AutoBioCAD

AutoBioCAD designs and automates the computational construction of synthetic regulatory networks in Escherichia coli to predict and produce nucleotide-encoded gene circuits with specified dynamic behaviors for experimental validation.

Key Features:

• Automated Design: Assembles regulatory circuits and outputs nucleotide sequences that encode circuits with targeted dynamic behaviors.
• Model Testing and Validation: Generates mathematical models for testing regulatory principles and predicting circuit dynamics for experimental comparison.
• Incorporation of Complex Biological Factors: Integrates stochastic effects, robustness considerations, qualitative dynamics, multiobjective optimization, and degenerate nucleotide sequences into its modeling process.
• Exploration of Genetic Contexts: Employs evolutionary design strategies to explore alternative genetic contexts and design variants automatically.

Scientific Applications:

• Design of synthetic regulatory circuits: Creation of gene regulatory circuits for Escherichia coli with specified dynamic behaviors.
• Predictive modeling of circuit dynamics: Prediction of circuit behavior under stochastic and robustness constraints.
• Experimental implementation: Production of nucleotide sequences for experimental construction and validation of designed circuits.
• Testing regulatory principles: Use of generated models to test regulatory principles within natural systems.

Methodology:

Loads a curated library of genetic element models, employs evolutionary design strategies to explore genetic contexts, integrates stochastic effects, robustness considerations, qualitative dynamics, multiobjective optimization, and degenerate nucleotide sequences into modeling, and generates mathematical models and nucleotide sequences for testing.