Network Workbench (NWB) Tool 1.0.0 Official Release
Release Notes
September 17, 2009

The Network Workbench Team

1. Introduction
2. General Description
3. Downloading and Installing
4. What’s New

1. Introduction

The Network Workbench team is pleased to announce the release of Network Workbench Tool 1.0.0! This release includes many new features from our previous 1.0.0 beta releases, as well as new features and improvements unavailable in any other version. New features include support for network community detection, two fast new implementations of Pathfinder Network Scaling, Weighted Page Rank, HITS, and a suite of algorithms for analyzing weighted networks.

The NWB tool 1.0.0 release also includes an updated and expanded 77-page tutorial, and a full walkthrough describing how Network Workbench community members can develop their own NWB/CIShell algorithms.

2. General Description

The Network Workbench Tool is a network analysis, modeling, and visualization toolkit for biomedical, social science, and physics research. It is a standalone desktop application requiring Java 1.4+ JRE. The tool installs and runs on Windows, Mac, and Linux platforms.

Network Workbench uses the Cyberinfrastructure Shell (CIShell) to bring together various algorithms used in the Network Science community. CIShell enables data and algorithms from disparate sources to work together, integrating with Java-based algorithms as well as algorithms developed in other programming languages such as FORTRAN, C, and C++.

CIShell, and by extension Network Workbench, is based on OSGi, a Java framework for plugin-based service-oriented architectures.

A listing of many of the algorithms available in Network Workbench can be found on the NWB Community Wiki.

If you would like to learn more about the Network Workbench project and the tool in general, please visit our main website http://nwb.slis.indiana.edu.

3. Downloading and Installing

Download the NWB tool at http://nwb.slis.indiana.edu/download.html. Once the file has completed downloading, unzip the .zip file and the NWB tool will be installed on your system.

In order to utilize NWB's plotting functionality, Mac and Linux users should install Gnuplot.

Note that certain versions of Mac OS X are not able to run some visualization algorithms in the NWB tool. The built-in GUESS visualization tool should be sufficient for most needs.

If you use the Network Workbench Tool or information at nwb.slis.indiana.edu for any publication, please cite as follows:

NWB Team. (2006). Network Workbench Tool. Indiana University, Northeastern University, and University of Michigan, http://nwb.slis.indiana.edu

4. What’s New

4.1 New since NWB 1.0.0 beta-5

4.1.1 Blondel Community Detection and Hierarchical Circular Viz

The NWB Tool now includes the ability to detect communities in networks at both high and low levels of detail. The results of Blondel Community Detection can be visualized in the Hierarchical Circular Visualization, which displays a network's communities and the connections between them.

4.1.2 Weighted Page Rank and HITS

The Network Workbench Tool now supports both the Weighted Page Rank and HITS algorithms, which are useful for rating the importance of nodes in networks based on their connections.

4.1.3 Pathfinder Network Scaling

Two new and improved Pathfinder Network Scaling algorithms are available in Network Workbench 1.0.0: Fast and MST Pathfinder Network Scaling. Both are useful for discovering the most important connections in a network, allowing the essential underlying structure to be viewed and analyzed more easily.

4.1.4 Discrete Network Dynamics Toolkit performance improvements

The Discrete Network Dynamics (DND) toolkit is a collection of algorithms for working with boolean and other logic networks with discrete states. Recent research, especially in the biological sciences, has shown that the dynamics of networks based on boolean and other discrete logics can mimic the dynamics of many complex processes as well as or better than approaches using complicated differential equations and complex timing rules. This release includes significant performance improvements to the Discrete Network Dynamics toolkit, supporting large networks via on-disk analysis, and decreasing overall runtime.

4.1.5 Additional features and fixes

Network Workbench 1.0.0 also includes many smaller improvements, including fixes for scientometrics functionality, better time slicing capabilities, improved tool stability, and more!

4.2 New since NWB 0.9.0

4.2.1 Improved GUESS Graph Visualization

Since our last stable release many small improvements have been made to the GUESS graph visualization, including more intuitive zooming capabilities and easier use of capabilities for resizing and colorizing by node values.

4.2.2 Weighted Network Suite

The Network Workbench Tool now includes 8 new fundamental algorithms for the creation and analysis of weighted networks.