow
+ non-Poisson statistics, characterized by bursts of rapidly occurring
+ events separated by long periods of inactivity(4-8). Here I show that
+ the bursty nature of human behaviour is a consequence of a
+ decision-based queuing process(9,10): when individuals execute tasks
+ based on some perceived priority, the timing of the tasks will be heavy
+ tailed, with most tasks being rapidly executed, whereas a few
+ experience very long waiting times. In contrast, random or priority
+ blind execution is well approximated by uniform inter-event statistics.
+ These finding have important implications, ranging from resource
+ management to service allocation, in both communications and retail.
+C1 Univ Notre Dame, Ctr Complex Networks Res, Notre Dame, IN 46556 USA.
+ Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+RP Barabasi, AL, Univ Notre Dame, Ctr Complex Networks Res, Notre Dame, IN
+ 46556 USA.
+EM al...@nd...
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+NR 28
+TC 32
+PU NATURE PUBLISHING GROUP
+PI LONDON
+PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND
+SN 0028-0836
+J9 NATURE
+JI Nature
+PD MAY 12
+PY 2005
+VL 435
+IS 7039
+BP 207
+EP 211
+PG 5
+SC Multidisciplinary Sciences
+GA 924ZO
+UT ISI:000229021100041
+ER
+
+PT J
+AU Barabasi, AL
+TI Network theory - The emergence of the creative enterprise
+SO SCIENCE
+LA English
+DT Editorial Material
+ID COMPLEX NETWORKS
+C1 Univ Notre Dame, Ctr Complex Network Res, Notre Dame, IN 46556 USA.
+ Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+RP Barabasi, AL, Univ Notre Dame, Ctr Complex Network Res, Notre Dame, IN
+ 46556 USA.
+EM al...@nd...
+CR ALBERT R, 2002, REV MOD PHYS, V74, P47
+ ASIMOV I, 1991, FDN EMPIRE
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+ BARABASI AL, 2002, PHYSICA A, V311, P590
+ BARABASI AL, 2004, NAT REV GENET, V5, P101
+ BENNAIM E, 2004, COMPLEX NETWORKS
+ BOLLOBAS B, 2001, RANDOM GRAPHS
+ BORNHOLDT S, 2003, HDB GRAPHS NETWORKS
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+ PASTORSATORRAS A, 2004, EVOLUTION STRUCTURE
+ STROGATZ SH, 2001, NATURE, V410, P268
+NR 14
+TC 7
+PU AMER ASSOC ADVANCEMENT SCIENCE
+PI WASHINGTON
+PA 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA
+SN 0036-8075
+J9 SCIENCE
+JI Science
+PD APR 29
+PY 2005
+VL 308
+IS 5722
+BP 639
+EP 641
+PG 3
+SC Multidisciplinary Sciences
+GA 922BO
+UT ISI:000228810900032
+ER
+
+PT J
+AU Vazquez, A
+ Oliveira, JG
+ Barabasi, AL
+TI Inhomogeneous evolution of subgraphs and cycles in complex networks
+SO PHYSICAL REVIEW E
+LA English
+DT Article
+ID MOTIFS
+AB Subgraphs and cycles are often used to characterize the local
+ properties of complex networks. Here we show that the subgraph
+ structure of real networks is highly time dependent: as the network
+ grows, the density of some subgraphs remains unchanged, while the
+ density of others increase at a rate that is determined by the
+ network's degree distribution and clustering properties. This
+ inhomogeneous evolution process, supported by direct measurements on
+ several real networks, leads to systematic shifts in the overall
+ subgraph spectrum and to an inevitable overrepresentation of some
+ subgraphs and cycles.
+C1 Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+ Univ Notre Dame, Ctr Complex Network Res, Notre Dame, IN 46556 USA.
+ Univ Aveiro, Dept Fis, P-3810193 Aveiro, Portugal.
+RP Vazquez, A, Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+CR ALBERT R, 2002, REV MOD PHYS, V74, P47
+ BARABASI AL, 2002, PHYSICA A, V311, P590
+ BEARMAN P, 1997, AM J SOCIOL, V102, P1383
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+ BIANCONI G, CONDMAT0310339
+ BIANCONI G, CONDMAT0408349
+ BIANCONI G, 2003, PHYS REV LETT, V90
+ DOROGOVTSEV SN, 2002, PHYS REV E 2, V65
+ MARINARI E, CONDMAT0407253
+ MILO R, 2002, SCIENCE, V298, P824
+ PASTORSATORRAS P, 2001, PHYS REV LETT, V87
+ PETERMANN T, 2004, PHYS REV E 2, V69
+ ROZENFELD HD, CONDMAT0403536
+ SERGI D, CONDMAT0412472
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+ VAZQUEZ A, 2004, P NATL ACAD SCI USA, V101, P17940
+ WUCHTY S, 2003, NAT GENET, V35, P118
+ YOOK SH, UNPUB
+NR 21
+TC 5
+PU AMERICAN PHYSICAL SOC
+PI COLLEGE PK
+PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA
+SN 1063-651X
+J9 PHYS REV E
+JI Phys. Rev. E
+PD FEB
+PY 2005
+VL 71
+IS 2
+PN Part 2
+AR 025103
+DI ARTN 025103
+PG 4
+SC Physics, Fluids & Plasmas; Physics, Mathematical
+GA 914RV
+UT ISI:000228246200003
+ER
+
+PT J
+AU Makeev, MA
+ Derenyi, I
+ Barabasi, AL
+TI Emergence of large-scale vorticity during diffusion in a random
+ potential under an alternating bias
+SO PHYSICAL REVIEW E
+LA English
+DT Article
+ID DISORDERED MEDIA; MOLECULAR MOTORS; FIELD; RATCHETS; SYSTEMS; DRIVEN;
+ MOTION
+AB Conventional wisdom indicates that the presence of an alternating
+ driving force will not change the long-term behavior of a Brownian
+ particle moving in a random potential. Although this is true in one
+ dimension, here we offer direct evidence that the inevitable local
+ symmetry breaking present in a two-dimensional random potential leads
+ to the emergence of a local ratchet effect that generates large-scale
+ vorticity patterns consisting of steady-state net diffusive currents.
+ For small fields the spatial correlation function of the current
+ follows a logarithmic distance dependence, while for large external
+ fields both the vorticity and the correlations gradually disappear. We
+ uncover the scaling laws characterizing this unique pattern formation
+ process, and discuss their potential relevance to real systems.
+C1 Univ Notre Dame, Dept Phys, Notre Dame, IN 46566 USA.
+ Lorand Eotvos Univ, Dept Biol Phys, H-1117 Budapest, Hungary.
+RP Makeev, MA, Univ Notre Dame, Dept Phys, Notre Dame, IN 46566 USA.
+EM ma...@us...
+ de...@el...
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+ LOPEZ E, 2003, PHYS RE...
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