Business & Operations

Federated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ),

Wren Engine CLI workflow guide for AI agents. Answer data questions end-to-end using the wren CLI: gather schema context, recall past queries, write SQL through the MDL semantic layer, execute, and learn from confirmed results. Use when: user asks a data question, requests a report or analysis, asks about metrics, revenue, customers, orders, trends, or any business data; user says 'how many', 'show me', 'what is the', 'top N', 'compare', 'trend', 'growth', 'breakdown'; user wants to explore, ...

Generate a Wren MDL project by exploring a database with available tools (SQLAlchemy, database drivers, MCP connectors, or raw SQL). Guides agents through schema discovery, type normalization, and MDL YAML generation using the wren CLI. Use when: user wants to create or set up a new MDL, onboard a new data source, or scaffold a project from an existing database.

Augment a Wren project with business context that DB schema cannot carry — enum value meanings, units (USD vs cents, ms vs sec), NULL semantics, magic sentinels (-1 = unknown), soft-delete default filters, business synonyms, time-grain / TZ conventions, cross-system identifiers, currency rules, canonical-table preferences, AND named aggregation metrics (ARR, churn, DAU, WAU, NRR) proposed as cubes. Runs in one of two modes selected at session start: `grill` (one question at a time, user-drive...

Upload a local file to ClawLink server and return the file reference for sending in chat. Whenever you need to send a file to someone, you must use this skill, including: the owner asks "send xxx to them", in a ClawLink negotiation conversation the other Claw requests "send me the file", "send the xxx file", "share the file", etc. Never read the file content and send it as a text message. You must upload the file and send a file reference.

Notify colleagues via ClawLink network. Use when user says things like "contact xxx", "tell xxx", "ask xxx", "notify xxx", "have xxx help", "check with xxx", or any statement that requires another person's assistance.

Flow.bio API bridge — authenticate, browse pipelines/samples/projects, search, upload data, launch pipeline executions,

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.

Detect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence identity falls into the twilight zone (<35% pairwise), when BLAST fails to find homologs that should exist, when working at metagenomic scale (DIAMOND, MMseqs2), or when structure beats sequence (Foldseek). Covers PSI-BLAST (iterative PSSM), jackhmmer (iterative HMM), HHblits/HHsearch (profile-profile), DIAMOND, MMseqs2, and Foldseek (3Di structural alphabet, van Kempen 2024).

Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6 structural variants), Aldy, Stargazer; applies Caudle 2020 activity-score translation. Use when implementing pharmacogenomic-guided prescribing, applying CPIC vs DPWG guidance, screening HLA risk alleles for ICI / antiepileptics / abacavir, or interpreting compound TPMT+NUDT15 thiopurine risk.

Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution. Use when building portable pipelines with container support, running workflows on cloud platforms (AWS, Google Cloud), or leveraging nf-core community pipelines.

End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal, denoising with OBITools3 or DADA2, contamination filtering, taxonomy assignment, Hill number diversity, and constrained ordination. Use when processing environmental DNA samples for biodiversity assessment or ecological surveys.

Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

Create and inspect Shader Graph assets

Manage Unity Package Manager (UPM) packages

Set up and manage SSO, SCIM provisioning, and MFA for startup teams using Google Workspace, Okta, or Azure AD. Use when centralizing authentication, onboarding SSO, or meeting compliance requirements.

Manage Cloudflare R2 buckets, lifecycle, and signed URLs. Use for low-egress object storage and media delivery.

Reduce AWS spend with rightsizing, autoscaling, commitment planning, and storage lifecycle policies. Use when running FinOps reviews, lowering cloud bills, or improving cost-per-request metrics.

Build AI-focused SRE incident response practices for LLM outages, degraded quality, runaway cost events, and safety regressions.

Implement incident management processes and escalation procedures. Configure on-call schedules and post-incident reviews. Use when managing production incidents.

Implement disaster recovery strategies and runbooks. Configure RPO/RTO targets and failover procedures. Use when planning for business continuity.

Develop business continuity plans and impact analysis. Implement BCP testing and communication procedures. Use when building organizational resilience.

Create and edit Excel .xlsx workbooks (sheets, cells, formulas, formatting) via Python `openpyxl`. Use to generate spreadsheets or write/update cells. Reading is via os.fs.read_document.

Manipulate PDF files — merge, split, extract pages/text, PDF↔images, OCR, info — via the `qpdf` / `poppler` / `ocrmypdf` CLIs. Use to combine, slice, convert, or OCR PDFs.