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 easily be set in the pathway diagram and
tested by simulations or sensitivity analysis where the results are presented
in the pathway diagrams.
Mathematica Application
Package for PathwayLab
PathwayLab integrated with
Mathematica provides a powerful
environment for advanced modeling and computational analysis of biochemical
reaction networks.
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for more information.
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.
Online collaboration
Online collaboration allows multiple users to view, discuss, and edit
pathway information over the internet.
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.
Standards Compatible
PathwayLab is compatible with standard MS-Office products making it easy
for anyone to open and view the PathwayLab documents. It also supports
several standard XML formats.
Advanced Search Functions
PathwayLab has abilities to search to make it easy for the user to find
different biochemical pathways as well as any information annotated to
pathways.
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.
Automated gene expression mapping
PathwayLab can import gene expression data and annotate it in relation to
the pathways. This gives researchers a fast overview of the results, ideas
of where to look for targets, and where to do more focused experiments.
Easy Integration of Database Information
PathwayLab enables researchers to easily create dynamic pathway graphs, to
integrate both proprietary pathway information and information from public
sources, and to make that combined information available to the entire
organization, through an easy-to-use web-based interface.
Sensitivity Analysis
Biochemical Pathways are complex constructions with often many
interactions and feedback loops, that make them hard to intuitively grasp
for researchers. PathwayLab offers sensitivity analysis, that points out
which enzyme that has the largest impact on a specific factor, e.g., a
metabolite level. This makes it easier to sort out the most interesting
enzymes that are affecting a disease state.
Metabolic Control Analysis (MCA)
PahtwayLab has MCA analysis capabilities which makes it possible to test
hypotheses as:
- What happens with the metabolic fluxes if a specific protein is
knocked-out?
- What happens if the level of a metabolite increases by 10%?
Comparative Analysis
With PathwayLab it is possible to compare pathways from different
organisms. If your are analyzing a disease in a model organism
environment, it is possible to get it compared with other animal or human
disease pathways, which can lead to new insights.
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.
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.
Automated Parameter Scanning
Parameters of a pathway model often have a high impact on the behavior of
the model. In order to find correct values of these parameters, PathwayLab
provides an automated mechanism for searching parameter values.
Easy to Create and Manage Pathway Information
PathwayLab Publish 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 the structured pathway model builder
making the pathway diagrams and models accessible and searchable for the
whole organization.
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.
Easy to Create and Manage Pathway Information
