Category Cross-Omics>Pathway Analysis/Tools

Abstract The CADLIVE (Computer-Aided Design of LIVing systEms) System is a comprehensive group of computational tools that analyzes and rationally designs large-scale 'biochemical networks' at the molecular interaction level.

It provides a rule-based automatic way to convert 'biochemical network' maps into dynamic models, which enables simulating their dynamics without going through all of the reactions down to the details of exact kinetic parameters.

The simulator supports the biochemical reaction maps that are generated by a GUI editor.

To directly link biochemical network maps to the dynamic simulation, the manufacturer has created the strategy of three layers and two stages with efficient conversion rules in an Extensible Markup Language (XML) representation.

This strategy divides a molecular network into three layers, i.e., gene, protein, and metabolic layers, and partitions the conversion process into two stages.

Once a biochemical map is provided, CADLIVE automatically builds a mathematical model, thereby facilitating one to simulate and analyze it.

CADLIVE consists of multiple software modules/programs which include the CADLIVE GUI Network Constructor, the Pathway Search Program for Virtual Knockout Mutants, the CADLIVE Grid Layout Program, the CADLIVE Dynamic Simulator, and CADLIVE Metabolic Engineering Tools.

1) The CADLIVE Network Constructor enables one to construct large- scale biological networks (metabolic and gene regulatory networks) using a GUI (Graphic User Interface) and saving them as regulator reaction equations in a database in a format compatible to the Dynamic simulator.

2) The Pathway Search Program for Virtual Knockout Mutants explores all possible pathways between two species, and can be applied to knockout mutants.

The manufacturers developed the pathway search module for virtual knockout mutants as a built-in application of CADLIVE.

This module analyzes gene function in the same way as molecular genetics, which simulates a change in mutant phenotypes or confirms the validity of the network map.

3) The CADLIVE Grid Layout Program automatically lays out 'biochemical networks' on a two-dimensional square grid. A grid layout is a special kind of graph layout, where all graph nodes are placed on a 2-dimensional square grid.

The manufacturer has developed an algorithm to compute grid layouts for graphs.

In their approach, a graph is modeled as a system of interacting particles (nodes) on a given grid. The nodes interact according to a 'cost function' which is designed based on the topological structure of the network.

In such a system, closely related nodes attract each other, and remotely related nodes repulse each other.

The manufacturer expresses their network layout method as an 'optimization algorithm' which aims at finding optimized solutions of a certain ‘objective cost’ that is a function of the layouts of the input network.

The network is modeled as a system of interacting particles which are placed on a 2-dimensional square grid. The network is confined within an area L.

The particles (nodes) interact according to a predefined energy function based on the network topological structure. A configuration of the particles represents a layout of the network, in which all edges are simple straight lines.

The energy of a configuration is the 'cost score' of the corresponding layout. A stable configuration has low energy; equivalence, and an acceptable layout has a low cost score.

4) The CADLIVE Dynamic Simulator automatically converts biochemical network maps into dynamic mathematical models and simulates their dynamics.

The Dynamic Simulator consists of:

5) The Metabolic Engineering Tools are developed as elementary mode based algorithms.

The manufacturer offers two (2) new tools for elementary mode analysis in metabolic engineering --

System Requirements

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Manufacturer Web Site CADLIVE

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G6G Abstract Number 20469

G6G Manufacturer Number 104094