Network Workbench Tool User Manual 1.0.0 Getting Started General Tutorial Domain Specific: Information Science Tutorial Domain Specific: Social Science Tutorial Domain Specific: Scientometrics Tutorial Updated 09.16.2009 Project Investigators: Dr. Katy Börner, Dr. Albert-László Barabási (Northeastern University), Dr. Santiago Schnell (University of Michigan), Dr. Alessandro Vespignani, Dr. Stanley Wasserman, and Dr. Eric A. Wernert Programmers: Weixia (Bonnie) Huang, Russell J. Duhon, Micah W. Linnemeier, Patrick Phillips, Chintan Tank, Joseph Biberstine, Timothy Kelley, Duygu Balcan, Mariano Beiró (Universidad de Buenos Aires, Argentina), Bruce W. Herr II, Santo Fortunato (Institute for Scientific Interchange Foundation, Torino, Italy), Ben Markines, Felix Terkhorn, Heng Zhang, Megha Ramawat, César A. Hidalgo (Harvard University), Ramya Sabbineni, Vivek Thakre, Ann McCranie, Alessandro Vespignani, and Katy Börner Users, Testers & Tutorial Writers: Katy Börner, Angela Zoss, Hanning Guo, Scott Weingart, Ann McCranie, Mark A. Price (at Indiana University unless otherwise specified) Cyberinfrastructure for Network Science Center School of Library and Information Science Indiana University, Bloomington, IN http://cns.slis.indiana.edu For comments, questions or suggestions, please post to the [email protected] mailing list. 1 Table of Contents 1. GETTING STARTED.............................................................................................................................................4 1.1 INTRODUCTION .....................................................................................................................................................4 1.2 DOWNLOAD AND INSTALL ....................................................................................................................................4 1.3 CUSTOMIZING NWB.............................................................................................................................................6 1.4 USER INTERFACE ..................................................................................................................................................7 1.5 WORKFLOW DESIGN.............................................................................................................................................8 2. SAMPLE DATASETS AND SUPPORTED DATA FORMATS.........................................................................9 2.1 SAMPLE DATASETS...............................................................................................................................................9 2.2 DATA FORMATS..................................................................................................................................................10 3. CODE LIBRARY ..................................................................................................................................................11 3.1 OSGI PLUGINS....................................................................................................................................................11 3.2 CISHELL PLUGINS ..............................................................................................................................................11 3.3 CONVERTER PLUGINS .........................................................................................................................................12 3.4 ALGORITHM PLUGINS .........................................................................................................................................12 3.4.1 Preprocessing .............................................................................................................................................12 3.4.2 Analysis.......................................................................................................................................................13 3.4.3 Modeling.....................................................................................................................................................13 3.4.4 Visualization ...............................................................................................................................................14 3.5 SUPPORTING LIBRARIES......................................................................................................................................14 3.6 INTEGRATED TOOLS ...........................................................................................................................................14 3.6.1 GUESS........................................................................................................................................................14 3.6.2 Gnuplot .......................................................................................................................................................14 4. GENERAL TUTORIAL .......................................................................................................................................14 4.1 LOAD, VIEW, AND SAVE DATA...........................................................................................................................14 4.2 DATA CONVERSION SERVICE..............................................................................................................................16 4.3 COMPUTE BASIC NETWORK STATISTICS.............................................................................................................16 4.4 MODELING..........................................................................................................................................................17 4.4.1 Random Graph Model ................................................................................................................................17 4.4.2 Watts-Strogatz Small World........................................................................................................................18 4.4.3 Barabási-Albert Scale Free Model .............................................................................................................19 4.5 TREE VISUALIZATIONS .......................................................................................................................................20 4.5.1 Tree View Visualization..............................................................................................................................20 4.5.2 Tree Map Visualization...............................................................................................................................20 4.5.3 Balloon Graph Visualization ......................................................................................................................21 4.5.4 Radial Tree Visualization ...........................................................................................................................22 4.5.5 Radial Tree/Graph with Annotation ...........................................................................................................23 4.6 GRAPH VISUALIZATIONS ....................................................................................................................................23 4.6.1 JUNG-based Circular, Kamada-Kawai, Fruchterman-Rheingold, and Spring Layouts............................23 4.6.2 Prefuse-based Specified, Radial Tree/Graph, Force Directed, and Fruchterman-Rheingold, and Small World Layouts......................................................................................................................................................24 4.6.3 GUESS Visualizations ................................................................................................................................24 4.6.4 DrL Large Network Layout.........................................................................................................................27 4.6.5 LaNet ..........................................................................................................................................................27 4.6.6 Circular Hierarchy .....................................................................................................................................28 4.7 SAVING VISUALIZATIONS FOR PUBLICATION......................................................................................................28 5. DOMAIN SPECIFIC: INFORMATION SCIENCE..........................................................................................28 5.1 READ AND DISPLAY A FILE HIERARCHY.............................................................................................................28 5.2 ERROR AND ATTACK TOLERANCE OF NETWORKS ..............................................................................................28 5.3 STUDYING PEER-TO-PEER NETWORKS ...............................................................................................................28 2 6. DOMAIN SPECIFIC: SOCIAL SCIENCE ........................................................................................................28 6.1 LOAD DATA........................................................................................................................................................29 6.2 BASIC NETWORK PROPERTIES ............................................................................................................................29 6.3 NETWORK ANALYSIS..........................................................................................................................................30