Engineering

Our engineering approach follows the iterative DBTL (Design-Build-Test-Learn) process to optimize synthetic biology solutions through systematic refinement and validation.

Overview

Our engineering approach focuses on three key components that work together to create a robust and efficient system. Through multiple cycles of refinement, we've developed predictive models and experimental validations that enhance the performance and reliability of our biological constructs.

The DBTL process allows us to systematically improve our designs based on empirical data and computational predictions, leading to innovative solutions for real-world challenges. Each component undergoes rigorous testing and optimization to ensure maximum efficiency and stability.

Engineering Components

SCR-D Structure Prediction

Computational modeling of protein structures with limited sequence information

Aptamer-Controlled SCR

Genetic regulation modulated by aptamer binding

Development of Tadpole

Software tool for automatised semi-rational design

Determine SCR-D's Structure - Cycles

Cycle 1: SCR-D Structure Prediction

Structure Prediction with Bioinformatics Tools and Coevolutionary Analysis

Cycle 2: Coevolutionary Analysis of SCR

Manual Conservation Analysis, Automation, and Key Element Identification

Creation of an aptamer-controlled SCR - Cycles

Cycle 1: SCR element

SCR-D as Switch Candidate, Selecting New SCR Element, and Choosing DIO2 SECIS

Cycle 2: Aptamer

Selecting Theophylline Aptamer and Choosing Theo-ON-5 Variant

Cycle 3: SCR riboswitch

Joining all the parts together to design a switch, using the model and the software.

Development of Tadpole - Cycles

Cycle 1: Algorithm Refinement

Brute-Force Search, Genetic Algorithm (GA), and Clustering

Cycle 2: Deployment and Accessibility

Python Scripts, Streamlit Interface, Render Deployment, and Docker

DBTL Visualization

Scroll down to see the iterative DBTL process or use the navigation arrows

       

References

       
             
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Iteration 1 of 3
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