「sem」の検索結果

Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

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。

Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

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。

Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

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。

半导体芯片制造工艺 (Semiconductor Process Engineering / 半导体芯片制造工艺 — 以「物理化学极限 + 良率经济双重约束」为特征的集成电路前道/后道制造工艺认知操作系统：从「器件架构与微缩路线（planar→FinFET→GAA nanosheet→CFET、等效微缩 DTCO/STCO、背面供电 BSPDN）→ 工艺整合（FEOL/MOL/BEOL 模块协同、PDK、流片 tape-out）→ 单元工艺（光刻 litho（DUV 浸没式 193i / EUV 13.5nm / 多重曝光 SADP-SAQP / OPC / mask）、刻蚀 etch（RIE/ICP/原子层刻蚀 ALE）、薄膜沉积 depo（CVD/PECVD/LPCVD/ALD/PVD/外延 epi/电镀 Cu）、掺杂 doping（离子注入 ion implant / 退火 RTA-laser anneal）、CMP 化学机械抛光、清洗 cleaning）→ 量测检测 metrology（CD-SEM / OCD / overlay / 椭偏 ellipsometry / 缺陷检测 defect inspection / e-beam）→ 良率工程 yield（缺陷密度 / SPC 统计过程控制 / FDC / APC / DOE 实验设计 / 良率爬坡 yield ramp）→ 先进封装 advanced packaging（2.5D/3D、CoWoS、HBM、混合键合 hybrid bonding、chiplet、TSV）」的完整器件-工艺-良率-量产决策链。覆盖 (a) 第一性张力 — **物理/化学/材料的硬约束（量子隧穿、短沟道效应、RC 延迟、热预算、缺陷物理、ppb 级污染控制）⇄ 良率/成本/产能的经济约束（每片晶圆成本、良率是主经济指标、D0 缺陷密度、wafer-per-hour、折旧）**；**持续微缩/摩尔定律（dimensional + equivalent scaling、节点路线图 N5/N3/N2/A16/A14、high-NA EUV）⇄ 物理极限/微缩放缓（原子尺度、漏电、功耗墙、成本墙、'摩尔定律已死'之争）**；**协同优化/整合（DTCO 设计-工艺协同、STCO 系统-工艺协同、模块间 trade-off）⇄ 单模块极致优化（单一 unit process 工艺窗口）**；**工艺配方的 tacit 手艺（process recipe 调试、工艺窗口、缺陷根因分析、量产 ramp 的经验）⇄ 可建模/可仿真/数据驱动（TCAD 仿真、ML 良率分析、APC/FDC、数字孪生）**；**性能-功耗-面积-成本 PPAC 四角权衡 ⇄ 良率/可制造性 DFM 优先**；**自主可控/国产替代（卡脖子、EUV 出口管制、设备/材料/EDA 国产化、SMIC/长江存储/长鑫/中微/北方华创/上海微电子）⇄ 全球高度分工（ASML 光刻垄断、AMAT/Lam/TEL/KLA 设备、TSMC/Samsung/Intel 代工、全球供应链）**。(b) 核心工作流 / pipeline（最标准、最易蒸高质量 + CLI 化）— 新节点/新工艺导入：器件目标与 PPAC 定义 → 工艺整合方案与 PDK → 单元工艺开发与配方调试（DOE 找工艺窗口）→ 量测建立与 SPC → 良率爬坡（缺陷分类 + 根因分析 + 工艺改善）→ 量产移交与持续改善。具体单元工艺 SOP：光刻（曝光条件 / OPC / overlay 控制 / 多重曝光分解）、刻蚀（选择比 / profile / loading effect / ALE）、沉积（台阶覆盖 / 应力 / 均匀性）、CMP（去除速率 / 碟形 dishing / 侵蚀 erosion）、量测与缺陷分析、良率分析与 FA 失效分析。(c) 工具栈 — 设备（光刻 ASML/上海微电子 SMEE；刻蚀+沉积 AMAT/Lam/TEL/中微 AMEC/北方华创 Naura；离子注入 AMAT/Axcelis；CMP AMAT/荏原 Ebara；量测检测 KLA/AMAT/中科飞测/上海精测）、EDA/TCAD/仿真（Synopsys Sentaurus/Silvaco/Coventor SEMulator3D、OPC Calibre/Synopsys）、良率与制造软件（SPC、MES、FDC/APC、缺陷分析 yield management、PWS）、材料（光刻胶 photoresist、CMP 浆料 slurry、特气、靶材、掩膜 mask blank）。(d) 知识正典 — 半导体工艺 canon 横跨器件物理与制造工程：核心教材（Plummer/Deal/Griffin《Silicon VLSI Technology》、Sze《Physics of Semiconductor Devices》《VLSI Technology》、Wolf & Tauber《Silicon Processing for the VLSI Era》、Campbell《Fabrication Engineering at the Micro and Nanoscale》、May & Spanos《Fundamentals of Semiconductor Manufacturing and Process Control》、Quirk & Serda《Semiconductor Manufacturing Technology》、肖国勇/施敏中文教材）、路线图（ITRS/IRDS、IEEE 国际器件与系统路线图）、顶会论文（IEDM、Symposium on VLSI Technology、IRPS 可靠性、SPIE Advanced Lithography、ISSCC、DAC）、行业分析（SemiAnalysis、TechInsights、IC Knowledge）。(e) figures/流派 — 学术与器件奠基（Gordon Moore 摩尔、Robert Dennard 登纳德微缩、胡正明 Chenming Hu FinFET/UTB-SOI 发明人 UC Berkeley、刘明 Tsu-Jae King Liu Berkeley、Krishna Saraswat Stanford、Mark Bohr Intel 工艺架构）、产业领袖与工艺大师（张忠谋 Morris Chang TSMC、林本坚 Burn-Jeng Lin 浸没式光刻、Martin van den Brink ASML、米玉杰/梁孟松 SMIC/三星工艺、Mark Liu/魏哲家 TSMC）、行业分析师（Dylan Patel SemiAnalysis、Scotten Jones IC Knowledge、TechInsights 拆解、Handel Jones）、科普与拆解（Asianometry、The Chip Letter、半导体行业观察）。流派分歧：等效微缩派 vs 摩尔定律已死派、前道微缩 vs 先进封装 chiplet 异构集成、dimensional scaling vs DTCO 协同优化、IDM vs 纯代工 foundry 模式、自主可控/国产替代路线 vs 全球分工。(f) 行业话术/黑话 — 制程节点 node / 流片 tape-out / 工艺窗口 process window / 良率 yield / 缺陷密度 D0 / 关键尺寸 CD / 套刻 overlay / 掩膜 reticle-mask / 光刻胶 PR / 浸没式 immersion / EUV/DUV / 多重曝光 multi-patterning SADP-SAQP / OPC / 刻蚀选择比 selectivity / profile / loading effect / 原子层刻蚀 ALE / 台阶覆盖 step coverage / 外延 epi / 离子注入 implant / 退火 anneal / RTA / CMP / dishing-erosion / FEOL-MOL-BEOL / FinFET / GAA / 纳米片 nanosheet / CFET / 背面供电 BSPDN / high-NA / PPAC / DTCO-STCO / DFM / SPC / FDC-APC / DOE / WAT-PCM / 良率爬坡 yield ramp / FA 失效分析 / particle 颗粒 / 洁净室 cleanroom-级别 / 12寸-8寸 wafer / chiplet / CoWoS / HBM / 混合键合 hybrid bonding / TSV / PDK / 等效微缩. (g) 争议/批判 — 「摩尔定律是否已死 vs 等效微缩继续」、「节点命名营销化（N3/N2 ≠ 物理 3nm/2nm，gate pitch/metal pitch 才是真尺度）」、「前道微缩 vs 先进封装异构集成谁是未来」、「自主可控/国产替代的现实（EUV 卡脖子、设备/材料/EDA 国产化进度、出口管制 entity list、良率与成熟度差距）」、「良率/成本/性能三角权衡」、「人才稀缺与工艺 know-how 的 tacit 性」、「中国大基金/产能扩张是否过剩」、「制裁与技术封锁」。(h) 大量隐性工艺手艺（process recipe 调试与工艺窗口寻找、缺陷根因分析与 FA、量产良率爬坡的经验判

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。

Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.

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。

Query the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover, gene lookups, and cross-references. Use when the user needs to annotate variants with VEP (consequence, CADD, REVEL, SpliceAI), check Ensembl Regulatory Build overlap for ENCODE regions, convert coordinates between GRCh37 and GRCh38, resolve gene IDs (Ensembl ↔ symbol ↔ RefSeq), look up gene phenotype associations, or cross-reference ENCODE targets with Ensembl annotations. Also use when the user mentions Ensembl, VEP, variant effect predictor, liftover, assembly conversion, regulatory build, gene lookup, or cross-references between databases.

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。

Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.

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。

Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.

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。

Runs a Semgrep security scan over a codebase: detects languages, selects rulesets, presents the plan for explicit approval, then runs every approved ruleset through scripts/run-scans.sh, which batches the semgrep processes and writes scans.json, and merges the output to SARIF. Supports two scan modes, "run all" for full ruleset coverage and "important only" for security findings at medium-to-high confidence and impact. Uses Semgrep Pro for cross-file taint analysis when it is available. Use when asked to scan code for vulnerabilities, run a security audit with Semgrep, find bugs, or perform static analysis. For the same scan without the approval gate, use the /static-analysis:semgrep-scan workflow.

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。

Configure AssemblyAI keys, regional endpoints, and server-versus-browser authentication safely. Use when installing or authenticating an integration. Trigger with "AssemblyAI auth", "AssemblyAI API key", or "AssemblyAI endpoint setup".

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。

Analyze and control AssemblyAI model, feature, duration, retry, concurrency, and LLM Gateway spend using measured usage. Use when setting budgets or investigating anomalies. Trigger with "AssemblyAI cost", "AssemblyAI billing", or "reduce AssemblyAI spend".

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。

Run a bounded AssemblyAI pre-recorded smoke test with explicit model fallback and safe output. Use when proving a new integration. Trigger with "AssemblyAI hello world", "first AssemblyAI transcript", or "AssemblyAI smoke test".

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。

Analyze and control AssemblyAI account request limits, concurrency, backoff, and admission queues. Use when handling 429s or planning throughput. Trigger with "AssemblyAI rate limit", "AssemblyAI concurrency", or "AssemblyAI backoff".

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。

Analyze and design a typed AssemblyAI adapter that isolates SDK drift, regional routing, polling, and streaming lifecycles. Use when integrating an official SDK. Trigger with "AssemblyAI SDK pattern", "AssemblyAI adapter", or "wrap AssemblyAI".

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。

Assembles microbial-community sequencing into metagenome-assembled genomes (MAGs) with metaFlye (ONT), metaSPAdes/MEGAHIT (Illumina), and hifiasm-meta/metaMDBG (PacBio HiFi), then recovers genomes via multi-binner consolidation (MetaBAT2, MaxBin2, CONCOCT, SemiBin2, VAMB -> DAS_Tool) and QCs them against MIMAG with CheckM2, GUNC, and GTDB-Tk. Covers why a metagenome is not a genome (uneven coverage, micro-diversity, strain collapse to consensus), differential-coverage binning, co-assembly vs per-sample, the rRNA-operon collapse that fails short-read MAGs, and strain resolution with inStrain. Use when reconstructing genomes from a microbiome, soil, ocean, or gut community, recovering MAGs, or resolving strain-level variation.

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。

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.

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。

Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.

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。

Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.

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。

Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when evaluating assembly completeness and quality.

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。

Entity-aware code change analysis using the pi-sem tools. Use when the user asks what changed, wants blast radius or affected tests, needs focused context for a function/class, wants review help on a commit/branch/PR, or asks to compare semantic diff with raw git diff. Prefer sem_context and sem_impact; use sem_diff selectively for summaries and reviews.

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。

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.

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。

Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.

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。

Expert-level semiconductor materials covering band theory, silicon processing, compound semiconductors, wide bandgap materials, and semiconductor device fundamentals.

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。

Full lifecycle expense reimbursement: single invoice intake and staging, batch aggregation to generate reimbursement drafts, approval workflow, ledger and dashboard. Trigger when user mentions reimbursement, expenses, invoices, travel reimbursement, approval workflow, or needs to organize / verify / approve expense records. Also applies when user needs to enter invoices, view reimbursement dashboards, ledgers, or compliance checks.

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。