PaViAn Files

This is the ReadMe for PaViAn 1.1

	What is it?
  	-----------

PaViAn is a tool to quickly retrieve and visualize biological pathways. 
Using the visualization different analysis techniques can be applied.


	Author
	------

PaViAn was developed by Raffael Fassler and Aspasia Ploubidou at the Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) in Jena, Germany.


 	The Latest Version
  	------------------

Details of the latest version can be found on the SourceForge web site.
http://sourceforge.net/projects/pavian-project/


  	Documentation
  	-------------

PaViAn has been published as a Diploma Thesis in the Faculty of Mathematics and Informatics of the Friedrich-Schiller-Universität Jena.


	Installation
  	------------

Simply copy all files into one directory and run the jar file.
http://sourceforge.net/projects/pavian-project/


	Contacts
	--------

Please see the support information on 
http://sourceforge.net/projects/pavian-project/support
and use the tracker feature to report bugs or demand features
http://sourceforge.net/tracker/?group_id=513771



1.	System Requirements
	a. Input Specifications
2.	Quick Start
3.	Load a Data File
	a.	Enter Proteins manually
4.	Display a Pathway
	a.	Score and Sort
	b.	Load an existing Pathway
5. 	Integrate Data
6.	Display Controls
7.	Features

1 . System Requirements:

Java 1.6 Update 24 or later
15MB free disk space 
Internet connection
All files in one directory with write access


2. Quick Start

Run the ?PaViAn x.x.jar? file.  Open the menu and click ?Load Example Data Set?.
After a couple of seconds the drop-down box will be filled with the retrieved 
pathways. Select the pathway of choice and the visualization starts.
Click the Color by E(X)presion button and then Records to show data inetgration.
See 5. Display Controls and 6. Features for more details.


3. Load a Data File

Open the menu and click Load Data File. After the file was selected a dialog 
will pop up. Enter the columns and rows of the IDs and the data values. 
Also enter the number of the first row with an data record and the number of 
the worksheet. The file will be loaded and the retrieval starts afterwards.


3.a. Enter Proteins Manually

Open the menu and click Load a single Protein. A dialog will pop up.
Enter a valid ID and the corresponding expression value. Enter 0 if no data 
is available. If a file is loaded then the protein is added to the existing list.
If not a new list is created. Multiple IDs can be added this way. Retrieval 
starts after the last record is submitted.


4. Display a Pathway

Displaying a pathway requires a loaded data file or a manually entered protein.
Matching pathways are listed in the drop-down box. Select the pathway of choice
and the visualizations starts.


4.a Scoring and Sorting of Pathways

Click the Score and Sort button. A dialog will pop up. Select select to sorting
options. Either with respect to the number of included records or the total
amount of expression lavel changes. the results are copied automatically into
the clip board (use the paste function of the operating system). Click the check
box if the resulst should be presented in an extra panel. 
Even if it can be used beforehand, the scoring and sorting is only valid for 
the entire data set if the retrieval has stopped!


4.b Load an existing Pathway

Displaying a pathway requires a loaded data file or a manually entered protein.
Open the menu and click Load an existing Pathway. Select a KGML file and the 
visualization starts.


5. Data Integration

After loading a data file or entering a protein manually and displaying a
pathway data can be integrated into the visualization.
Click the Color by E(X)presion button and then Records to show data inetgration.



6. Display Controls

	- Hit the space bar in order to run the layout algorithm
	- left-click the background and drag it in any direction in order 
	  to pan the view
	- right-click the background and drag it up or down in order to
	  zoom in and out
	- click and drag a node to change its position
	- hold ctrl and drag a node to move the entire subgraph attached to
	  that node
	- hold shift and click a node to de/select a node
	- right-click anywhere to open the pop-up menu
	- hover over a node to view quick information at the left text panel
	- double click a node to get more information in an extra panel
	- select a single node, open the pop-up menu and search in Kegg and
	  UniProt for even more information in two browser tabs