The Sci2 Tool is an 'empty shell' filled with plugins. Some plugins run on the core architecture, OSGi and CIShell (see Section 7 Extending the Sci2 Tool). Others convert loaded data into in-memory objects, formatted for different algorithms to read it. The algorithm plugins themselves can be divided into different menus, in this case data preparation, preprocessing, analysis, modeling and visualization. Users are not limited to using pre-packaged plugins; instead, they can create, download, share, and import their own.

There are two ways plugins can be added to the menu. First, if an algorithm is listed in the default_menu.xml file, which is found in the configuration/ directory of a CIShell tool, it is added in the place specified by the default_menu.xml file. Second, if an algorithm is not listed in this file, but has specified a menu_path property in the algorithm.properties file, the menu manager CIShell service will add it to the appropriate menu, as described in the by the menu_path property's value. For example, Analysis/additions will place an algorithm on the bottom of the Analysis menu.

It is possible to extend Sci2 Tool, by adding plugins related to database functionalities and Cytoscape tool (open source software platform for visualizing networks).

By adding the plugins related to database functionalities, the Sci2 Tool can support the creation of databases from ISI and NSF files. Database loading improves the speed and functionality of data preparation and preprocessing. While the initial loading can take quite some time for larger datasets (see sections 3.4 Memory Allocation and 3.5 Memory Limits) it results in vastly faster and more powerful data processing and extraction.

Cytoscape (http://www.cytoscape.org) is an open source software platform for visualizing networks and integrating these with any type of attribute data. Although Cytoscape was originally designed for biological research, now it is a general platform for network analysis and visualization. A variety of layout algorithms are available, including cyclic, tree, force-directed, edge-weight, and yFiles Organic layouts. Cytoscape tool can also be added to the Sci2 Tool as a plugin, permitting that the networks generated at Sci2 be visualized in Cystoscape.

To add Database, Cytoscape, Congressional District Geocoder, and New ISI File Format plugins to Sci2

  1. Download these files that contain additional plugins to add Database, Balloon Graph, Cytoscape, Congressional District Geocoder, and New ISI File Format plugins to Sci2:
    1. Sci2 v. 0.5.2 beta or older
      1. Sci2 Database plugins - DatabasePlugins.zip (unzip to obtain the jar files that will be inside a folder named DatabasePlugins) - Note the Database plugins should only be used with Sci2 v0.5.2 alpha or older
      2. ISI Web of Science file format - WOS-plugins.zip - plugin provides the support for the newest version of the Web of Science data format, see ISI (*.isi) for more information
      3. UCSD Map of Science  - edu.iu.sci2.visualization.scimaps_0.1.0.jar - Note this plugin is for should only be used with Sci2 v1.0 beta or older
      4. Update Temporal Bar Graph for European dates - edu.iu.sci2.visualization.temporalbargraph_0.0.10.jar - plugin fixes the temporal bar graph plugin to work with European date format.
      5. Update Extract Word Co-Occurrence Network - edu.iu.nwb.composite.extractcowordfromtable_1.0.1.jar - plugin fix creates isolated nodes for unique record ID
      6. Twitter Reader - edu.iu.sci2.reader.twitter_1.0.0.jar pulls information from Twitter. For more information on how to use this algorithm, (currently not working) see Twitter Reader Documentation.
    2. Sci2 v. 1.0 beta or older
      1. ISI Web of Science file format - WOS-plugins.zip - plugin provides the support for the newest version of the Web of Science data format, see ISI (*.isi) for more information
      2. UCSD Map of Science  - edu.iu.sci2.visualization.scimaps_0.1.0.jar - Note this plugin is for should only be used with Sci2 v1.0 beta or older
      3. Update Temporal Bar Graph for European dates - edu.iu.sci2.visualization.temporalbargraph_0.0.10.jar - plugin fixes the temporal bar graph plugin to work with European date format.
      4. Update Extract Word Co-Occurrence Network - edu.iu.nwb.composite.extractcowordfromtable_1.0.1.jar - plugin fix creates isolated nodes for unique record ID
      5. Twitter Reader - edu.iu.sci2.reader.twitter_1.0.0.jar pulls information from Twitter. For more information on how to use this algorithm, (currently not working) see Twitter Reader Documentation.
    3. Current Release 
      1. Balloon Graph - BalloonGraph.zip (unzip to obtain the jar files that will be inside a folder named BalloonGraph)
      2. Cytoscape network visualization plugin - org.textrend.visualization.cytoscape_0.0.3.jar
      3. Congressional District Geocoder 
  2. You will have to extract these files before you copy them into plugins directory in the Sci2 folder
  3. Open the Sci2 folder and go to the plugins directory:

  4. Copy the plugin files themselves (not the folders that contain them) into the directory /plugins of Sci2 directory:



  5. Download the file default_menu.xml by right-clicking and saving the link as an XML file. Then copy this file into the directory configuration/ under Sci2 directory, replacing the older version of this file. This file specifies where each plugin added will be located at the menu. Note, this step only applies if you have downloaded the database plugins for Sci2 v0.5.2 alpha or older.
  6. The next time the Sci2 Tool is loaded after this modifications, these additional plugins will appear as new menu items.

Algorithms available at extended version

Menus at Extended Version

As stated before, this additional plugins will appear as new menu items in the Sci2 Tool.

Figure 2.1: Menus in the extended version of Sci2.

How Algorithms are Added to the Menu

There are two ways algorithms are added to the menu. First, if an algorithm is listed in the default_menu.xml file, which is found in the configuration/ directory of the Sci2 Tool, it is added in the place specified by the default_menu.xml file. Secondly, if an algorithm is not listed in this file, but has specified a menu_path property in the algorithm.properties file, the menu manager CIShell service will add it to the appropriate menu, as described in the by the menu_path property's value (for example, Analysis/additions will place an algorithm on the bottom of the Analysis menu).