45 skills · sorted by relevance
Design and review PCR and RT-qPCR primers, short DNA sequences used to start amplification. Assess predicted structures and unintended products under explicit reaction conditions, with reports that track reference sequences, coordinates, and search limits.
Analyze encrypted ZIP challenges in a CTF sandbox and use bkcrack to recover legacy ZipCrypto keys from known file contents. Create a decrypted archive, validate extraction, and preserve the commands and evidence needed to reproduce the result.
GPCR receptor pharmacology — agonist/antagonist/inverse-agonist/biased-agonist classification, GPCRdb structural data, receptor-ligand binding analysis, antibody-target interface (SAbDab). Use for GPCR drug discovery, biased-agonism analysis, receptor subtype selectivity questions, and orthosteric vs allosteric pocket characterization.
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Create, review, migrate, and simulate Python liquid-handling protocols for Opentrons Flex and OT-2 robots. Covers deck layout, labware, pipettes, modules, volumes, and tip policies, with checks for Opentrons App analysis and operator review before physical runs.
Plan and document studies that assess whether an analytical procedure suits its intended use. Select the governing framework, evaluate calibration, accuracy, precision, and detection limits, and compare methods using acceptance criteria defined before data collection.
Think and work like an expert Molecular Biologist. Use when a task calls for Molecular Biologist judgment. Reasons from central-dogma sequence flow, binding affinity (Kd/Km/kcat), gene regulation, and biological-versus-technical replicate structure through MIQE-compliant RT-qPCR, ddPCR, Western/flow/microscopy, CRISPR editing with rescue, and IWGAV antibody validation while treating off-target reagent effects, batch effects, mycoplasma and cell-line misidentification, and toxicity-driven artifacts as first-class failure modes.
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Think and work like an expert Molecular Geneticist. Use when a task calls for Molecular Geneticist judgment. Reasons from sequence-as-hypothesis, reference context (genome build, MANE/RefSeq transcript, HGVS), and allele-level molecular consequence through ACMG/AMP-ClinGen criteria, IGV/VEP/SpliceAI/gnomAD/ClinVar review, MIQE-compliant qPCR/ddPCR, and Sanger/NGS validation while treating allele dropout, pseudogene/paralog misalignment, FFPE deamination, contamination and barcode bleed, and transcript/build mismatch as first-class failure modes.
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Think and work like an expert Food Microbiologist. Use when a task calls for Food Microbiologist judgment. Reasons from food as a hurdle-governed matrix of water activity, pH, and redox through BAM/ISO reference methods, c/n/m/M sampling plans, PMA-v-qPCR, and ComBase kinetics while treating VBNC and injured cells, post-process contamination, matrix inhibition, and unconfirmed PCR hits as first-class failure modes.
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Expert-level molecular biology knowledge. Use when working with DNA replication, transcription, translation, gene regulation, cloning, PCR, sequencing, CRISPR, epigenetics, or molecular techniques. Also use when the user mentions 'DNA replication', 'transcription', 'translation', 'gene expression', 'PCR', 'cloning', 'restriction enzyme', 'gel electrophoresis', 'Western blot', 'CRISPR', 'epigenetics', 'promoter', 'enhancer', or 'RNA splicing'.
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Implements AWS Nitro Enclave-based confidential computing environments with cryptographic attestation, KMS policy integration using PCR-based condition keys, and secure vsock communication channels. The practitioner builds enclave images, configures attestation-aware KMS policies, validates attestation documents against the AWS Nitro PKI root of trust, and establishes isolated computation pipelines for processing sensitive data such as PII, cryptographic keys, and healthcare records. Activate...
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Integrate cryptocurrency exchanges into PHP applications with CCXT. Follow examples for market data, orders, authentication, and errors, with synchronous requests, ReactPHP asynchronous processing that avoids waiting on each request, and WebSocket connections for live updates.
Assess market sentiment using fear and greed measures, options activity, margin trading, foreign investment flows, and social media discussion. Combine indicators on a common scale to produce a dashboard and explain signs of excessive optimism or fear.
Helps create, explain, debug, and optimize regular expressions for finding, extracting, or replacing text. Accounts for differences between programming languages and checks matching and nonmatching examples to identify overly broad patterns and potential performance problems.
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, low-input RNA-seq, or targeted sequencing to distinguish PCR from biological duplicates.
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Generates complete cross-disease shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction. Always use this skill whenever a user wants to design, plan, or build a multi-dataset study linking two related diseases through shared DEGs, enrichment, PPI hub genes, public validation, regulatory-network analysis, immune infiltration, drug-gene interaction screening, and optional qRT-PCR or cell-line validation. Covers five study patterns (shared-DEG discovery, hub-gene prioritization, regulatory-network interpretation, immune/drug follow-up, bioinformatics-plus-validation) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path, and a strictly verified reference literature retrieval layer with real references only.
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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.
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Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.
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Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.
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Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
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WeChat Mini Program development skill for building, debugging, previewing, testing, publishing, and optimizing mini program projects (小程序开发、调试、预览、发布). Covers project structure and config (`project.config.json`, `appid`, `miniprogramRoot`, `tabBar`, routing/navigation, icon assets), WeChat Developer Tools Nightly workflows (`wechatide` CLI, WeChat IDE Skills/MCP), `miniprogram-ci` preview/upload, console/network debugging, message push (消息推送) and customer-service auto-reply (客服消息), mini program SEO / search indexing (小程序搜索优化、页面收录、搜索推广、mpcrawler), and CloudBase integration (`wx.cloud`, 腾讯云开发, 云开发) when explicitly used. Use when users create, develop, modify, debug, preview, deploy, publish, or promote WeChat Mini Programs. NOT for Web frontend (use web-development), pure backend services (use cloudrun-development / cloud-functions), or UI-design-only tasks (use ui-design).
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Opentrons Protocol API v2 for OT-2/Flex: Python protocols for pipetting, serial dilutions, PCR, plate replication; control thermocycler, heater-shaker, magnetic, temperature modules. Use pylabrobot for multi-vendor.
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Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic trees (Phylo). Use for gene family studies, phylogenomics, comparative genomics, NCBI pipelines. For PCR/restriction/cloning use biopython-molecular-biology; for SAM/BAM use pysam.
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Think and work like an expert Molecular Ecologist. Use when a task calls for Molecular Ecologist judgment. Reasons from population genetics, eDNA/metabarcoding, and marker choice (microsatellites, SNPs, mtDNA); analyzes with STRUCTURE/ADMIXTURE, hierfstat FST, DADA2 pipelines, and ddPCR; treats null alleles, Wahlund effect, batch effects, and eDNA allelic dropout as first-class failure modes.
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Think and work like an expert Medical Parasitologist. Use when a task calls for Medical Parasitologist judgment. Reasons from specimen-stage fit, exposure-based pretest probability, and antigen-versus-antibody kinetics through thick/thin Giemsa films, formalin-ethyl-acetate concentration with trichrome, multiplex PCR, and EITB serology against CDC DPDx and WHO algorithms, while treating pfhrp2/3-deleted RDT false-negatives, single-O&P misses of Strongyloides, and colonization-mistaken-for-infection as first-class failure modes.
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