TERANODE Design Suite (TDS) Biological Modeler

Category Cross-Omics>Pathway Analysis/Tools

Abstract Biological Modeler is a software application for modeling biological systems such as metabolic and signaling pathways. Biological Modeler has a graphical environment that suits the needs of both informatics and scientific users. Biological Modeler has a wide range of model and data import, export and annotation capabilities for integrative and qualitative modeling.

Biological Modeler also has strong support for kinetic simulations and data analyses based on rigorous biochemical and biophysical theories. Biological Modeler enables users to import pathway models from a number of sources or create their own using a graphical editor.

Biological Modeler's key features/capabilities include:

Graphical Pathway Editor --

1) Visual Editing - Graphical palette of objects and relationships can be used to schematically define a pathway.

2) Cut-and-Paste - Pathways or portions of pathways are easily copied or deleted using familiar graphical cut-and-paste procedures with the mouse.

3) Hierarchical Pathways - Functional and physical hierarchies can be definable at any level and can be nested together.

4) User-defined Properties - Pathway objects and relationships can be modified to track data about entities in the pathway. Property types include numeric, text, formulas, images, files, and others.

5) Import and Export - Pathways can be imported from external repositories such as Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be shared with other applications through the Systems Biology Markup Language (SBML).

6) Broad Pathway Support - Metabolic pathways, signaling pathways, biochemical reactions, gene regulation, protein interactions, and more can be imported or created.

Pathway Analytics --

1) Data Visualization - Data can be mapped and color-coded to pathways to visualize expression and concentration levels from experiments.

2) Scientific Plotting - Simulation results and experiment data can be plotted and visualized including both discrete and time-series data.

3) Programming-free Simulation - Kinetic simulations are automatically created for pathways. Simulations are performed with state-of-art numerical methods for comparison with experiment data.

4) Scientific Plotting - Simulation results and experiment data can be plotted and visualized including both discrete and time-series data.

5) Parameter Sets - Behavioral analysis can be performed by varying parameters of the pathway. Parameter sets provide a means to investigate behavior of a pathway (e.g., sensitivity analysis).

6) Curve-fitting and Optimization - Pathway parameters can be automatically estimated to fit simulated results to experiment data.

7) Customizable Reports - Data and pathway properties reports are easily defined and available for searching, sorting, export, or printing.

Data Integration --

1) Dynamic Data Set - Biological Modeler is fully integrated with Protocol Modeler (an additional module) allowing data from the lab to automatically link to analysis.

2) Import and Export - Data can be imported for analysis from Affymetrix, Excel, Microarray Gene Expression Markup Language (MAGE-ML), comma-separated values (CSV), and other formats, and can be exported in the CSV format.

Collaboration --

1) Search - Pathways and the objects in pathways are fully searchable by properties and property values.

2) Annotation - Objects in a pathway can be annotated with file attachments, drawings, text notes, web links, and more to provide contextual or historical information about analysis and findings.

3) Check-in/Check-out. Revision control over changes to pathways in a multi-user environment is controlled using check-in/check-out of the TERANODE Model Server.

System Requirements

Hardware

Recommended Teranode Database System Setup

Application Server Setup

Manufacturer

Manufacturer Web Site TERANODE Design Suite (TDS) Biological Modeler

Price Contact manufacturer.

G6G Abstract Number 20156

G6G Manufacturer Number 102589