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End-to-end bulk time-course analysis from an expression matrix to temporal gene modules and per-cluster pathway enrichment. Orchestrates temporal DE (limma splines or DESeq2 LRT), Mfuzz/tslearn soft clustering of expression-profile shapes, GAM trajectory fitting, per-cluster GO enrichment against a temporal-gene background, and an OPTIONAL circadian rhythm-detection branch (MetaCycle/CosinorPy) that runs only when the design covers >=2 full cycles with >=6-8 evenly spaced samples per cycle. Use when analyzing a bulk time-series expression experiment from any omics platform and deciding limma-splines vs DESeq2-LRT for temporal DE, soft vs hard clustering, whether the sampling design even licenses rhythm detection, and which background to use for enrichment. Not for single-cell pseudotime (see temporal-genomics/trajectory-modeling for the bulk-vs-pseudotime boundary) or unknown-period discovery (see temporal-genomics/periodicity-detection).

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Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata. Use when investigating outbreaks for who-infected-whom, defining SNP-cluster outbreak definitions, accounting for unsampled intermediates, choosing between outbreaker2 (rich epi data) and TransPhylo (genomic-only after dated phylogeny), running source attribution between host populations, calling HIV-TRACE thresholds appropriate to the local subtype, or distinguishing recent transmission from reactivation in TB / chronic HIV.

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Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata. Use when investigating outbreaks for who-infected-whom, defining SNP-cluster outbreak definitions, accounting for unsampled intermediates, choosing between outbreaker2 (rich epi data) and TransPhylo (genomic-only after dated phylogeny), running source attribution between host populations, calling HIV-TRACE thresholds appropriate to the local subtype, or distinguishing recent transmission from reactivation in TB / chronic HIV.

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通过uc命令行在多台机器组成的Uncloud集群中部署和管理服务，涵盖公开端口、Caddy路由、实例数量调整、日志查看和存储卷管理。

• 从Compose文件部署服务
• 通过HTTPS公开网页应用
• 配置通往NAS或路由器的路由

按共同根本原因整理GitHub中积累的故障报告，建立父议题和设计文档，并协助将相关修复与防止问题复发的测试合并到一个拉取请求。

• 合并具有共同原因的故障报告
• 根据未处理议题制定修复计划
• 将新故障归入已有计划

Reduce data with many features into fewer dimensions using UMAP. Create 2D or 3D views, prepare inputs for clustering, compare parameter settings, and project new samples while checking whether the results remain stable and meaningful.

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• Visualizing data with many features in 2D or 3D
• Preparing reduced features for HDBSCAN clustering
• Guiding dimensionality reduction with partial labels

Process molecular datasets in Python through a simpler interface to RDKit, a chemistry toolkit. Convert and standardize structures, calculate molecular properties, compare and cluster compounds, generate 3D conformations, and visualize results for drug discovery workflows.

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• Load and standardize molecular datasets
• Calculate molecular properties and similarities
• Cluster compounds and select diverse subsets

Set up and run kube-bench to check Kubernetes configuration against CIS security benchmarks. Select the appropriate benchmark and cluster components, then export JSON or JUnit results for automated pipelines and troubleshoot skipped checks or incorrect detection.

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• Setting up kube-bench for the first time
• Selecting benchmark versions and scan targets
• Exporting JSON or JUnit results for CI

Analyze Kubernetes API server audit logs to identify pod access, secret reads, permission changes, privileged pods, and anonymous requests. Use the event patterns to reconstruct suspicious activity and develop detection rules for security monitoring systems.

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• Tracing API activity during a suspected cluster compromise
• Reviewing access to Kubernetes secrets
• Investigating permission changes and privileged pods

Set up and manage AlloyDB for PostgreSQL clusters, instances, and backups. Includes guidance for MCP integration, a way for agents to operate databases, plus references for application connections, Terraform, authentication, and AI search capabilities.

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• Create an AlloyDB cluster and primary instance
• Manage AlloyDB backups
• Automate database operations through MCP

Plan what content to create using business goals, customer questions, and competitor gaps. Organize related topics, prioritize ideas for search or sharing, and turn them into content calendars or briefs with clear audiences and purposes.

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• Planning core themes for a company blog
• Prioritizing topics from customer questions
• Grouping related articles into topic clusters

Finds the base image needed to create a custom GKE node image. It translates requirements such as GKE version, operating system, processor architecture, accelerators, and sandbox settings into a matching image name.

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• Finding a base image for custom GKE nodes
• Looking up images for GPU or TPU configurations
• Matching images to COS, Ubuntu, ARM64, or X86_64

Configure Backup for GKE to protect Kubernetes configurations and persistent data. Set backup schedules, retention periods, and customer-managed encryption keys, then prepare restore plans with explicit policies for handling existing resources.

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• Setting scheduled backups and retention periods
• Backing up persistent data and Secrets
• Encrypting backups with customer-managed keys

Adjust application capacity on GKE through manual scaling, HPA for changing the number of running pods, and VPA for adjusting CPU and memory allocations. Includes configuration templates and a workflow for reviewing resource requests against actual usage.

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• Scale application capacity automatically as demand changes
• Review CPU and memory allocations against actual usage
• Change the number of application replicas manually

Diagnose why GKE Pods cannot authenticate to Google Cloud APIs. Inspect cluster settings, service account bindings, resource permissions, and metadata server health, then provide evidence and concrete fixes for a human to apply.

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• Investigate Pod authentication failures and 403 errors
• Check Kubernetes service account identity bindings
• Diagnose metadata server connectivity problems

Diagnose failures in GKE HorizontalPodAutoscaler (HPA), which adjusts Pod counts automatically. Investigate missing metrics, unexpected scaling behavior, and slow reactions, then receive proposed configuration fixes or commands for review before deployment.

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• Investigating unknown metrics and HPA errors
• Diagnosing workloads that will not scale up or down
• Troubleshooting scaling to and from zero

Plan and configure a shared GKE cluster for multiple teams or environments. Set up namespaces, team permissions, resource limits, and network separation, then use labels and GKE cost allocation to track spending by team.

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• Design a GKE cluster shared by multiple teams
• Separate development, staging, and production workloads
• Set team permissions and resource quotas

Create and validate Terraform alerts for GKE using PromQL, a monitoring query language. Cover response times, errors, traffic, memory usage, and cluster health, with checks for alert timing, duplicate signals, and metric ingestion costs.

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• Create alerts for GKE service latency and errors
• Detect frequent container restarts and unhealthy nodes
• Review existing Terraform alert configurations

Create and administer AlloyDB for PostgreSQL databases, including clusters, instances, backups, secure connections, and access permissions. It also covers command-line operations, infrastructure configuration, and MCP tools that let agents automate database tasks.

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• Create an AlloyDB cluster and primary instance
• Manage backups and plan recovery
• Configure secure connections and access permissions

Review BigQuery capacity, table layouts, storage retention, and SQL to improve cost efficiency. Compare billing options, plan partitioned tables, and evaluate search indexes, stored aggregation results, and BI Engine for suitable workloads.

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• Compare On-Demand pricing with Editions
• Review storage billing models and retention periods
• Design table partitioning and clustering

Manage KubeSphere’s Traefik-based Gateway API extension for external access to applications. Install, upgrade, or remove it across selected clusters, and inspect GatewayProxy resources, which manage proxy instances, to investigate deployment failures and unhealthy gateways.

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• Install or upgrade the extension on selected clusters
• Inspect GatewayProxy status by scope
• Investigate Traefik startup and update failures

Install, upgrade, and remove the ingress-nginx-based KubeSphere Gateway extension, which manages external access to applications. Inspect gateways across cluster, workspace, and project scopes, and investigate stalled operations, Helm installation failures, or pod problems.

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• Installing or upgrading the Gateway extension
• Checking gateways by cluster, workspace, or project
• Investigating stalled gateway operations and pod failures

Inspect live development or staging traffic to find an identifier that distinguishes one developer’s requests across services. Produce a matching mirrord HTTP filter and a report showing where the identifier survives, disappears, or cannot be observed.

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• Find a filter for personal requests on a shared staging cluster
• Check whether request IDs survive across services
• Build mirrord filters using JWT claims or cookies

Install and configure mirrord Operator for team use on Kubernetes. The skill covers licensing, access permissions, feature settings, internal registries, and offline deployments, with guidance for upgrades and troubleshooting across supported cluster platforms.

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• Install mirrord Operator for a development team
• Configure cloud authentication or offline licensing
• Enable preview environments and database branches