Week 6: Genetic Circuits Part I

Context
Week 6 kicks off genetic circuits: specifying a behavior (truth table), choosing parts, drawing a design (SBOL Visual), and validating it in silico with design tools.

Goals

• Pick a simple function (e.g., a 1–2 input logic gate that controls a reporter).
• Select candidate parts (promoter, RBS, CDS/reporters, terminator) from a public registry.
• Draw the construct using SBOL Visual glyphs.
• Validate the design concept with a circuit tool and record assumptions/limitations.

Part A — Specify the function

Describe the circuit you want (one paragraph + a truth table). Examples: NOT, AND, NAND controlling a fluorescent reporter. Keep scope modest so results are interpretable.

• Deliverables: plain-language description, inputs/outputs, and a truth table.

Part B — Choose parts (catalog references)

Pick plausible parts (or families) for each role; note alternatives and why you chose them.

• Where to look: the iGEM Registry of Standard Biological Parts (promoters, RBSs, reporters, terminators, inverters, etc.). Cite the entry pages you consult. :contentReference[oaicite:0]{index=0}

• Deliverables: a small parts table (name or ID, role, brief note, source link).

Part C — Sketch the construct (SBOL Visual)

Create a block diagram of your design using SBOL Visual glyphs (promoter → RBS → CDS → terminator; plus regulators/interactions as needed). Keep it consistent and readable.
If you don’t use a drawing tool, a neat hand sketch is fine—just label elements clearly.

• Reference: SBOL Visual v2 overview/specification for glyphs and best practices. :contentReference[oaicite:1]{index=1}

• Deliverables: a single figure (PNG/SVG) and 3–5 bullet notes explaining the design.

Part D — In-silico sanity check (choose one)

Use one tool (or both) to reason about your design. Keep this exploratory—document what you tried and what you learned.

1. Cello (design automation) — encode logic and map to a part library to synthesize candidate DNA circuits; summarize the output design and limitations. :contentReference[oaicite:2]{index=2}
2. iBioSim (model/analysis) — build a small model for your construct and explore qualitative behavior. Screenshots of your setup are enough for this week. :contentReference[oaicite:3]{index=3}

• Deliverables: 1–2 screenshots and a short paragraph interpreting the result.

What to turn in

• Problem statement + truth table
• Parts table (IDs, roles, links)
• SBOL Visual diagram (with a few explanatory bullets)
• In-silico check (tool used, screenshots, 4–6 sentence interpretation)
• One limitation you’d address next week

Handy references

• iGEM Registry of Standard Biological Parts (browse/search parts). :contentReference[oaicite:4]{index=4}
• SBOL Visual v2 (glyph standard). :contentReference[oaicite:5]{index=5}
• Cello (genetic circuit design automation; Cello 2.0 paper). :contentReference[oaicite:6]{index=6}
• iBioSim (modeling/analysis). :contentReference[oaicite:7]{index=7}
• Background review: “Synthetic Gene Circuits: Design, Implement, and Apply.” :contentReference[oaicite:8]{index=8}