01 · Describe
Start from behavior, not a blank canvas
Say what you want the cell to do, in plain language. Reef proposes a candidate genetic circuit you can read, edit, and reason about.
Living cells are the most powerful computers we know. They sense, decide, and build. Reef is the interface for designing them: describe the behavior you want, and design, simulate, and pressure-test the genetic circuit before you ever touch the bench.
We put the IO in bIO.
For researchers and builders. No spam, just an early look.
Reef closes the gap between knowing what you want a cell to do and having a design that actually works.
Say what you want the cell to do, in plain language. Reef proposes a candidate genetic circuit you can read, edit, and reason about.
Predict the design's behavior and surface likely failure modes, so DNA and bench time go to designs that are likely to work.
Built on open formats (SBOL) and meant to plug into the tools and foundries you already use.
Flip the inducers below. Reef's behavior engine propagates the signal through the genetic logic and predicts the reporter, live in your browser.
Click an inducer node to toggle it on / off.
Running live in your browser on Reef's behavior engine. In the studio, designs flow into quantitative simulation, failure-mode checks, and AI-assisted design.
A 3-gene oscillator, designed and simulated in Reef. One run drives all three views at the same instant: the logic ring, the share-of-expression stream, and the genetic loop. Reef predicts how a circuit behaves over time, not just its truth table. Click any gene and the change ripples through every view.
Cells run programs written in DNA. A genetic circuit is a specific wiring of genetic parts that produces a behavior. Read it however you like:
Think of a cell as a tiny computer and its DNA as the source code. Genes are like functions: each one makes a protein that does a job. Promoters are the if-statements: little switches in front of a gene that decide when it runs, and other proteins can flip those switches on or off.
String these together and you get programs: a toggle switch that flips between two states and remembers which one (a light switch with memory), an oscillator that pulses on and off on a rhythm (like a blinking cursor), or a logic gate that only acts on the right combination of signals (glows green only if sugar is high and oxygen is low). Reef lets you describe the behavior you want, then designs, simulates, and checks the genetic program before you build it.
Genetic circuits are engineered regulatory networks assembled from standardized parts (promoters, RBSs, coding sequences, terminators) wired so the protein products of one transcriptional unit regulate others. Transcription factors act as activators or repressors on downstream promoters; tuning promoter strength, RBS-determined translation-initiation rate, and degradation lets you build defined dynamics: bistable toggle switches, repressilator-style oscillators, and combinatorial logic (NOR being the most natural to implement as tandem operators on a single promoter).
Reef recommends characterized parts (quality-scored across the iGEM Registry and SynBioHub), assembles a topology, and simulates it: Hill-function ODE kinetics for deterministic population dynamics, with stochastic (Gillespie) modeling for noise and bistability. Designs are SBOL/SBML-native and export to GenBank/FASTA. Reef flags failure modes before you build: leaky expression, resource competition and metabolic burden, retroactivity at module interfaces, toxicity, and synthesis feasibility. Where Cello compiled Boolean logic into static gate assignments for one chassis, Reef targets dynamic, quantitative, characterization-grounded design across the full design-build-test loop.
The market already pays for biology software. The circuit-design layer, the wiring above proteins, is still served by academic tools a generation behind.
We keep the deep research out of public view: the full 40+ tool teardown, the academic timeline, and where we attack. Request the brief and we'll send it over.
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Reef is an early-stage effort to give biology a real design interface: the layer between human intent and living systems. We're building it carefully, in the open, with the scientists who'd actually use it.