Week 11 — Bioproduction & Cloud Labs
Cloud laboratories are making science accessible, affordable, and reproducible. Our aim this semester is to showcase how they can enable human creativity at scale, and how they provide a platform for collaboration and community.
How To Grow (Almost) Anything is about synthetic biology, bioengineering, robotics, automation, art, and AI. But it is also about friendship, shared purpose, and the freedom to build beyond what we know and to be inspired by what can be. To that end, the goal with this cloud lab unit and homework assignment is to inspire collaboration and creativity while designing a scientifically rigorous cell-free fluorescent protein optimization experiment together.
Lecture (Tues, Apr 14)
Bioproduction & Cloud Labs
(▶️Recording)
Reshma Shetty
Recitation (Wed, Apr 15)
Cloud laboratories
(▶️Recording | 💻Slides)
Ronan Donovan
Lab (Thurs-Fri, Apr 16 - 17)
Tip
As you plan for final projects, you may want to refer to the provided non-exhaustive list of common Nebula protocols and their parameters in the “Reading & Resources” section below.
Homework — DUE BY START OF APR 28 LECTURE
Info
Note that this homework is due a week later than it ordinarily would due to its release a week later than normal.
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork
Assignees for this section
| MIT/Harvard students | Required |
| Committed Listeners | Required |
- Contribute at least one pixel to this global artwork experiment before the editing ends on Sunday 4/19 at 11:59 PM EST.
- A personalized URL was sent to the email address associated with your Discourse account, and you can discuss the artwork on the Discourse.
- If you did not have a chance to contribute, it’s okay, just make sure you become a TA this fall! 😉
- Make a note on your HTGAA webpages including:
- what you contributed to the community bioart project (e.g., “I made part of the DNA on the bottom right plate”)
- what you liked about the project, and
- what about this collaborative art experiment could be made better for next year.
Part B: Cell-Free Protein Synthesis | Cell-Free Reagents
Assignees for this section
| MIT/Harvard students | Required |
| Committed Listeners | Required |
Referencing the cell-free protein synthesis reaction composition (the middle box outlined in yellow on the image above, also listed below), provide a 1-2 sentence description of what each component’s role is in the cell-free reaction.
E. coli Lysate
- BL21 (DE3) Star Lysate (includes T7 RNA Polymerase)
Salts/Buffer
- Potassium Glutamate
- HEPES-KOH pH 7.5
- Magnesium Glutamate
- Potassium phosphate monobasic
- Potassium phosphate dibasic
Energy / Nucleotide System
- Ribose
- Glucose
- AMP
- CMP
- GMP
- UMP
- Guanine
Translation Mix (Amino Acids)
- 17 Amino Acid Mix
- Tyrosine
- Cysteine
Additives
- Nicotinamide
Backfill
- Nuclease Free Water
Describe the main differences between the 1-hour optimized PEP-NTP master mix and the 20-hour NMP-Ribose-Glucose master mix shown in the Google Slide above. (2-3 sentences)
Bonus question: How can transcription occur if GMP is not included but Guanine is?
Part C: Planning the Global Experiment | Cell-Free Master Mix Design
Assignees for this section
| MIT/Harvard students | Required |
| Committed Listeners | Required |
Given the 6 fluorescent proteins we used for our collaborative painting, identify and explain at least one biophysical or functional property of each protein that affects expression or readout in cell-free systems. (Hint: options include maturation time, acid sensitivity, folding, oxygen dependence, etc) (1-2 sentences each)
The amino acid sequences are shown in the HTGAA Cell-Free Benchling folder.
Create a hypothesis for how adjusting one or more reagents in the cell-free mastermix could improve a specific biophysical or functional property you identified above, in order to maximize fluorescence over a 36-hour incubation. Clearly state the protein, the reagent(s), and the expected effect.
The second phase of this lab will be to define the precise reagent concentrations for your cell-free experiment. You will be assigned artwork wells with specific fluorescent proteins and receive an email with instructions this week (by April 24). You can begin composing master mix compositions here.
Important
In order to be eligible for this, make sure that your final project slide is in the “2026 Committed Listener ONE FINAL PROJECT IDEA” slide deck.
The final phase of this lab will be analyzing the fluorescence data we collect to determine whether we can draw any conclusions about favorable reagent compositions for our fluorescent proteins. This will be due a week after the data is returned (date TBD!). The reaction composition for each well will be as follows:
- 6 μL of Lysate
- 10 μL of 2X Optimized Master Mix from above
- 2 μL of assigned fluorescent protein DNA template
- 2 μL of your custom reagent supplements
Total: 20 μL reaction
Part D: Build-A-Cloud-Lab | (optional) Bonus Assignment
Assignees for this section
| MIT/Harvard students | Optional |
| Committed Listeners | Optional |
Ginkgo Nebula Cloud Laboratory Rendering, 2025
- Use this simulation tool to create an interesting looking cloud lab out of the Ginkgo Reconfigurable Automation Carts. This is just a minimal implementation so far, but I would love to see some fun designs!
Tip
Note from Ronan: If you are interested in helping me build out future HTGAA cloud lab software, please fill out this form!