Sci 2

SCIENCE OF SCIENCE (SCI2) TOOL

A tool for science of science research & practice http://sci2.cns.iu.edu

Scott Weingart, Hanning Guo, Katy Brner, Kevin W. Boyack, Micah W. Linnemeier, Russell J. Duhon,
Project Investigators: Katy Brner and Kevin W. Boyack (SciTech Strategies Inc.) Patrick A. Phillips, Chintan Tank, and Joseph Biberstine (2010) Science of Science (Sci2) Tool User
Programmers: Micah W. Linnemeier, Russell J. Duhon, Patrick A. Phillips, Chintan Tank, and Joseph Biberstine Manual. Cyberinfrastructure for Network Science Center, School of Library and Information Science,
Users, Testers & Tutorial Writers: Scott Weingart, Hanning Guo, Katy Brner Indiana University, Bloomington.

Cyberinfrastructure for Network Science Center Katy Brner and Angela Zoss (2010) Plug-and-Play Macroscopes Tutorial. International Conference on
School of Library and Information Science Social Computing, Behavioral Modeling and Prediction, Bethesda, MD.
Indiana University, Bloomington, IN
http://cns.slis.indiana.edu Katy Brner (2010) Science of Science Research and Tools (12 Tutorials). Reporting Branch, Office of
Extramural Research/Office of the Director, National Institutes of Health, Bethesda, MD.
Introduction
The Science of Science (Sci2) Tool (http://sci2.cns.iu.edu) is a modular toolset specifically designed for the study of Tutorial #01: Science of Science Research
science. It supports the temporal, geospatial, topical, and network analysis and visualization of datasets at the Tutorial #02: Network Science / Information Visualization
micro (individual), meso (local), and macro (global) levels. Tutorial #03: CIShell Powered Tools: Network Workbench and Science of Science Tool
The web site at http://sci2.cns.iu.edu supports free registration and download as well as topic queries via Ask an Tutorial #04: Temporal AnalysisBurst Detection
Expert forms. Tutorial #05: Geospatial Analysis and Mapping
Tutorial #06: Topical Analysis & Mapping
Functionality Tutorial #07: Tree Analysis and Visualization
Users of the tool can Tutorial #08: Network Analysis and Visualization
Read datasets in many different formats including CSV. Tutorial #09: Large Network Analysis and Visualization.
Perform extensive data preprocessing - data cleaning, deduplication, filtering, network extraction. Tutorial #10: Using the Scholarly Database at IU
Run different types of analysis with some of the most advbanced algorithms available. Tutorial #11: VIVO National Researcher Networking
Use visualizations to interactively explore, understand, and communicate results. Many visualizations use an Tutorial #12: Future Developments
easy to read reference system, automatic legend design, and 'fine print' that documents who created the
visualization when using what data set. Agency Adoption
Automatically record their workflows via audit trail documentation. The tool is actively used in peer reviewed research and agencies such as the National Science
Compare results across agency as the very same analyses workflows can be applied to agency internal and/or Foundation, the National Institutes of Health, and the US Department of Energy.
proprietary data.
Share datasets and algorithms across scientific boundaries, e.g., new algorithm plugins can be easily added by
non computer scientists.
In November 2010, more than 150 different preprocessing, analysis, modeling, and visualization algorithms are
available, see listing on back.

System Architecture
The Sci2 Tool is built on the Cyberinfrastructure Shell (CIShell) (CIShell.org), an open source software framework
for the easy integration and utilization of datasets, algorithms, tools, and computing resources. CIShell is based
on the OSGi R4 Specification and Equinox implementation (OSGI.org).

Three other tools: Network Workbench (http://nwb.slis.indiana.edu), TEXTrend (http://www.textrend.org) lead by

George Kampis, Etvs University, Hungary a tool with natural language processing (NLP), classification/mining,
and graph algorithms for the analysis of business and governmental text corpuses, and the Epidemiology Tool
under development are CIShell powered and plugins from these efforts/tools can be plug-and-played in the Sci2
Tool. Simply copy a *.jar file from the /plugin directory of one tool into the /plugin directory of another tool and
the algorithm or tool becomes available in the menu system. As the functionality of OSGi/CIShellbased software Please cite as
frameworks improves and the number and diversity of dataset and algorithm plugins increases, the capabilities Sci2 Team. (2009). Science of Science (Sci2) Tool. Indiana University and SciTech Strategies,
of custom tools will expand. http://sci2.cns.iu.edu.

Documentation Acknowledgements
The tool comes with extensive documentation such as a 110 page user manual that exemplifies how to use the This work is supported in part by the Cyberinfrastructure for Network Science Center and the School
tool for science of science research and science policy and 12 two hour tutorials originally designed for the of Library and Information Science at Indiana University, the National Science Foundation under
National Institutes of Health. Grant No. SBE-0738111 and IIS-0513650, and the James S. McDonnell Foundation.
 2
Data Preparation 3
Sci2 Sample Workflows
Data Formats
Database
ISI Preprocessing 5
GraphML (*.xml or *.graphml) Merge Identical ISI People General Networks Modeling
Extract Top N% Records Extract Top Nodes Networks
XGMML (*.xml) Suggest ISI People Merges
Extract Top N Records Extract Nodes Above or Below Value Random Graph
Pajek .NET (*.net) Merge Document Sources
Delete Isolates
Create Document Source Merging Table Aggregate Data Watts-Strogatz Small World
Pajek .Matrix (*.mat) Extract Top Edges
NWB (*.nwb) Match References to Papers Barabsi-Albert Scale-Free
Temporal Extract Edges Above or Below Value ---------------------------------------------
TreeML (*.xml) ---------------------------------------------
Slice Table by Time Remove Self Loops TARL (Topics, Aging and Recursive Linking)
Extract Authors
Edgelist (*.edge) Trim by Degree
Extract Documents
Scopus csv (*.scopus) Geospatial MST-Pathfinder Network Scaling
Extract Keywords
NSF csv (*.nsf) Extract ZIP Code Fast Pathfinder Network Scaling
Extract Document Sources
CSV (*.csv) ---------------------------------------------
---------------------------------------------
ISI (*.isi) Topical Snowball Sampling (N nodes)
Extract Authors by Year
Normalize Text Node Sampling
Bibtex (*.bib) Extract References by Year
Edge Sampling
1 Endnote (*.enw) Extract Original Author Keywords by Year
Extract New ISI Keywords by Year
---------------------------------------------
Symmetrize
File ---------------------------------------------
Extract Authors by Year for Burst Detection
Dichotomize
Multipartite Joining
Load Extract Documents by Year for Burst Detection
---------------------------------------------
Load and Clean ISI File Extract Original Author Keywords by Year for Burst Detection
Merge 2 Networks
--------------------------------------------- Extract New ISI Keywords by Year for Burst Detection
Read Directory Hierarchy Extract References by Year for Burst Detection
--------------------------------------------- ---------------------------------------------
Save Extract Longitudinal Summary
--------------------------------------------- ---------------------------------------------
View Extract Co-Author Network
View with ---------------------------------------------
--------------------------------------------- Extract Author Citation Network
Merge Node and Edge Files Extract Document Citation Network (Core Only)
Split Graph to Node and Edge Files Extract Document Citation Network (Core and References)
--------------------------------------------- Extract Document Source Citation Network (Core Only)
Preferences Extract Document Source Citation Network (Core and References)
--------------------------------------------- ---------------------------------------------
Converter Graph Extract Document Co-Citation Network (Core Only)
--------------------------------------------- Extract Document Co-Citation Network (Core and References)
Exit Extract Document Source Co-Citation Network (Core Only)
Extract Document Source Co-Citation Network (Core and References)
Extract Author Co-Citation Network
---------------------------------------------
Extract Author Bibliographic Coupling Network
Extract Document Bibliographic Coupling Network

Micro
Extract Document Source Bibliographic Coupling

NSF
Individual Level Studies Merge Identical NSF People

NSF awards for one scholar

---------------------------------------------
Extract Investigators
Extract Awards
4 Analysis Degree & Strength
are analyzed to understand Extract Organizations Temporal Average Weight vs End-point Degree
--------------------------------------------- Burst Detection Strength Distribution
temporal patterns and Extract Co-PI Network Weight Distribution
co-investigator network.
6
Geospatial Randomize Weights
General Geocoder ---------------------------------------------
Create Merging Tables Yahoo Geocoder Blondel Community Detection Visualization
Meso Merge Entities
--------------------------------------------- Topical
---------------------------------------------
HITS
General
GnuPlot
Burst Detection
Institution Level Studies Custom Table Query
Custom Graph Query Unweighted & Directed
Image Viewer

--------------------------------------------- Networks Node Indegree Temporal

ISI publication data from four Extract Raw Tables from Database Network Analysis Toolkit (NAT) Node Outdegree Horizontal Bar Graph
Unweighted & Undirected Indegree Distribution
network science researchers Text Files Node Degree Outdegree Distribution Geospatial
are studied to understand Remove ISI Duplicate Records Degree Distribution --------------------------------------------- Geo Map (Circle Annotations)
Remove Rows with Multitudinous Fields --------------------------------------------- K-Nearest Neighbor
temporal patterns and --------------------------------------------- K-Nearest Neighbor (Java) Single Node In-Out Degree Correlations
Geo Map (Colored-Region Annotations)

co-author networks. Extract Directed Network Watts-Strogatz Clustering Coefficient

Watts Strogatz Clustering Coefficient over K
--------------------------------------------- Topical
Extract Bipartite Network Dyad Reciprocity RefMapper
Extract Paper Citation Network --------------------------------------------- Arc Reciprocity ---------------------------------------------
Diameter
Macro Extract Author Paper Network
--------------------------------------------- Average Shortest Path
Shortest Path Distribution
Adjacency Transitivity
---------------------------------------------
Science Map via 554 Fields
Science Map via Journals
Extract Co-Occurrence Network Weak Component Clustering
Global Level Studies Extract Word Co-Occurrence Network Node Betweenness Centrality
---------------------------------------------
Strong Component Clustering
---------------------------------------------
Networks
Extract Co-Author Network GUESS
Extract Reference Co-Occurrence Weak Component Clustering Extract K-Core ---------------------------------------------
USPTO patent data on (Bibliographic Coupling) Network Global Connected Components Annotate K-Coreness Radial Tree/Graph (prefuse alpha)
---------------------------------------------
influenza downloaded from ---------------------------------------------
Extract K-Core
--------------------------------------------- Radial Tree/Graph with Annotation (prefuse beta)
Extract Document Co-Citation Network HITS Tree View (prefuse beta)
the Scholarly Database is --------------------------------------------- Annotate K-Coreness PageRank Tree Map (prefuse beta)
---------------------------------------------
geolocated by country of patent Detect Duplicate Nodes
HITS Weighted & Directed
Force Directed with Annotation (prefuse beta)
Update Network by Merging Nodes Fruchterman-Reingold with Annotation (prefuse beta)
holder. Number of patents and HITS ---------------------------------------------
Weighted & Undirected Weighted PageRank
patent citations are shown. Clustering Coefficient
DrL (VxOrd)
Specified (prefuse beta) Output formats:
Nearest Neighbor Degree --------------------------------------------- JPEG (*.jpg)
Strength vs Degree Circular Hierarchy PDF (*.pdf)
PostScript (*.ps)