ToolBus/PathPort Tool and Visualization Plugins
Beta Release

The following is a list of plugins that can be downloaded for use with the ToolBus/PathPort system. These are beta versions of the plugins and thus might well contain major bugs and other problems, so user beware. To install a beta version of a plugin, simply copy the bin version to the plugins directory of your ToolBus installation (install newer versions by overwriting the older version). [ NOTE: Do NOT put the src version in the plugins directory! ]

The default locations for the plugins directory are:

Windows		C:\Program Files\ToolBus\ToolBus-Distribution\ToolBus.app\Contents\Resources\Java\plugins
Mac OSX		/Applications/ToolBus/ToolBus-Distribution/ToolBus.app/Contents/Resources/Java/plugins
Linux/Solaris		$HOME/ToolBus/ToolBus-Distribution/ToolBus.app/Contents/Resources/Java/plugins

There is no requirement that you download all (or any) of the following plugins, though we strongly recommend it. Most are quite small and fast to download. For your convenience, we also make a combined download available from the ToolBus/PathPort beta version download page. Please check back periodically for new beta versions of plugins, or join the pathport-announce mailing list.

All plugins are open sourced under the LGPL except where noted.

• Local File System - Last updated 22Oct2004: bin (33.4 K), src (33.9 K)

  Makes the local file system of your desktop available via ToolBus. This ability is specifically NOT built into ToolBus so that it can be updated easily as there are a variety of ways that users are accustomed to viewing their file organizations. For example, MS Windows and Mac OSX users see very different interfaces for this task.

• DNA and Annotations - Last updated 13Jan2005: bin (908.2 K), src (541.7 K)

  View large DNA sequences, including whole bacterial chromosomes, along with their annotations (e.g. genes, SNPs). Shows multiple, and adjustable, zoom levels along with GC content. You can specify how each type of feature should be displayed and hide those features you don't want to see. Search for features of interest and select all or part of them for inclusion in groups.

• Small Sequence Manipulation - Last updated 13Jan2005: bin (736.2 K), src (3723.4 K)

  View and edit short nucleotide and amino acid sequences. Editing is supported by both text-based and graphical editors which allow feature-based editing. Provides simple analysis tools including translation, ORF finding and dot-plot analysis. Allows import and export of sequences in a variety of common sequence formats.

• Agarose Gel Electrophoresis - Last updated 22Oct2004: bin (99.2 K), src (72.5 K)

  Provides a simulation for a gel given a set of digested DNA. The user can adjust the voltage, time, and gel percentage and see what the resulting gel should look like before its actually run. This can be used to plan a gel run.

• Pathogen Background Information - Last updated 04Jan2005: bin (970.4 K), src (556.4 K)

  Browse through the background information for your (least?) favorite pathogen from CDC's or NIAID's A, B, or C lists. Major information categories (e.g. taxonomy, epidemeology, lab work, host list) are presented in a tabbed pane, with traversable web links provided you also have installed the "HTML Rendering" plugin (see below).

• Microarray - Last updated 13Jan2005: bin (7297.8 K), src (1139.5 K)

  View the results of both one and two color microarray, including time series, experiments. This plugin is able to visualize a wide variety of analysis results, including: dendograms, hierarchical and other types of clusterings, principle component analysis, raw data in tabular form, T and F test results, clasification profiles, and similarity nets. You can also build your own clusters around similarities to specific genes and compare different cluster results with one another.

• Sequence Alignment - Last updated 22Oct2004: bin (285.2 K), src (221.3 K)

  Examine (multiple) sequence alignments. You can edit the alignment, view the concensus sequence, as well as see overviews of the degree of concensus and hydrophocity.

• Phylogentic Tree - Last updated 14Jan2005: bin (655.1 K), src (199.9 K)

  This plugin also comes with a tool interface that supports the dynamic quering of a phylogenetic tree database for all the sequence bacteria (including archea) from RefSeq based on organism and gene annotation. In addition, you can query with your own DNA or protein sequences to include in the tree. The visualization also shows you the aligned sequences that gave rise to the tree.

• PCR and Hybridization Probes - Last updated 13Jan2005: bin (396 K), src (228 K)

  See the original sequence and both the PCR and hybridization probes that you designed. Shows all the probes in relationship to one another so you can pick the ones that give the best coverage. You can see the data in either graphical or tablular text form.

• Protein Interactions - Last updated 04Jan2005: bin (268.3 K), src (150.8 K)

  Examine the protein interactions of a particular pathway. VBI's protein network (pathway) web-service contains a growing database of infection pathways for the pathogens on the A, B, and C lists of the CDC and NIAID. Three different views give you a choice of how to visualize the network.

• BLAST/FASTA Similarity - Last updated 13Jan2005: bin (468.5 K), src (273 K)

  Displays the results of either a BLAST of FASTA search of one or more query sequences. You can see the data in either graphical or tablular text form. Links to web resources are also available for BLAST results.

• Large Sequence Comparison - Last updated 13Jan2005: bin (1197.4 K), src (271.4 K)

  Provides two ways of viewing the comparison (e.g. via MUMmer) of two large DNA sequences (e.g. bacterial chromosomes). One view shows the two sequences one above the other with their own features (e.g. genes, SNPs) shown, as well as the correspondences identified by the comparison. The second view is a scatter plot of correspondences.

• Generic XML - Last updated 04Jan2005: bin (27.4 K), src (37.4 K)

  This is primarily useful for developers of web-services so that they can examine the results returned to ToolBus by their services. It can also be used to examine data not recognized by any other plugin.

• Tutorial Example - Last updated 22Oct2004: bin (31.6 K), src (36.4 K)

  This is the plugin described in the tutorial. If you are thinking about writing your own plugin, you'll definitely want to get this one.

• Gene Group Suggestion (Prototype) - Last updated 22Oct2004: bin (767 K), src (715.3 K)

  This is a new variety of plugin that is designed to listen in on all of the data that comes into ToolBus and to find links between gene related items for the same or similarly annotated genes. The visualizer displays this information and makes it easy for the user to create new ToolBus groups that contain the various items so linked. Formation of these groups also depends upon support from the other visualizers containing this data. Currently, only the DNA and Annotations visualizer supports group suggestion.

• 2D-Gel + Mass Spectroscopy (Prototype) - Last updated 10Jan2005: bin (3127.9 K), src (2283.8 K)

  Visualizes 2D-Gels or proteins along with mass spectroscopy data obtained from cut spots taken from the gels. Both single MS and tandem MS experiments are supported.

• 2D-Gel Comparisons (Prototype) - Last updated 10Jan2005: bin (4887.6 K), src (3222.4 K)

  Visualizes multiple 2D-Gels and enables the comparison of spots between gels. This is intended as an aid in determining which spots to cut from a time series set of gels.