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Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planarity, vdW overlap, bond/angle distortion), and pose-energy reasonableness. Filters AI-docking outputs (DiffDock, EquiBind, NeuralPLexer) where ~50% of poses fail physical-validity tests. Use when QC-ing docking results, comparing classical vs ML docking outputs, or filtering pose lists before SAR analysis.

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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

日本語の概要は準備中です。原文の説明を表示しています。

Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

日本語の概要は準備中です。原文の説明を表示しています。

Audit required bioinformatics command-line tools against Lmod or Environment Modules on Linux HPC clusters, resolve executable and version requirements, and reproducibly deploy missing software through a site-approved EasyBuild, Spack, Bioconda/micromamba, Apptainer, binary, or source-build workflow. Use when Codex must inspect module availability, diagnose a missing or wrong-version bioinformatics tool, install scientific software on Slurm/PBS clusters, publish or validate modulefiles, or produce an auditable and rollback-ready cluster software deployment.

日本語の概要は準備中です。原文の説明を表示しています。

Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

日本語の概要は準備中です。原文の説明を表示しています。

Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization.

日本語の概要は準備中です。原文の説明を表示しています。

Use when a driver has been involved in a crash — regardless of preventability or injury — and the carrier needs to handle the immediate, post-investigation, and return-to-work phases. Covers trauma response, post-accident testing under 49 CFR 382.303, paid time off, retraining, light duty, and re-entry planning.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when the user asks about CMV maintenance program requirements under 49 CFR 396.3 — what records must be kept, retention periods (12-18 months on vehicle file + 1 year after disposal), what counts as systematic inspection/repair/maintenance, preventive maintenance scheduling, brake adjustment records, and what auditors look for in vehicle files. Cite 49 CFR 396.3 + 396.21.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when the user asks about getting/maintaining motor carrier operating authority — USDOT number, MC number, BOC-3 process agent, insurance filing (MCS-90, BMC-91/91X), Unified Carrier Registration (UCR), International Registration Plan (IRP), International Fuel Tax Agreement (IFTA), state-level permits (NY HUT, KY weight distance, OR weight-mile, NM weight distance), new entrant safety audit, intra vs interstate, for-hire vs private. Cite 49 CFR 365, 387, 390.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when the user asks about International Fuel Tax Agreement (IFTA) compliance — quarterly returns, jurisdiction reporting, fuel + miles reconciliation, IFTA-100/101 forms, base jurisdiction selection, IFTA license + decals, recordkeeping requirements, common IFTA audit findings, or how to handle non-IFTA jurisdictions. Cite IFTA Articles of Agreement.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill to understand FMCSA hearing standards for CMV drivers. Covers the forced whisper test, audiometry alternative, and certification for hearing-impaired drivers.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when you receive an IFTA audit notification and need to defend your records. Covers preparation, common arguments, and dispute escalation.

日本語の概要は準備中です。原文の説明を表示しています。

Use when a driver has been disqualified or is at risk of disqualification — major offense convictions (DUI, leaving the scene, drug trafficking with CMV), serious traffic violations, RR-grade-crossing violations, imminent-hazard out-of-service, or Clearinghouse positive-test prohibited status. Also use when planning a return-to-duty pathway, SAP process, or reinstatement timeline. Covers 49 CFR 383.51, Part 40 Subpart O, and Part 391.15.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when your carrier is selected for an IFTA audit. Covers what records to produce, how the audit is conducted, and common findings.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when the user asks about hazardous materials (hazmat) transportation under 49 CFR 171-180 — placarding requirements, segregation tables, hazmat employee training (49 CFR 172 Subpart H), Hazmat Safety Permit (HMSP), shipping papers, packaging groups, emergency response phone, security plans, hazmat endorsement on CDL, and bulk vs non-bulk distinctions. Cite specific 49 CFR section.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when the user asks specifically about preparing for the New Entrant Safety Audit (NESA) under 49 CFR 385 Subpart D — different from a Compliance Review. Covers what auditors look at, the 18-month window, automatic failure conditions, the 60-day fix window, what to NOT do, and how to convert from "new entrant" to permanent authority. Cite 49 CFR 385.301-321.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when selecting an MRO for drug testing program oversight. Covers MRO qualifications under Part 40, what the MRO does, and how to evaluate MRO services.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when sorting paperwork between a driver's personnel file and the regulated DQ file. Covers FMCSA-required documents vs employer documents, audit-scope vs HR-scope, retention differences.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when an owner-operator (single CDL driver, single operating authority) needs to comply with random testing. Covers consortium membership, pool size requirements, and self-employed driver rules.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when the user asks about onboarding a new CDL driver — pre-hire process, day-zero requirements, application + DQF setup, road test, drug & alcohol pre-employment, Clearinghouse Full query, MVR initial pull, PSP report, ELDT verification, sequence of activities + timing, and what NOT to do (handing keys before testing complete). Cite 49 CFR 391, 382.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when interpreting a drug test result that comes back as 'diluted negative,' 'diluted positive,' 'refusal,' or 'adulterated.' Covers what constitutes a refusal vs. retest vs. confirmed positive.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when the user asks about commercial driver drug & alcohol testing under 49 CFR 382 + 40 — the six testing reasons (pre-employment, random, post-accident, reasonable suspicion, return-to-duty, follow-up), MRO process, SAP/return-to-duty process, post-accident triggers, random selection rates, what panels are tested, refusal definitions, or testing programs and consortiums. Cite specific 49 CFR 382 or 40 subsection.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when the user asks about carrier-driver relationships — Independent Contractor (IC / 1099) vs Employee (W-2), Owner-Operator lease agreements, the AB5 California law, the DOL 2024 IC test, lease-purchase programs from the carrier side, settlement statements, deductions, and how to structure a compliant IC arrangement. Cite 49 CFR 376 + 1099 IRS rules.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when the user asks about Driver Qualification Files (DQF) — what must be in a DQ file under 49 CFR 391, retention periods, what's required pre-hire vs ongoing, document expiration tracking, audit-readiness for driver files, common DQF deficiencies that auditors find, or how to handle missing documents on existing drivers. Always cite the specific subsection of 49 CFR 391.

日本語の概要は準備中です。原文の説明を表示しています。