Bootcamp Part 1 — Bio Basics, Phage Therapeutics, DNA Designs, Genetic Circuits

Topics & Agenda

• Bio Basics (Time Stamp: 13:59) — Speaker: Anna‑Thérèse Mehra
  Subtopics: Tree of life, DNA/RNA/proteins, central dogma.
  2025‑BioBootCamp‑1.1 — Bio Basics (PDF)

• DNA Design & Genome Engineering Methods (Time Stamps: 1:06:06, 1:30:40) — Speakers: Dominika Wawrzyniak, Michelle Yue
  Subtopics: DNA/gene structure, mutations, vectors, CRISPR, and other DNA modifiers.
  2025‑BioBootCamp‑1.2 — DNA Design (PPTX) · 2025‑BioBootCamp‑1.3 — Genome Engineering Methods (PPTX)

• Phage Therapeutics (Time Stamp: 1:49:15) — Speaker: Lisa Riedmayr
  2025‑BioBootCamp‑1.4 — Phage Therapeutics (PPT)

• Genetic Circuits (Time Stamp: 2:19:12) — Speaker: Johannes Stein
  2025‑BioBootCamp 1.5 — Genetic Circuits (PDF)

Most‑updated slides: Part I (Google Drive)
Recording: MIT Zoom

Resources

• Central dogma of molecular biology

• Precision Health — The Central Dogma (2‑min) — YouTube

• What is the ‘Central Dogma’? — YourGenome

• Enzymes — Amoeba Sisters — YouTube

• DNA and RNA (nucleic acids)

  • DNA and RNA: Differences in Form and Function — Stated Clearly — YouTube
  • DNA vs RNA — Biology Dictionary

• DNA Design

  • An Introduction to Genetic Engineering — Cambridge — cambridge.org
  • Eukaryotic Genome Complexity — Nature Scitable — nature.com

• Phages — Bacteriophages: The Deadliest Being on Planet Earth — YouTube

• Genetic Circuits — Talks by Voigt/Lu — YouTube

Bootcamp Part 2 — Scientific Method, Experimental Design & Lab Techniques

Topics & Agenda

• Scientific Method & Experimental Design (30 min) — Speaker: Rana Said
  2025‑BioBootCamp‑2.1 — Scientific Method & Experimental Design (PPTX)

• Literature Research (15 min) — Speaker: Dominika Wawrzyniak
  2025‑BioBootCamp‑2.2 — Literature Research (PPTX)

• Tools for Molecular Biology (30 min) — Speakers: Adrian Filips & Rana Said
  2025‑BioBootCamp‑2.3 — Databases (PPTX)

• Wet Lab Methods (90 min) — Speakers: Jieming Chu, Adrian Filips, Martina Armas, Benjamin Arias
  2.4 — Biosafety & Sterile Techniques · 2.5 — Culturing Microorganisms · 2.6 — DNA Extraction · 2.7 — DNA Sequence Analysis · 2.8 — Lab Methods 3

• Scientific Figures (15 min) — Speaker: Dominika Wawrzyniak
  2025‑BioBootCamp‑2.9 — How to Create Scientific Figures (PPTX)

Most‑updated slides: Part II (Google Drive)
Recording: MIT Zoom

Resources

• Image practice & guides

  • Effective image visualization for publications — F1000Research
  • Community‑developed checklists for publishing images and image analyses — Nature Methods
  • 3 ways to make your scientific images accurate, informative and accessible — Nature Index

• Literature research

  • Google Scholar advanced search — SEMO Guide
  • PubMed keyword search — Harvard Library Guide

Bootcamp Part 3 — Python, Colab, Benchling & Accessible Biolabs

Topics & Agenda

• Python Fundamentals & Colab (60 min) — Speaker: Paul Kao
  2025‑BioBootCamp‑3.1 — Python Basics (PPTX)

• Colab Examples & AI Tools (45 min) — Speaker: Suvin Sundararajan
  2025‑BioBootCamp‑3.2 V2 (PPTX)

• Benchling Basics (60 min) — Speaker: Cholpisit (Ice) Kiattisewee
  2025‑BioBootCamp‑3.3 — DNA Languages, Reading & Editing (PPTX)

• Accessible Biolabs (15 min) — Speaker: Adrian Filips
  2025‑BioBootCamp‑3.4 — Accessible Protocols (PPTX)

Presentation Slides: Part III (Google Drive)
Recording: (link will be updated when posted)

Resources

Supporting Colabs

• Walkthrough: Python‑Basics‑HTGAA‑Bootcamp‑2025.ipynb
• Example 1: Rosetta: (Remake) — L‑Protein — Point‑Mutation‑Scan.ipynb
• Example 2: Opentrons Lab: HTGAA25 Opentrons Colab
• Part 2: Python‑HTGAA‑Bootcamp‑2025.ipynb
• Part 2 Opentrons: HTGAA25 Opentrons Bare Code

AI Tools

• Connected Papers