Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools

Abstract BiologicalNetworks is a Systems Biology software platform for biological pathways analysis, querying and visualization of gene regulation and protein interaction networks, metabolic and signaling pathways.

It is equipped with filtering and visualization tools, to provide high quality, easily understood scientific presentations of your pathway analysis results.

BiologicalNetworks includes PathSys (see G6G Abstract Number 20068), a general-purpose scalable warehouse of biological information, which integrates over 20 curated and publicly contributed data sources, experimental biological data and PubMed data for the eight (8) representative genomes (S. cerevisiae, D. melanogaster, etc.).

BiologicalNetworks is also supported with curated pathways from a number of public databases like KEGG and various scientific studies.

BiologicalNetworks identifies relationships among genes, proteins, small molecules and other cellular objects, and draws pathways, linked to the original sources of information.

BiologicalNetworks is equipped with an enhanced graphic manipulation and query language, data mining and filtering tools, a storage mechanism and a generic data-importing mechanism through schema-mapping.

BiologicalNetworks Features/Capabilities:

Build Pathways features - Assemble your pathway using multiple search algorithms:

1) expend pathways;

2) find the shortest path between two genes or all the shortest paths covering a group of genes;

3) find only direct interactions;

4) find common targets or find common regulators;

5) find intersections with known curated pathways (for example with KEGG pathways).

Use filtering to include in your pathway only specific types of biological objects, such as genes, proteins, complexes, small molecules, cellular processes and others.

Use filtering to include in your pathway only specific types of biological interactions such as binding interactions, post-translational regulation, genetic interaction, expression regulation, enzymatic activity, molecular synthesis, transport, and others.

File Formats features -

1) You can export your pathway in several text (SIF, GML, XML, tab delimited) based formats;

2) SBML compatible: Level 1 & 2;

3) You can export your pathway in several graphical based formats.

Explore Pathways -

1) You can move, drag and drop biological components on the workspace, apply different intelligent layout algorithms, change and customize the shape and color of visual components;

2) Its automatic graphical optimization allows large pathways to be resized for optimal viewing;

3) You can add, modify or redefine interactions to further validate associations;

4) You can add Notes and Annotation to the model workspace;

5) You can Cut, Copy, Paste and Delete biological components;

6) Offers Undo and Redo operations. Up to 10 operations can be undone and redone using the icons in the toolbar;

7) You can zoom in /out/fit and Zoom in a selected region to investigate different types of associations and reference source descriptions. This feature becomes useful when the model size becomes big;

8) Offers direct links to the PubMed abstract and exact source sentence where findings are referenced;

9) You can view a variety of preloaded curated common pathways such as MAPK, p53, apoptosis, Wnt, Cell Cycle and all KEGG pathways; or specific networks and pathways from different scientific studies;

10) You can also export publication quality graphics in a variety of file formats.

Visual Data Abstraction features -

1) Offers Meta-Network, in which a node (Meta-Node) has its own internal network structure, supports multi-scale visualization of bio-networks, and is ideal for the ‘network’ of functional modules;

2) Meta-Nodes and Meta-Edges make the effective analysis of cellular processes and dealing with their complexity a lot easier;

3) You can double click the Meta-Nodes to collapse them to simplify your network, and then, double click the Meta-Nodes again to recover the original network;

4) Meta-Edges are automatically recalculated based on the connections of the 'nodes' inside the Meta-Nodes.

Network Analysis and Statistics features - Offers

1) Network statistics;

2) Finding cycles;

3) Pathway Homology;

4) Node and Connector Tables.

Import Gene/Protein Lists features -

1) Product can import Lists of Genes, Proteins and other biological entities from Yeast, Fly, etc;

2) Supports multiple ID types including: Unigene IDs, Accession Numbers, LocusLink, Swiss-Prot, Affymetrix GeneChip IDs, Gene Names and Gene Symbols;

3) Has the ability to create gene lists that are exportable for manipulation in other software packages.

Use your Microarray Gene Expression Data for Pathway Analysis -

1) Import your microarray gene expression data sets;

2) Filter, Normalize, make Data Transformations with your expression data;

3) Sort and search your expression data;

4) Apply different clustering methods to your experimental data;

5) Do clustering analysis in the context of biological pathways;

6) Overlay Expression Experiment results onto an existing pathway diagram;

7) Derive microarray expression correlation networks;

8) Extract pathways from expression data;

9) Find up or down regulated genes through various biological states and identify key regulators or targets of interest;

10) Build Pathways for selected expression values;

11) Work with groups/clusters and pathways in conjunction with expression experiments; and more.

BiologicalNetworks Recent Software Releases --

BiologicalNetworks v. 2.0 alpha --

01 May 2009 -

New features added:

1) New NetBeans professional platform from SUN Microsystems. The NetBeans platform is acknowledged as a standard by hundreds of thousands of developers of project oriented systems around the world, developing applications of all sizes and complexity:

2) Intuitive and customizable Visual Interface --

3) Research and analysis enhancements --

BiologicalNetworks v. 2.0 Beta --

07 January 2010 -

1) Sequence Analysis environment integrated into the main Window of BiologicalNetworks.

2) All the functionality of the older version 1.9 is carried over to the new platform.

3) Tested on Java 5 and 6, Windows and Mac OS X

4) Back end database now reaches 2 TB of data integrated from over 100 public data sources.

01 April 2010 -

1) Several additional functions and search options introduced into BuildPathwayWizard for extensive network navigation.

2) In addition to Gene Ontology (GO) annotations multiple additional ontology annotations were added:

3) MetaNodes functionality extended with representation of Curated Pathways as MetaNodes in MetaNetworks.

4) JMol viewer for 3D protein structure visualization added.

5) Network visualization and navigation extended: Layouts, Scaling, and Editing.

6) Sequence Analysis Module extended:

System Requirements

Contact manufacturer.


Manufacturer Web Site BiologicalNetworks

Price Contact manufacturer.

G6G Abstract Number 20067U

G6G Manufacturer Number 101833