ProViz User Manual

LaBRI

Developer: Florian Iragne

Developer: Bertrand Mathieu

Developer of the Tulip library: David Auber

1.1

This program is licensed under the terms of the GNU General Public License.

This documentation is licensed under the terms of the GNU Free Documentation License.

Abstract

Analysis of protein-protein interaction networks (PPIN) requires a combination of algorithmic and visualization tools, ideally integrated within a software platform that is itself integrated with access to local and distant data banks. We present a software tool called ProViz that provides highly-interactive visualization of large networks of interactions, integrated with data model under development in the intact european project.


Table of Contents

1. What is ProViz
What is ProViz?
2. ProViz interface
The main window
The graph view window
Zooming in and out
Moving in the view
Scaling elements
Chosing an element
The zoom box mouse mode
The selection box mouse mode
The move mouse selection mode
The mouse selection expand graph mode
The contextual menu
The Views tab
The views tree
View options
The menu and the toolbar
Opening a file
Importing PSI data files
Expand graph with local dataset
Saving files
Exporting PSI data files
Setting up user preferences
The recent file list
Printing and saving images
Obtaining help
Center view
Changing the layout of a view
The controlled vocabulary tree
Color code
Selection mecanisms
Using term selection
Finding CV terms in the tree
The properties tab
The property list
Links to external information
Using the comment field
Finding proteins with the properties panel
3. Tutorial
Introduction
Description of the ProViz interface
The menu bar
The tool bar
Right panel
Left panel
Using ProViz with a dataset in Tulip file format
Opening the file
Filtering Data
Saving modifications
Using graph layout
Using ProViz with a dataset in PSI-MI canonical format
Importing a PSI-mi canonical file
Saving modifications
Conclusion
4. Graph Extraction Policies
Definition
Introduction
Prerequisites
Available Policies
Tutorial
Example with a Two-Hybrid in Yeast Experiment
Example with data from high troughoutput methods
5. Graph fusion and datasets merging
Definition
Use of graph fusion
How to add interactions to a graph with queries over online databanks
6. Credits and License
A. ProViz installation
Requirements
Compiling from the sources

List of Tables

4.1.

List of Examples

2.1.