Summary: The third session dives into coding and software tools for bioinformatics. Participants will practice Python fundamentals, explore Google Colab for biological data analysis, and learn how to perform in silico cloning using Benchling.

Cost for Attendance: $33 (payment links @ door or in advance to @elliot-roth // @thatmre)

Part III Topics & Agenda

• Python Fundamentals & Colab (60 min)

  • Subtopics: Fundamentals of Python, Basic Syntax, Setting up Colab

• Colab Examples and AI Tools (45 min)

  • Subtopics: From Code to Lab: Practical Applications with CoLab & Opentrons

• Benchling Basics (60 min)

  • Subtopics: Reading DNA sequences, in silico cloning by scenario, essential Benchling features

• Accessible Biolabs (15 min)

Subtopics: Setting up labs with limited resources, accessible protocols for external students

Slides: https://drive.google.com/drive/u/0/folders/12kdCFoHJ2Wrj58xG-MoJl8dHMDx8l2A3

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: https://www.connectedpapers.com/

• 📝Research Rabbit: https://www.researchrabbit.ai/

Benchling Example Project: 📝Benchling Basics