catalog

1. Introduction

2. Getting Started

[2.1] System Requirements

[2.2] Java WEB START Instructions

[2.3] Installation Instructions

[2.4] Download Microarray Data files

3. Quick Tour of BiologicalNetworks

[3.0] Features and Functionality of BiologicalNetworks

[3.1] Graphical User Interface

[3.2] Creating Pathway/Model

[3.3] Defining Pathways/Models

[3.3.1] Defining a Node

[3.3.2] Defining a Interaction/Process

[3.4] Exploring Curated Pathways

[3.5] Network statistical analysis

4. BiologicalNetworks Graphical User Interface

[4.1] BiologicalNetworks Components

[4.2] BiologicalNetworks Panes

[4.2.1] Project Pane

[4.2.2] Project Folders

[4.2.3] Pathways Pane

[4.2.4] Search Result Pane

[4.2.5] Palette Pane

[4.3] Menu, Toolbar and Model Kit

[4.3.1] Node Properties Editor

[4.3.2] Interaction/Process/Reaction properties Editor

[4.3.3] Compartment Editor

[4.4] Overview of Context Menus

5. BiologicalNetworks Modelling Environment

[5.1] Building a Pathway/Model

[5.1.1] Adding Biological Components

[5.1.2] Adding Interaction/Processes/Reactions

[5.1.3] Adding Compartments

[5.1.4] Editing Pathway/Model

[5.2] Managing Pathways/Models and SBML Support

[5.2.1] Saving Pathways/Models

[5.2.2] Importing Pathways/Models

[5.2.3] Exporting Pathways/Models

[5.3] Network statistical analysis

6. Data Management

[6.1] Pathway Representation

[6.2] Workspace

[6.3] Database Search

[6.3.1] Context Search

[6.3.2] Search by Attributes

[6.3.3] Quick Search

[6.3.4] Querying database to explore gene relationships

7. Working with Microarray Data

[7.1] Loading Microarray Data

[7.2] Color schemes and Visual styles settings

[7.3] Expression Experiment Viewer

[7.4] Expression viewer toolbar

[7.5] Filtering, Normalization and Data Transformation

[7.6] Sorting and searching over expression data

[7.7] Clustering of Experimental Data

[7.8] Clustering analysis results viewers

[7.9] GeneOntology terms overrepresentation analysis

8. Explore gene relationships with expression data

[8.1] Color network by expression values.

[8.2] Extract pathways from expression data.

[8.3] Build Pathways for selected expression values