Homework #3 🤖

Part 1: Opetron art - Model designs with the Opentrons T2 during lab practice.

• 96 well-plate under fluorescent light

• 96 well-plate under normal light

Part 2: Python code for the petri dish design

• Link of colab: https://colab.research.google.com/drive/1mFtRMx0jfea2qvEGCu0XQWX7JPL9NNc4?usp=sharing

Part 3: Post Lab Questions

One of the great parts about having an automated robot is being able to precisely mix, deposit, and run reactions without much intervention. This year, a greater emphasis will be placed on utilizing the Opentrons to accelerate your final projects.

For this week, we’d like for you to do the following

1. Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode or Python scripts, procedures you may need to automate, 3D printed holders you may need, and more.

Automation in reaction synthesis through the use of robots (eg. Opentrons):

Whether it is to dispense liquids or perform some specific reactions: to control contamination and increase accuracy, help improve the efficiency of transformation processes on a larger scale, or improve reproducibility.

• PCR (e.g. rt-PCR)
• Bacteria culture
• Mo. transformation and development of the constructs as plasmids

Automation in the detection of markers: This could be done using software such as ImageJ, or Matlab, to automate image analysis and improve accuracy.

• Gel Electrophoresis Analysis
• Fluorescence quantification
• High-Resolution Image processing

An example of this could be the models from Thermo Fisher for reading microtiter plates in fluorescence, absorbance, and luminescence assays. (Varioskan™ ALF Multimode Microplate Reader)

https://www.thermofisher.com/order/catalog/product/VA000010C?SID=srch-srp-VA000010C

Automation in data analysis

Bioinformatics and machine learning tools enable the analysis of expression data and large-scale evaluation of statistics in experiments (RStudio, Python, IBM SPSS Statistics, Stata).

• Gene/protein expression trends
• Results comparations —> Biostatistics

1. Find and describe a published paper that utilizes the Opentrons or similar automation tools to achieve novel biological applications (eg automated PACE)

• DNA assembly: AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots (2023)

The article presents a Python code package (AssemblyTyron) that is designed with the aim of automating the DNA assembly process using the Opentrons OT-2 robot. This facilitates the construction of plasmids and DNA fragments by homology or Golden Gate, reducing human intervention to a minimum.

LINK:

https://academic.oup.com/synbio/article/8/1/ysac032/6956284

Aditional: REVIEW —> Automated high-throughput DNA synthesis and assembly https://www.cell.com/heliyon/fulltext/S2405-8440(24)02998-0#fig1

Efficient SARS-CoV-2 Quantitative Reverse Transcriptase PCR Saliva Diagnostic Strategy utilizing Open-Source Pipetting Robots

The study deals with a novel method for the diagnosis of SARS-CoV-2 by quantitative reverse transcriptase PCR (RT-qPCR) in saliva samples, this presents improvements by working with robots for the pipetting process. This provides an efficient and cost-effective alternative to conventional pipetting methods that are also subject to human experimental error. In addition to facilitating large-scale processes.

LINK: https://pmc.ncbi.nlm.nih.gov/articles/PMC9199378/#SM1

• Automation of inoculation in culture media for the microbiology laboratory

The article deals with the creation of a blueprint for an automated system to inoculate culture media. In this way reducing risks of contamination and mishandling. This study describes the use of robots from the beginning stages of the production chain such as inoculation to the disposal of the media.

https://recit.uabc.mx/index.php/revista/article/view/285/510