SimPheny™

Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools and Cross-Omics>Agent-Based Modeling/Simulation/Tools

Abstract SimPheny (for Simulating Phenotypes) is an enterprise-level software platform developed by Genomatica that enables the development of predictive computer models of organisms, from bacteria to humans.

SimPheny provides an unparalleled tool for exploring all the capabilities and limitations of a biochemical network.

Genomatica utilizes it in the field of chemical bio-manufacturing, and GT Life Sciences has exclusive commercial rights to the software for life science applications.

With cellular metabolism at its core, SimPheny can build virtual cells from their basic molecular components, and can simulate the activity of the cell’s complete reaction network.

SimPheny has been developed over a period of ten (10) years, and it has become the premier metabolic modeling and simulation software available.

SimPheny serves as an advanced biological knowledge management system with proven predictive capabilities.

High-throughput data, such as genomic sequence, gene expression, proteomic and metabolomic data can all be integrated, analyzed and dynamically visualized within these computer models.

This integration provides a natural bridge between experimental and computational research efforts within an organization.

In addition, SimPheny enables models to be refined and improved as more data for an organism become available.

With SimPheny, researchers are able to use computer models of metabolism to drive research and discovery.

SimPheny thus enables:

1) Predictive model development and ongoing curation;

2) Network-based simulation of metabolism;

3) Pathway oriented data visualization;

4) Integrative analysis of high throughput experimental data;

5) Biological knowledge management;

6) Informed strategic decision making; and

7) Scientific collaboration throughout an organization.

Most importantly, SimPheny can use a ‘metabolic model’ as the basis for simulations of the biological system in silico.

These simulations calculate the phenotypic behavior of the biological system represented by the model.

The capabilities of the system can be explored; using simulation methods, to ask “what if” questions and examines the effects of changing genetic and environmental conditions.

These conditions may reflect diseased states, or controlled-process conditions.

Within SimPheny researchers can:

1) Predict growth, substrate uptake, and product formation rates;

2) Predict characteristics of knock-out phenotypes and identify essential genes;

3) Predict the outcomes of adaptive evolution;

4) Identify undiscovered pathways or reactions in the network based on necessary biomass components;

5) Test the effect of adding genes or reactions to the network;

6) Design metabolic networks to support and optimize the production of a specific metabolite or protein;

7) Find “minimal perturbation” phenotypes; and

8) Examine conditions consistent with disease and healthy states.

System Requirements

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Manufacturer

Manufacturer Web Site SimPheny

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G6G Abstract Number 20629

G6G Manufacturer Number 104229