Assignments

An open-source tool that combines multi-omics data with large language model reasoning to accelerate biological discovery and improve accessibility in bioinformatics analysis.

Hands-on exercise designing and simulating DNA “gel art” using in-silico restriction digests in Benchling, demonstrating principles of DNA reading, writing, and editing through creative gel electrophoresis visualization.

Python-based lab automation exercise using the Opentrons OT-2 platform to design, simulate, and analyze a liquid-handling protocol in Google Colab, emphasizing precision, reproducibility, and workflow optimization in automated experimentation.

In-silico protein exploration and introductory design—choose a protein, visualize structure/features, optionally predict or mutate with ColabFold, and document screenshots plus brief insights.

Peptide-binder design workflow—generate SOD1-targeting peptides with PepMLM, model complexes in AlphaFold-Multimer, compare ipTM scores, and select top candidates with brief analysis.

Intro to genetic circuit design—define a simple logic-based function, select biological parts, visualize the construct with SBOL symbols, and validate the concept using in-silico tools like Cello or iBioSim.

Continuation of genetic circuit design—contrast RNA-level and protein-level regulation (endoribonucleases vs proteases), explore layered and dynamic control, and connect these mechanisms to final project planning.

Introduction to cell-free protein synthesis—exploring transcription–translation systems outside living cells to enable faster, safer, and more controllable protein production for prototyping, biosensing, and on-demand applications.

Exploration of bioproduction and automation—analyzing lycopene and β-carotene synthesis in E. coli, linking pathway design to scale-up thinking, and reflecting on automation’s impact on protein manufacturing and iteration cycles.

Designing and reasoning about genome-scale DNA assembly—plan a multi-fragment Gibson construct, explore large-scale design strategies like recoding and tRNA relocation, and analyze lessons from minimal and synthetic genome projects such as JCVI-syn3.0 and Sc2.0.

Protein characterization and measurement—analyzing eGFP using LC–MS data from Waters Immerse Cambridge to interpret structure, peptide coverage, and post-translational modifications through chromatographic and mass spectrometric analysis.

Engineered living materials—survey key ELM classes, draft a use-case concept (organism, matrix, function, lifecycle), and outline feasibility and safety/containment considerations.

No-homework consolidation week—polish docs and projects, with optional explorations in frugal science (Foldscope, Paperfuge) and microbiome primers to inform design under real-world constraints.