PathwayLab

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

Abstract PathwayLab is InNetics' product suite designed to analyze, visualize, and document biochemical pathways. PathwayLab is enabling discovery researchers to visualize and document pathways and associated data related to their disease focus.

By building pathway models that can integrate kinetic, gene expression, and functional data, PathwayLab becomes an efficient hypothesis test bench for prediction and analysis of disease pathways.

This will enable scientists to generate new insights and to better understand biological disorders and potential drug targets.

PathwayLab helps scientists to more efficiently elucidate disease pathways and protein functionality, empowering them to put targets into context. This supports better-informed decisions.

It is also possible to use the software as a communication and documentation tool, in order to capture and analyze large quantities of complex information from different sources and to make it available for those involved in common projects.

PathwayLab is an in silico pathway analysis tool, enabling pharmaceutical R&D to reach their target decisions faster and with higher accuracy.

PathwayLab allows visualization, documentation and in silico analysis of biochemical pathways.

Products overall features/capabilities include:

1) Easy to create and store new reaction objects with user specified kinetics.

2) Efficient transient analysis (simulation) and Metabolic Control Analysis (MCA).

3) Drag-n-drop component libraries based on Systems Biology Graphical Notation (SBGN).

4) Web export deployment of pathway drawings.

5) Exports to Mathematica, MATLAB, and SBML.

PathwayLab Research Edition --

Biosimulation - Advances Understanding of Pathway Mechanisms --

PathwayLab Research Edition reduces the complexity of pathways and gives you the ability to improve the quality of new hypothesis resulting in more efficient use of wet-bench experiments.

PathwayLab provides you with the tools to generate, analyze, and predict behavior in biochemical pathways. The knowledge about reaction behavior can be easily set in a pathway diagram and tested by simulations or sensitivity analysis where the results are presented in pathway diagrams.

1) Easy to Create and Manage Pathway Information - PathwayLab Publishing Edition is your intuitive tool for drawing pathways and is the entry point for the PathwayLab suite.

The tool serves both as the easy to use pathway drawer as well as a structured pathway model builder making the pathway diagrams and models accessible and searchable for the whole organization.

2) Easy Integration of Database Information - PathwayLab enables researchers to easily create dynamic pathway graphs, to integrate both proprietary pathway information with information from public sources, and to make that combined information available to the entire organization, through an easy-to-use web-based interface.

3) Flexible and Open Solution - The PathwayLab suite is a flexible solution that offers many customization opportunities. It supports multiple data types, which can be imported into PathwayLab.

Models and data developed in PathwayLab can also be easily exported to other existing applications.

4) Standards Compatible - PathwayLab is compatible with standard MS-Office products making it easy for anyone to open and view PathwayLab documents. It also supports several standard Extensible Markup Language (XML) formats.

5) Drawing and Layout Optimization - PathwayLab can be used to build structured pathways from ready made building blocks representing any combination of pathway substances and reactions, and makes them easy to arrange by optimization algorithms.

6) Dynamic Simulation of Biochemical Pathways - By building a pathway model, that incorporates the known pattern of reactions of enzymes and metabolites, it's possible to simulate how the cell reactions will change during different conditions.

Even if the kinetic data is difficult to obtain, PathwayLab Research Edition modeling technology can be used to accurately predict the gene and protein functions and characteristics under changing conditions.

7) Metabolic Control Analysis (MCA) - PathwayLab has MCA analysis capabilities, which makes it possible to test hypotheses as:

8) Export to Mathematica and MATLAB - PathwayLab can export the pathway models into MATLAB or Mathematica formats.

This makes it possible for the user to model the biological system using standard biological notions and symbols in PathwayLab and in the next step export the complete mathematical description to MATLAB or Mathematica tools for further analysis.

9) Export to SBML - PathwayLab can export pathway models into the Systems Biology Markup Language (SBML). This facilitates model reuse and sharing of models with other software that are SBML compatible.

10) Support of Systems Biology Graphical Notation (SBGN) - Ready made component libraries based on the Systems Biology Graphical Notation (SBGN), which facilitates communication between researchers by using clearly defined graphical symbols for biochemical entities and processes.

11) Automated Parameter Scanning - Parameters of a pathway model often have a high impact on the behavior of the model. In order to find the correct values of these parameters, PathwayLab provides an automated mechanism for searching parameter values.

Mathematica Application Package for PathwayLab --

PathwayLab integrated with Mathematica provides an environment for advanced modeling and computational analysis of biochemical reaction networks.

A pathway model defined in PathwayLab can be exported to a Mathematica m-file as a pathway model object.

The PathwayLab application package for Mathematica allows even more advanced and customizable computational analysis such as transient and steady state analysis, stability analysis, sensitivity analysis, and parameter estimation.

Key Benefits and Capabilities of PathwayLab integrated with Mathematica:

1) Access Mathematica's advanced numerical, symbolic, and graphical capabilities for analyzing complex systems biology models.

2) Reduce error prone model authoring using a state of the art modeling environment for biological systems.

3) Capitalize on Mathematica’s advanced file export (XML) features to transform your pathway models into high quality reports and graphics ready for publication.

Mathematica Notebooks -- Included in PathwayLab Illustrate:

1) Time course simulation for transient analysis;

2) Approximate and exact steady state computations;

3) Linearization of non-linear models;

4) Non-linear stability analysis;

5) Stoichiometric matrix computations;

6) Parameter sweeping;

7) Model reduction utilizing moiety conservation relations;

8) Symbolic transformations of reaction rate equations; and

9) Formatting reaction rate equations using standard mathematical notation.

Highly integrated with any Microsoft Office tool - Since PathwayLab is using Microsoft Visio as the drawing tool and interface; it makes the product very easy to integrate with other Microsoft Office applications.

Drawing and Layout Optimization - PathwayLab can be used to build structured pathways from ready made building blocks representing any combination of pathway substances and reactions, and makes them easy to arrange by optimization algorithms.

System Requirements

Manufacturer

Manufacturer Web Site PathwayLab

Price Contact manufacturer.

G6G Abstract Number 20122R

G6G Manufacturer Number 101448