PhD_thesis_cm967

Chapter 1 - Introduction

• Published work: "The Context Matrix: Navigating Biological Complexity for Advanced BioDesign"
  • CrossRef
  • Context Matrix GitHub Repo

Chapter 2 - Motivation and Constraints of Single-Cell Assays and Project Aims

1. MFD experiments [crossref]
   • cm967 (latest) image pre-processing pipeline
   • cm967 (latest) image analysis pipeline
2. Plate reader experiments [crossref]
   • pre-processed data
   • analysis Jupyter Notebooks

Chapter 3 - Next-Generation Microfluidic Devices for Single-Cell Analysis of Engineered Cells

[crossref]

1. MFD DXF design files for standard photo-lithography [crossref]
2. MFD design files [crossref]
   1. for Nanoscribe nano3D printing
      1. AutoDesk Fusion 360/Inventor files [dimensions: 3D]
      2. DeScribe files [dimensions: 3D]
      3. NanoWrite files [dimensions: 3D]
   2. for standard photo-lithography master blue prints (MBPs) [dimensions: 2D; file format: DXF]
3. Python scripts for Blender MFD feature design automation of STLs for Nanoscribe [dimensions: 3D; file format: .py] [crossref]

Chapter 4 - OptoSelect: An Optogenetic Selection Platform in Microfluidic Devices

• Design and assembly files for reusable OptoSelect-BLADE system [crossref]

Chapter 5 - In situ Genotyping Techniques for Throughput Increase

• Novel Spectra Viewer [crossref]
• Fluorophore Set Orthogonality Evaluator [crossref]
• De Novo Orthogonal Oligo Generator [crossref]
• FISH Barcode Architecture Modelling [crossref]

Chapter 6 - Automated, Low-Cost, Dynamic, High-Throughput Experimentation

1. iBF:DNAA-OT2 : Jupyter Notebooks for DNA assembly using the Opentrons OT-2 [crossref]
2. iBF:DNAA-Echo : Jupyter Notebooks for DNA assembly using the Labcyte Echo [crossref]
3. iBF:ExPrep-OT2 : Jupyter Notebooks for experiment preparation using the Opentrons OT-2 [crossref]

Chapter 7 - Discussion and Conclusion

Steps for future work, in the first instance, generating Hill Plot part characterisations at single-cell, time-lapse detail:

1. Design of sequential inducer assay
2. Design of gradient inducer assay
   1. MFD DXF design files for gradient mixer

PhD_thesis_cm967