Javadoc: http://gsocpaver.github.io/Paver/

Installation:

There are 2 options for installation:
1. use the released .jar file. For a tutorial on the installation see “Get it!” tutorial here.

2. compile the source code from the online repository directly(https://github.com/GSOCPathbuilder/PathBuilder)

Using PathBuilder:

Pathbuilder is made up of two parts: building a pathway and changing the layout.

Building a pathway:

Building a pathway can be done using the menu item Plugins>>PathBuilder>>Build Pathway. This will get you to the following input window:

input window
input window

Settings:

Input Source: This can either be by a tab delimited text file, or by using the text box for manual input.

Input Type: This can either be connections or nodes. Connections are 2 data nodes connected by a line, nodes are individual data nodes which can later be connected by hand.

Input syntax:

connections:

SystemCode[:]Id [tab]  LineType [tab] SystemCode[:]Id

e.g: En:12340     normal      S:P123456

For connections, the syntax has to be exactly right, it has to contain all elements. It has to be a start node, followed by the line type, followed by the end node. A node contains a system code and an id, separated by colons.

The system code is the abbreviation of a public data source used to identify it. A full list of data sources with system codes can be found here. The id is the identifier used by the data source to identify the biological element. The line type can be a normal line with a straight line and ending with an arrow. Or a MIM-type interaction, all MIM-types available in the main PathVisio program are also available in PathBuilder. For more information on mim-types, see the PathVisio documentation here.

nodes:

Label [tab] Id [tab] DataSource

e.g: HSP90     3324      Entrez Gene

The syntax for individual nodes normally contains 3 elements, a label, an identifier and a data source.  A data source can be given by it’s full name, or by system code. An individual data node does not require all 3 elements to be given. Just 2 elements, the label and the identifier can also be used as input. Or a data node can be created based on just a label, or just an identifier. If just an identifier is given, this identifier will be the label as well.

Layout:

The layout can be changed by using Plugins>>PathBuilder>>Layout. The layout of the pathway is then reorganized with an algorithm. The algorithm used is the inverted self-organising map(ISOM) layout algorithm from the JUNG 2.0 Java library.