Guy Torbet.

Reverse Engineering Biology

Guy Torbet
Guy Torbet

July 26, 2021

🔬 Biology 💻 Software Notes
nucleotide byte
genome bytecode
translation disassembly 3 byte wide instruction set with arbitrary "reading frames"
protein function a polyprotein is a function with multiple pieces
protein secondary structure basic blocks 80% accuracy in prediction
protein tertiary structure This seems like the hard one to predict: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205819
quaternary structure compiled function with inlining https://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction_prediction
gene library bacteria are statically linked, viruses are dynamically linked
transcription loading
protein structure prediction library identification
genome analysis static analysis
molecular dynamics simulations of protein folding dynamic analysis Simulation doesn't seem to work yet. Constrained by tooling and compute.
no equivalent execution We are reverse engineering a CAD format. Runs more like FPGA code, all at once. No serial execution. (What are the FPGA reverse engineering tools?)

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