Notes
Method notes with the parameters, thresholds and decision rules. Work in progress is marked.
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What a design campaign has to record
Record types and identity fields for a computational antibody design run, the three artefacts that must agree before a run is admissible, and the gate order that front-loads the cheap failures.
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Primery: turning BLAST mismatches into species-specific primers
Stage parameters, the composite scoring function, chemistry presets, benchmark results across 21 loci, a diagnosis checklist for loci that return no clusters, and how to take a designed pair to the bench.
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Placing a primer on a mismatch cluster
Computing cluster density from a query-anchored alignment, four thresholds worth holding, and converting the resulting melting-temperature gap into a gradient PCR window.
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Assembling a plant genome from short reads
Profiling order and k selection, three assembler architectures compared on contiguity, two ways to spend borrowed long reads, and four things to read off a pairwise alignment to detect chimerism.
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A three-locus workflow for Fusarium identification in feed
Why ITS screens but does not identify, the bench decisions that cost read length, four metrology checks for a capillary analyser, and the trimming choices that decide a species call.
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Ordering the filters in a de novo nanobody pipeline
Filter order against per-stage cost, where to set the interface-confidence cut and what happens either side of it, correlated proxies across a five-stage cascade, and why humanisation belongs inside the loop.