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API + Python SDK for ordering cell-free protein expression and binding assays. Submit sequences for expression (10–100 µg), measure binding affinity (KD) against targets, track status, and retrieve results programmatically — no wet-lab setup. Built for ML-guided directed evolution and antibody/nanobody optimization. Requires Adaptyv account and API key.
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How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.
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Task sequences, progressive disclosure, and the pacing of an experience over time. Use when designing multi-step flows, evaluating onboarding, or diagnosing why users get lost.
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Create polished, validated architecture, workflow, sequence, data-flow, and lifecycle/state diagrams as explorable standalone HTML with inline SVG, dark/light themes, optional trace motion, and PNG/JPEG/WebP/SVG/WebM export. Accept plain-language requirements or pasted Mermaid flowchart, sequenceDiagram, and stateDiagram input; inspect repository evidence when the diagram must reflect real code. Use when the user asks to visualize system architecture, infrastructure, cloud/security/network topology, technical workflows, API call sequences, request lifecycles, data pipelines, ETL/ELT, data lineage, state machines, or to convert/beautify Mermaid.
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Pixel-based motion and UI change analysis from frame sequences or screenshots using computer vision and visual comparison. Use when `.transition` or visual effects are not observable via MotionEyes logs, when you only have screenshots/video, when you need regression diffs across builds, or when you need to summarize on-screen changes without instrumentation. Do not use when MotionEyes traces are available and you need precise timing/values; use `motioneyes-animation-debug` instead.
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Build 2D games and animations using SpriteKit. Use when creating game scenes with SKScene and SKView, adding sprites with SKSpriteNode, animating with SKAction sequences, simulating physics with SKPhysicsBody and contact detection, creating particle effects with SKEmitterNode, building tile maps, using SKCameraNode, or integrating SpriteKit scenes in SwiftUI with SpriteView.
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Guide for using renderers — the bridge between chat-style messages and token sequences. Covers renderer setup, TrainOnWhat, vision inputs, model family matching, and custom renderers. Use when the user asks about renderers, tokenization, message formatting, or vision inputs.
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When the user wants to optimize post-signup onboarding, user activation, first-run experience, or time-to-value. Also use when the user mentions "onboarding flow," "activation rate," "user activation," "first-run experience," "empty states," "onboarding checklist," "aha moment," or "new user experience." For signup/registration optimization, see signup-flow-cro. For ongoing email sequences, see email-sequence.
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Uses Microsoft RESTler to perform stateful REST API fuzzing by automatically generating and executing test sequences that exercise API endpoints, discover producer-consumer dependencies between requests, and Bul: security and reliability bugs. The tester compiles an OpenAPI specification into a RESTler fuzzing grammar, configures authentication, runs test/fuzz-lean/fuzz modes, and analyzes results for 500 errors, authentication bypasses, resource leaks, and payload injection vulnerabilities. ...
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Architecture Decision Records — context, decision, consequences, supersession trail.
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Generates sourced, BDR-ready account research briefs for named target accounts in B2B SaaS ABM and outbound motions. Use after a target account list is built and before outreach sequences are written. Best for Tier 1, Tier 2, and intent-qualified accounts where BDRs need a clear "why this account, why now, why this persona" hypothesis. Designed for B2B SaaS teams selling compliance, security, GRC, risk, or other technical platforms into mid-market and enterprise buyers. Not intended for broad list building or mass enrichment.
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This skill covers detecting anomalies in Modbus/TCP and Modbus RTU communications in industrial control systems. It addresses function code monitoring, register range validation, timing analysis, unauthorized client detection, and deep packet inspection for malformed Modbus frames. The skill leverages Zeek with Modbus protocol analyzers, Suricata IDS with OT rules, and custom Python-based detection using Markov chain models for normal Modbus transaction sequences.
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Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, methylation, proteomics) under negative-binomial count models using RNASeqPower, PROPER, and simulation via powsimR, distinguishing per-gene from marginal (transcriptome-wide) power, the role of mean expression and dispersion, and the sequencing-depth-versus-replicate tradeoff. Covers simulation as the honest default for overdispersed counts, FDR-aware average power versus single-test power, observed/post-hoc power as an anti-pattern, and the winner's-curse / Type-S / Type-M consequences of underpowering. Use when planning replicate number for a sequencing experiment, deciding whether to add depth or samples, choosing closed-form versus simulation power, estimating power from pilot dispersions, or justifying replication in a grant. For clinical-trial power see clinical-biostatistics/power-and-sample-size; for the inverse sample-size question see experimental-design/sample-size.
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Query physics databases — NIST CODATA constants, NIST Chemistry WebBook, Materials Project, Particle Data Group (PDG), OEIS sequences. Always use these instead of hardcoding physical constants.
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Orchestrates an end-to-end CRISPR editing experiment design from target gene to delivery-ready, validatable constructs. Sequences guide design, off-target assessment, edit-modality selection (knockout, base editing, prime editing, HDR knock-in), and template/donor design, with a QC checkpoint at each handoff. Use when designing a complete CRISPR experiment for knockout, point correction, or tagging and the order of operations, the modality decision, and the cross-cutting traps are needed rather than a single step. Defers each step's mechanics to the genome-engineering skills.
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End-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction QC (RSeQC, MaxEntScan, SpliceAI), runs rMATS-turbo and leafcutter for concordant differential analysis, optionally MAJIQ V3 for complex events / heterogeneous cohorts, isoform-switching with NMD/ORF/domain consequences (IsoformSwitchAnalyzeR v2 + DRIMSeq+DEXSeq+stageR DTU), and sashimi visualizations. Use when performing comprehensive splicing analysis from raw bulk RNA-seq data; for variant-driven splice prediction see splice-variant-prediction; for rare-disease single-patient outlier detection see outlier-splicing-detection; for full-isoform PacBio/ONT analysis see long-read-splicing.
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When the user wants to optimize post-signup onboarding, user activation, first-run experience, or time-to-value. Also use when the user mentions "onboarding flow," "activation rate," "user activation," "first-run experience," "empty states," "onboarding checklist," "aha moment," or "new user experience." For signup/registration optimization, see signup-flow-cro. For ongoing email sequences, see email-sequence.
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Record PlayMode keyboard and mouse input to JSON. Use to capture gameplay, bug repro, or E2E input sequences for replay.
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Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.
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Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, methylation, proteomics) under negative-binomial count models using RNASeqPower, PROPER, and simulation via powsimR, distinguishing per-gene from marginal (transcriptome-wide) power, the role of mean expression and dispersion, and the sequencing-depth-versus-replicate tradeoff. Covers simulation as the honest default for overdispersed counts, FDR-aware average power versus single-test power, observed/post-hoc power as an anti-pattern, and the winner's-curse / Type-S / Type-M consequences of underpowering. Use when planning replicate number for a sequencing experiment, deciding whether to add depth or samples, choosing closed-form versus simulation power, estimating power from pilot dispersions, or justifying replication in a grant. For clinical-trial power see clinical-biostatistics/power-and-sample-size; for the inverse sample-size question see experimental-design/sample-size.
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Assigns pathogen lineages (SARS-CoV-2 Pangolin via UShER mode; Nextclade clade + QC; pango-designation alias_key.json resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage fitness modelling (Wenseleers / Bedford-Figgins multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data version pinning (mandatory for reproducibility), Nextclade dataset versioning (lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme version churn (V3 / V4 / V4.1 / V5.3.2 / Midnight 1200) with documented dropout regions, recombinant X-prefix Pango designation lag, GISAID vs INSDC dual-deposition tensions, and the Karthikeyan 2022 wastewater early-detection signal with explicit reproducibility caveats. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater pooled samples into lineage frequencies with Freyja, tracking lineage frequencies and growth advantages over time, pinning pangolin-data / Nextclade dataset versions for reproducibility, handling ARTIC primer dropouts (V4.1 amplicons 64 / 76 / 88-90), or running variant surveillance for SARS-CoV-2 / influenza / Mpox / RSV / H5N1 / measles.
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Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling isoform suffixes, or filtering reviewed Swiss-Prot vs auto-annotated TrEMBL. Encodes the legacy URL migration (2022), the new JSON schema layout, and bulk-pull patterns.
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Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.
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Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopython SeqRecord/SwissProt objects. Covers nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar.
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