'logs' 검색 결과

Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

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Exclusive-choice UI: CheckButton radio groups in list rows, when to use them vs ComboRow vs ToggleGroup. Use when presenting mutually exclusive options in GNOME preferences or dialogs.

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Implement GNOME's 4-tier destructive-action pattern: undo toasts instead of confirmation dialogs, AdwAlertDialog for irreversible actions. Use when adding delete, remove, clear, or other destructive actions.

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Audit a GTK4/libadwaita app for GNOME HIG compliance across 12 categories (text, icons, layout, shortcuts, accessibility, color, dialogs, responsiveness, CSS, GSettings, i18n), then fix violations category by category. Use when asked to audit, review, polish, or "make HIG-compliant" a GNOME app, or before a release/Flathub submission.

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In-app notifications: AdwToast/ToastOverlay with undo buttons, when to use toasts vs banners vs dialogs. Use when giving feedback after user actions in a GNOME app.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Runs standard-format scenarios through ScenarioRunner — ASAM OpenSCENARIO 1.x (.xosc, via --openscenario, with catalogs and ParameterDeclaration overrides) and OpenSCENARIO 2.0 (.osc, via --openscenario2, the ANTLR/osc2 pipeline). Validates a file against the schema before running, lists the bundled examples, and reports which OSC features ScenarioRunner actually implements. Use when the user asks to "run an xosc", "run an OpenSCENARIO file", "use the OpenSCENARIO standard", "run a .osc / OSC2 scenario", or hands over a scenario file from another tool.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Figma REST API / Plugin API / Widget API / Code Connect / MCP Server / Dev Mode リファレンス OAuth / PAT / Plan Access Token, files, folders, variables, VariableComposedColor, webhooks, SCIM, Dev Resources, activity-logs, library-analytics FrameNode, TextNode, ComponentNode, figma.variables, figma.codegen, figma.ui, textWrapStyle, variable fonts Widget useSyncedState, useSyncedMap, usePropertyMenu, AutoLayout Code Connect template files (.figma.ts) / legacy parser / custom parsers / register / Storybook (React / SwiftUI / Compose / HTML) MCP Code to Canvas, Write to Canvas, html_to_figma, generate_image, get_motion_context, generative plugins / shaders, Figma Weave

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OpenAI API (developers.openai.com) の運用・管理リファレンス。 Administration API, admin API keys, RBAC, roles, groups, invites, projects, spend limits, audit logs, usage / costs API, Terraform provider (openai/openai), workload identity federation (WIF, OIDC / SPIFFE / X.509 / Idira), moderation API, misalignment monitoring, safety alerts / cases, safety best practices, under-18 guidance, ZDR Private Safety Processing (PSP), production best practices, deployment checklist, cost / latency optimization, fast / ultrafast mode, Realtime API costs。 rate limits・error handling・prompt caching・webhooks は openai-api-core、Codex WIF・管理は openai-codex。

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Clear Unity Console entries. Use before compile, tests, or debugging when stale logs would hide the current result.

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Map owned assets, attack surface, and inventory for systems the requester is authorized to assess. Use for asset discovery, service catalogs, and exposure reviews — never unauthorized scanning.

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Query and interpret security logs you are authorized to read. Build detections and investigations without leaking PII.

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Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNOG-mapper (orthology), InterProScan (domain signatures), and KofamScan (KEGG), routing specialized functions to dbCAN/antiSMASH/AMRFinderPlus/SignalP. Covers the orthology-vs-domain-vs-homology paradigms, the annotation-error percolation cascade, domain-presence-is-not-function, GO IEA circularity in enrichment, evidence tiering, and bit-score/coverage thresholds. Use when adding functional annotation to predicted genes, choosing between eggNOG-mapper and InterProScan, or judging how much to trust a functional label.

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Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.

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Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and when to defect to de novo computation.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Cell Reports 36:109597), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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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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Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, LOEUF interpretation, SV/CNV/mtDNA catalogs, and Whiffin max-credible-AF framework. Use when filtering rare variants, applying ACMG BS1/BA1, ranking genes by LoF intolerance, or selecting between v2 (GRCh37 + chrX/Y constraint) and v4 (GRCh38 + 807k samples).

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Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, Annoy MHFP6, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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Memory consolidation pass: orient on existing memories, gather signal from logs/transcripts, merge updates into topic files, prune index. Use on 'dream', 'consolidate memory', 'clean up memories', 'prune memories', 'memory maintenance', or when memories feel stale.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.