173 skills · sorted by relevance
Expert-level air quality engineering covering pollutant sources, atmospheric dispersion, air quality standards, emission controls, and air quality modeling.
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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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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.
The English summary is being prepared. Showing the original description.
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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Plan data ingestion and transformation workflows with Apache Airflow, Spark, and dbt. Get guidance on processing changed records, validating data quality, and rerunning failed or historical jobs without creating duplicate results.
Review the exact final set of changes for a LoopX goal, checking reuse, simplification, concrete risks, and project validations. Record and verify a quality receipt, a review record tied to those specific changes.
Check live air quality anywhere with zero API keys — Open-Meteo's air-quality API via curl, decoded from raw PM2.5 and AQI numbers into what they mean for going outside. Use when asked what's the air quality, is it safe to run outside, AQI in my city, or pollution levels right now. Produces the current AQI and pollutant levels, the plain-language health read with the standard bands, and the rerunnable command.
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Design scheduled AI workflows for document ingestion, batch processing, and model training using Prefect, Airflow, or Dagster. Compare orchestration tools and plan task dependencies, retries, caching, and monitoring through implementation fragments.
Validate FASTQ sequencing files, run local quality checks, and interpret reports to decide whether trimming is needed. Optionally remove adapters or low-quality read ends while preserving original reads and their quality reports.
Design and implement systems that collect, transform, validate, and store data for analysis. Covers scheduled and real-time processing, data warehouses, quality checks, monitoring, and cost tuning using tools such as Apache Spark, dbt, and Airflow.
Design systems that collect, transform, and store data. Choose between scheduled and continuous processing, generate workflow configurations, validate data quality, and analyze performance using guidance for tools including Python, SQL, Spark, Airflow, dbt, and Kafka.
Plan or run DNA analysis to find small genetic changes in tumors, using tumor samples alone or paired with normal tissue. Check sample pairing, contamination, data quality, filtering, and annotations that add information to detected variants.
Guides the design of data pipelines, continuous stream processing, and data quality checks. It compares tools such as Airflow, Dagster, and Flink, and provides implementation patterns and checklists for scheduling, retries, validation, and monitoring.
Think and work like an expert Air Quality Scientist. Use when a task calls for Air Quality Scientist judgment. Reasons from source emissions through transformation, transport, and dose using SMOKE/MOVES inventories, WRF-driven CTMs like CMAQ and CAMx, PMF/ME-2 apportionment, and concentration-response functions, while treating rotational PMF ambiguity, AOD-to-PM bias in humid regions, uncalibrated low-cost sensors, and untreated wildfire exceptional events as first-class failure modes.
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Move quality earlier in the development lifecycle. Covers dev/QA pairing patterns, Three Amigos sessions, TDD facilitation (Red-Green-Refactor), PR review checklists for testability, and Definition of Done with quality gates. Includes shift-left maturity model for team assessment. Use when: "shift left," "TDD," "dev-QA pairing," "definition of done," "testability," "quality culture," "QA in sprint planning." Not for: writing the unit tests themselves — use unit-testing; automated PR test-quality review at scale — use ai-qa-review; multi-quarter QA direction or roadmap — use test-strategy. Related: unit-testing, ai-qa-review, test-strategy.
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Review source code for readability, complexity, duplication, and maintainability without changing files. Receive a structured report with prioritized issues, refactoring suggestions, positive findings, and estimates of technical debt—the work needed to address accumulated code problems.
Generate RuVLLM settings for local language model inference and create MicroLoRA or SONA instances. Adjust their small internal weights using quality scores as feedback, with instances held in server memory for subsequent adaptation calls.
Audit a gbrain knowledge base for outdated pages, broken or missing links, inconsistent tags, and missing citations. Get issue counts and specific repair actions, with additional checks for search quality and maintenance status.
数据工程 — 数据平台从业者的认知操作系统, 覆盖把数据从源系统搬运成可靠 / 可查询 / 可信赖形态供分析 / ML / 数据产品消费的全生命周期 (生成 → 摄取 → 存储 → 转换 → 服务 + 安全/数据管理/DataOps/数据架构/编排/软件工程 六条暗流, Reis & Housley 框架): 摄取与集成 (批 + CDC 变更数据捕获 Debezium + EL 工具 Fivetran/Airbyte/Meltano/dlt + Kafka Connect + schema drift) / 存储与文件表格式 (对象存储数据湖 + 列存 Parquet/ORC/Arrow/Avro + 开放表格式 Apache Iceberg/Delta Lake/Apache Hudi + lakehouse + 分区/compaction) / 转换与建模 (ELT dbt/SQLMesh + Spark + 维度建模 Kimball + Inmon + Data Vault + 大宽表 OBT + 渐变维 SCD + 增量模型 + 语义/指标层) / 编排与工作流 (Apache Airflow/Dagster/Prefect/Mage/Kestra/Apache DolphinScheduler + DAG + 幂等 + 回填 backfill + 数据资产调度) / 批流与实时 (Apache Kafka/Apache Flink/Spark Structured Streaming/Kinesis/Pulsar/Redpanda + Lambda vs Kappa + watermark/窗口/exactly-once + 流式 SQL Materialize/RisingWave + 实时 OLAP ClickHouse/Apache Druid/Apache Pinot/StarRocks/Apache Doris) / 数仓与查询引擎 (Snowflake/BigQuery/Redshift/Databricks SQL/Trino/Presto/DuckDB/Polars + 存算分离 + MPP) / 数据质量测试与可观测性 (dbt tests/Great Expectations/Soda + 数据契约 + Monte Carlo data downtime + 新鲜度/量/schema 异常检测) / 数据治理编目与血缘 (DataHub/Amundsen/OpenMetadata/Unity Catalog + 列级血缘 + PII 分类 + 访问控制 + GDPR) / DataOps 与可靠性 (数据 CI/CD + 转换版本控制 + 环境隔离 + 幂等重处理 + 数据 SLA/SLO + 计算存储 FinOps) / 数据架构范式 (现代数据栈 + lakehouse + data mesh + data fabric + 去中心化 vs 中心化所有权) / 分析工程角色 (dbt 时代连接数据工程与分析的桥) — 不含 数据科学/ML 建模本身 (是下游消费者) / BI 仪表盘制作 (serving 下游) / 数据分析报表为终点 / 'data engineer = 跑 Hadoop 的' 过时窄化 / 通用后端应用开发 (平行学科) (Data Engineering — the cognitive operating system of practitioners who design, build, and operate the data platform: moving data from source systems into reliable, queryable, trustworthy form for analytics / ML / products, covering (a) the data engineering lifecycle (generation → ingestion → storage → transformation → serving, with the undercurrents security / data management / DataOps / data architecture / orchestration / software engineering — Reis & Housley framing), (b) ingestion & integration (batch + CDC change-data-capture with Debezium, EL tools Fivetran / Airbyte / Meltano / dlt, Kafka Connect, API + file + database sources, schema drift handling), (c) storage & file/table formats (object storage data lakes, columnar formats Parquet / ORC / Arrow / Avro, open table formats Apache Iceberg / Delta Lake / Apache Hudi, lakehouse architecture, partitioning / compaction / Z-ordering), (d) transformation & modeling (ELT with dbt / SQLMesh, Spark, dimensional modeling Kimball, Inmon CIF, Data Vault, One Big Table / wide tables, normalization vs denormalization, slowly changing dimensions, incremental models, the semantic / metrics layer), (e) orchestration & workflow (Apache Airflow, Dagster, Prefect, Mage, Kestra, Apache DolphinScheduler, DAGs, idempotency, backfills, data-aware / asset-based scheduling), (f) batch vs streaming & real-time (Apache Kafka, Apache Flink, Spark Structured Streaming, Kinesis / Pulsar / Redpanda, the Lambda vs Kappa debate, watermarks / windowing / exactly-once, streaming SQL Materialize / RisingWave, real-time OLAP ClickHouse / Apache Druid / Apache Pinot / StarRocks / Apache Doris), (g) warehouses & query engines (Snowflake, BigQuery, Redshift, Databricks SQL, Trino / Presto, DuckDB, Polars, decoupled storage & compute, MPP), (h) data quality, testing & observability (dbt tests, Great Expectations, Soda, data contracts, Monte Carlo / data downtime, freshness / volume / schema anomaly detection, unit / integration testing of pipelines), (i) data governance, catalog & lineage (DataHub, Amundsen, OpenMetadata, Unity Catalog, column-level lineage, PII / data classification, access control, GDPR / data privacy), (j) DataOps & reliability (CI/CD for data, version control of transformations, environments, idempotent reprocessing, SLAs / SLOs for data, cost / FinOps for compute & storage), (k) data architecture paradigms (modern data stack, data lakehouse, data mesh, data fabric, decentralized vs centralized ownership), (l) the analytics engineering role (the dbt-era bridge between data engineering and analysis); N
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Retrieve disease outbreak alerts and air-quality health warnings for countries and cities. Review disease summaries, alert levels, sources, and fine-particle pollution readings to understand reported public-health risks in a location.
Evaluate improvements to Archify diagrams using actual outputs and agent work records. Compare accuracy, readability, and total delivery time to investigate layout, connection routing, diagnostics, and authoring guidance, then document what the evidence supports.
Review Front-End Checklist rule files and improve their instructions, explanations, and code examples. Use the project's quality scorer and structure validator to identify gaps, replace vague prompts, and organize each rule into a usable reference for developers and agents.
Upgrade MSTest v1 or v2 projects to v3, including partially completed migrations. Update packages, repair affected assertions and test data, replace legacy settings, and compare test results while preserving the existing test runner.
Qualify the exact final diff for a LoopX-managed goal. Use when goal policy enables change_quality_qualification, before a non-trivial delivery or merge, and when producing or repairing an exact-scope quality receipt. The workflow is language-neutral, permits at most one policy-authorized safe-fix pass, and never grants merge or repository authority.
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