BiologicalNetworks


BiologicalNetworks Quick Start Guide

Quick Start Guide demonstrates:




1.1 Downloading and Install BiologicalNetworks

Downloading BiologicalNetwork will begin by clicking "Free download" for Windows or "Mac OS X" for MacOS. BiologicalNetworks (download size: ~60 MB; download time: depending on your internet connection ~2 minutes). After downloading install BiologicalNetworks on your own computer and start application. If BiologicalNetworks does not start, send a request to HELP.

1.2 Hardware Requirements

Minimal configuration:

Windows
2GHz Intel CPU
Microsoft Windows XP/Vista/Windows 7
2Gb RAM
300MB Free Disk Space

Macintosh
1.8MHz PowerPC G4 or IntelMac
Mac OS X 10.4 and above
2Gb RAM
300MB Free Disk Space


2.0 Welcome Page

BiologicalNetworks appears first on the screen with the Welcome Page See Figure 1 and Project Panel. Welcome page of BiologicalNetworks contains a list of Driving Projects created by our users. Driving Projects are selected for their scientific merit in answering important biological questions and represent a broad range of research endeavors. At the same time Driving Projects stimulate the BiologicalNetworks project to improve its technologies and provide feedback on our work. Open these projects by clicking on the respective thumbnail.

Fig.1 Welcome Page

Fig.1 Welcome Page

Project Panel shows the database and your project contents See Figure 2

Fig.2 Project Panel
Fig.2 Project Panel

2.1 Exploring Opened Project/ Pathway

Node Properties.

To explore opened Project/Pathway:

If you click on the Node Properties Paneit it will show you details of the chosen bioentity. See Figure 3

Fig.3 Node Properties Panel

Fig.3 Node Properties Panel

There are default, editable, expandable and reference fields on the Node Properties Pane.

Default fields: non editable fields for example GeneOntology annotation which are loaded with the data;

Editable fields: fields that could be edited or additional annotation could be added and saved either to local file or to database;

Expandable fields: fields that themselves have internal structure. See Figure 4

Fig.4 Properties in window

4 Properties in window

If you double click on the top of Node Properties Panel it will show you all information available for this bioentity. Figure 5

Fig.5 Expanded Node Properties

Fig.5 Expanded Node Properties

Reference fields: fields that refer to Internet resource that have information about this bioentity. See Figure 6

Fig. 6 Example of reference field

Fig. 6 Example of reference field


2.2 Interaction/Process/Reaction properties

Click on the Process/Reaction node. The Process/Reaction properties Panel will appear. See Figure 6

Fig. 6 Interaction/Process Properties

Fig. 6 Interaction/Process Properties




3.0 Querying Data in BiologicalNetworks


3.1 Quick Search

The General Search box is located at the top of the Properties Pane. See Figure 7

Fig. 7 Quick search field

Fig. 7 Quick search field

There is also Choose Organism Option in the Search. See Figure 8

Fig.8 Choose Organism Option
Fig.8 Choose Organism Option

You can also Load you gene list (tab delimeted or Comma separated) form a file to Search in the Database.

Type your favorite gene name or keywords to search for all available information about it presented in our database.

Your search results will be listed in the Search Results Pane. See Figure 9

Fig.9 List Pane: quick search results
Fig.9 List Pane: quick search results

You can copy/paste rows from the List Pane to your active pathway, or save the search results as an individual group in the Groups/Clusters folder.


3.2 Save Search results

You can Save Your Search Results to Excel File and Build a Pathway from selected group of bioentities. See Figure 10

Fig.10 List Pane context menu.
Fig.10 -------

3.3 Analyze Search Results for GO terms

GO analysis, generates a table that functionally characterize your set of genes. See Figure 11

Fig.10 Add GO
Fig.11 Add GO

3.4 Add property columns to Search Results

Add Column - You can add any attribute for the list of attributes collected from many external public databases.See Figure 12

Fig.12 Add Column
Fig.12 Add Column

3.5 Querying Curated Pathways and Interaction Networks.

Search in Curated Pathways and Interaction Networks. See Figure 13

Fig.13 Curated Pathways and Interaction Networks search field
Fig.13 Curated Pathways and Interaction Networks search field

3.6 Querying Microarray data.

To search in Microarray data, use Search Box at the top of the Microarray DataSource Pane.

Microarray Data Pane contains results found for your search from the compendium of the microarray expression data collected from several data sources (i.e. Gene Expression Omnibus). See Figure 14

Fig.14 Microarray Data search
Fig.14 Microarray Data search

3.7 Querying Database to Build Pathways and explore Interaction Networks and gene relationships

Choosing Build Pathway from Search Results list, from opened network or pathway, from microarray experiment and practically from any list of genes opens BuildPathwayWizard Panel. See Figure 10


Build Pathway Wizard

BuildPathwayWizard allows you to create pathways, using molecular interaction data from the database.

It starts by suggesting several ways to determine starting entities, and then opens the Build Pathway dialog box.

Check entities for your pathway, See Figure 15

Fig.15 Input Node Selection
Fig.15 Build Input Node Selection

Choose an algorithm for pathway building, See Figure 16

Fig.16 Search Mode Selection
Fig.16 Search Mode Selection

Check the Filter option and set up the filter, if needed, See Figure 17

Fig.17 Build Pathway Filters Wizard
Fig.17 Build Pathway Filters Wizard

Press the Finish button to start data mining. The new pathway diagram appears in the Pathway Pane.

Refer to the Tutorials to learn more about the BuildPathway Wizard.



4.0 Exploring Curated Project/ Pathway

To explore a repository of our Curated Pathways:

Click Pathways DataSource tap in the left panel of application window to bring up Curated Pathways. See Figure 18

Fig.18 Curated Pathways Pane. Fig.18 Curated Pathways Pane.
Fig.18 Curated Pathways Pane.

The Curated Pathways tab pane has database tree panel.

Click the KEGG node to show available organisms in KEGG database.

After retrieving the data, 213 most popular organism nodes are appeared. (Number of nodes may vary from this value.) See Figure 18

Double click one of the organism nodes to show the accompanying pathways. See Figure 19

Fig.19 Curated Pathways: Organisms, Pathways, Reactions, Metabolites.
Fig.19 Curated Pathways: Organisms, Pathways, Reactions, Metabolites.

Double click one of the pathways shows list of reaction nodes. See Figure 19

To load the pathways into the Pathway Panel simply click Open Network. See Figure 20

The loaded pathways containing reactions, compounds and their interactions are drawn in model workspace window.

To get nice positioning force-directed layout is used.

Fig.20 Open curated pathways in the Main Pathway Window
Fig.20 Open curated pathways in the Main Pathway Window


Fig.21 Curated pathways
Fig.21 Curated pathways

4.1 Viewing Pathways

Open the Public Pathways, or Curated Pathways folder in the Curated Pathways Pane;

The pathway diagram appears in the Pathway Pane;

Use the Zoom by Rectangle, or Magnifier option to zoom in on parts of the pathway; See Figure 22

Use Force-Directed or Hierarchical Layout option to layout the pathway by cell localization. Refer to the Tutorials to learn more about pathway editing.

Fig.22 Zoom options
Fig.22 Zoom options

5.0 Working with Microarray Data

Use search on the top of Microarray DataSource Windows to find Microarray Data. See Figure 23

Fig.23 Microarray DataSource Pane
Fig.23 Microarray DataSource Pane

Loaded Microarray data opening in new tab. See Figure 24

Fig.24 Microarray Data
Fig.24 Microarray Data

Apply different clustering algorithms available from Analysis> Clustering>K-Means/Medians Clustering. See Figure 25

Fig.25 Clustering
Fig.25 Clustering

Clustering analysis results appear in the Project Panel.

Functionalities available from Microarray submenu and Microarray Experiment Manager Menu bar, allows the user to:

- sort the experiment by a particular sample.

- Create new> pathways as well as new groups from an expression experiment.

- Select a number of genes and create a group or a pathway from them.

- Expression data can be visually displayed on an existing pathway diagram by showing different shades of green/red depending on the fold change of expression.


5.1 Color network by expression values.

To overlay Expression Experiment results onto an existing pathway diagram:

  • Open an expression experiment;
  • Open a pathway of interest;
  • Press the Coloring by Expression Values Toolbar button to color the active pathway by expression values;
  • From drop down menu choose the sample time point you would like to visualize on the active Pathway Pane
Fig.26 Search microarray Fig.26 Search Pathway Fig.26 Color network
Fig.26 Color network


6.0 Sequence viewer.

To open Sequence:

  • Just select and open an existing sequence file from any desired file location by using standard File Open dialog.
  • Currently supported sequence file format is GBK and such file should have the same extension. Please expect upcoming support for a number of other file formats.
  • Now supported both one-sequence and multi-sequence (with locus list) gbk file formats.
  • Viewer supports Zooming feature, Scrollbar navigation, Color change for annotations and Disable/Enable feature for any type of annotations.
Fig.27
Fig.27 Sequence shown as splited into pieces for easely navigation Fig.28
Fig.28 Multi-locus Sequence with locus tags and properties panel for colors tuning.