Welcome! Browse each week below. We’ll keep pages updated as slides/recordings post.
This week lays the foundation for ethics, safety, and governance in biotechnology — and we get hands-on in lab basics.
Slides will be shared after class.
Document your work clearly — sketches, screenshots, notes, even failed attempts (and how you addressed them).
Reflect on any ethical concerns that arose this week. Propose governance actions you think are appropriate to address them. Include this on your class page for Week 1.
Slides (Updated Feb 5):
Recording (Updated Feb 7):
Welcome to HTGAA! This first lab introduces pipetting and serial dilutions, foundational for precise liquid handling and solution preparation. This is a one‑day lab with two mini‑protocols (mixing colors and dilutions). By the end, you’ll confidently use pipettes, prepare solutions to target concentrations, and troubleshoot common errors.
This is a one‑day lab covering mixing colors and dilutions. By the end you’ll confidently use pipettes and prepare solutions at desired concentrations.
Lab Prep and Lab Answer Keys will be shared here after the lab.
Relevant segments of the recitation recording will be updated here after the class.
This week explores the read–write–edit toolkit: sequencing and synthesis workflows, restriction digests and gel electrophoresis, and early genome‑editing frameworks.
Slides:
Class Recording: Zoom
Document every step of your in‑silico and lab work — sketches, screenshots, notes, failures, and fixes. Your write‑up should help others reproduce your process.
Use the Gel Art: Restriction Digests and Gel Electrophoresis protocol as a guide.
Info
Optional for Committed Listeners with lab access; mandatory for MIT/Harvard students. Documentation due at the start of class Feb 18.
Perform the experiment you designed in Part 1 per the Gel Art protocol.
Slides (Updated Feb 12):
Recording:
A focused 3‑hour lab on restriction digests and agarose gel electrophoresis. You’ll create DNA gel art while mastering core techniques that underpin verification of DNA constructs.
3‑hour lab blending creativity and molecular biology: you’ll pour gels, set up restriction digests, run electrophoresis, and visualize DNA.
Quick Guide
This week focuses on lab automation using the Opentrons OT‑2. You’ll write Python to control the robot and create bio‑art patterns using fluorescent E. coli on black agar plates.
There was no live lecture this week per the source site. Check the Recitation and Lab sections for materials and recordings.
Submit your code BEFORE your lab time. You’ll run your protocol on an OT‑2 during scheduled lab time.
Slides: Google Slides
Recording: will be posted (per source).
Program the Opentrons OT‑2 to deposit fluorescent E. coli and create bio‑art on black agar plates.
In this two‑day lab you’ll program the Opentrons OT‑2 to deposit fluorescent E. coli on black agar plates, creating glowing bio‑art under UV light. It’s a hands‑on intro to automation + creative biotech.
This week begins Protein Design (Part I) — modern sequence/structure tools for evaluating and designing proteins.
This session introduces Protein Design foundations: what sequence/structure information is, how to find it, and how modern ML tools have changed design workflows.
(Slides and recording will be posted here when available.)
Homework details will be added here when posted on the course site.
Recitation slides and recording will appear here when posted.
This week’s lab is entirely in‑silico — no in‑person wet‑lab.
The protein design lab will be entirely in‑silico; you’ll run a variety of models to test different protein designs.
Picture source: Hou, Feenstra et al., 2022 — “Ten quick tips for sequence‑based prediction of protein properties using machine learning,” PLOS Comput Biol 18(12): e1010669.
No additional readings were posted on the course site at the time of conversion. This section will be updated if materials appear.
Continuing Protein Design, this week focuses on protein–peptide interactions using modern ML models (PepMLM) and AlphaFold‑Multimer.
Date: Tue Mar 4 (per schedule).
Slides: (will be posted when available)
Recording: Zoom
Mandatory for MIT/Harvard students and Committed Listeners. Due Tue, Mar 11 (before lecture).
Create a Hugging Face account → we’ll use PepMLM‑650M: model page.
Get the amino‑acid sequence for SOD1 on UniProt (ID: P00441). Make the A4V mutation.
Run PepMLM inference and generate 4 peptides (length 12 aa). (2 is acceptable if time‑limited.)
Add a known SOD1‑binding peptide to your list: FLYRWLPSRRGG (see Genes & Development reference).
genesdev.cshlp.org
Use AlphaFold‑Multimer (ColabFold notebook) to model the SOD1:peptide complex.
Open notebook: AlphaFold‑Multimer
model_type = alphafold2_multimer_v3 — shown to recapitulate peptide‑protein binding accurately.After running AF‑Multimer with your 5 peptides (4 generated + 1 known), plot the ipTM scores to compare relative binding confidence.
Write a 1‑paragraph summary of your results.
This is computationally heavy — start early.
More details: Final Project Page (external Notion): www.notion.so
Date: Wed Mar 5.
Slides: MS2‑Phage homework discussion (from Notion file reference)
Recording: Zoom
This week’s practical work is in‑silico and pairs with the Homework: design peptides with PepMLM and evaluate binding to SOD1 using AlphaFold‑Multimer.
Model protein–peptide interactions by generating peptide candidates (PepMLM‑650M) and predicting complexes (AlphaFold‑Multimer). Compare ipTM scores across candidates to select promising binders.
This week introduces design and assembly of genetic circuits, anchored around Gibson Assembly and the associated wet‑lab skills.
Date: Tue Mar 11.
Slides:
Recording: Zoom
These questions are based on the Gibson Assembly Lab and are mandatory for Committed Listeners and MIT/Harvard students.
Date: Wed Mar 12.
Slides: will be shared after the class.
Recording: Zoom
This week’s lab pairs directly with the Homework. Use the protocol and primer‑design notes below; document your process and results.
Practice DNA assembly by preparing linear fragments (via PCR and/or restriction digest) and assembling them with Gibson Assembly, followed by transformation into E. coli.
We continue Genetic Circuits with emphasis on regulatory logic, toggle switches, and practical pathways for implementing and testing circuits in cells.
Date: Tue Mar 18.
Slides: will be posted after class.
Recording: Zoom
This homework is based on the Week 7 Lab. It’s a good week to start honing final projects and focusing on developing / researching protocols.
Date: Wed Mar 19.
Slides: will be shared after class.
Recording: Zoom
This week’s lab focuses on genetic circuit design and testing workflows. Document your design rationale, parts selection, and test plans.
Translate design principles into an actionable workflow: from selecting promoters/regulators to drafting test plans for toggle switches or related motifs.
We explore cell‑free expression: building reactions from defined parts, tuning energy regeneration, and producing proteins without living cells.
Date: Tue Apr 1.
Slides: (will be posted when available)
Recording: Zoom
Mandatory for Committed Listeners and MIT/Harvard students.
Key readings:
Start exploring your final project in depth this week. The minimum requirement is completing Aim 1.
MIT/Harvard tracking
Key ordering dates (MIT/Harvard):
Date: Wed Apr 2.
Slides: will be shared here after class.
Recording: Zoom
MIT/Harvard: No in‑person lab protocol this week (per schedule).
Global Nodes: Use the PDF protocol below.
Induce a reporter in a cell‑free transcription‑translation (TX‑TL) system and quantify expression changes between treatments.
This week explores bio production—scaling from bench‑scale designs to strains and processes that produce carotenoids (e.g., lycopene, β‑carotene) and other biomolecules. Expect an emphasis on media design, carbon sources (e.g., fructose), and automation.
Tip This lab focuses on designing, ordering, and assembling DNA constructs that support your final project goals. Document Benchling files, provide FASTA sequences, and outline a precise cloning & validation plan.
Date: Tue Apr 8.
Slides: Will be shared after class.
Recording: Zoom
Part A is based on lecture prompts (Mandatory for Committed Listeners).
Part B is based on the Bio Production Lab (Mandatory for Committed Listeners and MIT/Harvard students).
Key Link:
Key Papers:
Answer the following:
Use this space to begin thinking through DNA design related to carotenoid pathways (targets, operon structure, promoter choices, and measurement plan).
Date: Wed Apr 9.
Slides: 2025: Lycopene & β‑Carotene Bioproduction
Recording: Zoom
This lab focuses on designing, ordering, and assembling DNA constructs that support your final project goals. Document Benchling files, provide FASTA sequences, and outline a precise cloning & validation plan.
From DNA design to building genomes and bioproduction: this week bridges sequence design with practical pathways to construct systems that produce carotenoids and other compounds.
Slides will be posted here after class; recording will appear once processed.
Recording: Zoom
Homework will be posted here when available.
Use this week to deepen your strain design plans and connect them to next week’s imaging/measurement workflows.
Recitation slides will be shared here after the class; recording will be linked below.
Recording: Zoom
In this two‑day lab, you’ll produce beta‑carotene and lycopene in E. coli and analyze growth (OD600) and pigment absorbance.
Work with E. coli carrying pAC‑LYC (lycopene) and pAC‑BETA (beta‑carotene) to optimize pigment production by tuning media, temperature, and carbon source.
We focus on imaging & measurement workflows that let us read biology to guide design: LC‑MS for intact mass & peptide maps and instrumentation for fluorescence & microscopy.
Date: Tue Apr 22.
Slides: Lecture Slides
Recording: Class Recording
Homework this week is based on data generated at Waters Immerse Cambridge. You’ll characterize eGFP structure (intact mass; peptide map) using LC‑MS. Data will be provided online for remote students.
Date: Wed Apr 23.
Slides: Recitation Slides
Recording: Recitation Recording
This week’s practical focuses on LC‑MS workflows for eGFP characterization (intact mass and peptide mapping). On‑site work takes place at Waters Immerse Cambridge; remote students will use the shared dataset.
Connect measurement to design by acquiring and interpreting LC‑MS data.
This week explores frugal science approaches (low‑cost, accessible tools) and the microbiome, with an emphasis on resource‑aware experimental design.
Lecture slides will be posted here after the class; recording will be linked when available.
Recording: Zoom
The Week 13 page currently lists “Add Note Here.” We’ll update this section with prompts and deliverables once the course site publishes them.
Suggestion: Draft a resource‑aware protocol for a measurement or assay relevant to your final project (cost, accessibility, robustness).
Recitation slides will be shared here after the class; recording will be updated once available.
Recording: Zoom
This week is reserved for make‑up labs and final‑project execution. Use lab time to run missing protocols, validate constructs, collect final measurements, or perform imaging.
Allocate bench time to complete experiments needed for your final project milestone(s).
We close the semester with Bio Design & Living Materials, plus final‑project wrap‑up and documentation.
Date: Tue May 6.
Slides: will be shared here after class.
Recording: Zoom
Focus on completing and documenting your final projects this week.
Date: Wed May 7.
Slides: will be shared after class.
Recording: Zoom
Use this week for final project experiments, measurements, and documentation. Confirm space/equipment needs with instructors.
Allocate bench time to complete any remaining experiments and finalize documentation for presentations.