DevOps & Infra

stanfish06 Bundle

Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and triage execution failures. Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.

stanfish06 Bundle

High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.

stanfish06 Bundle

Installs and uses the Render CLI for deploys, logs, SSH, psql, Blueprint validation, and automation. Use when the user needs to run Render CLI commands, script deploys in CI/CD, authenticate with an API key, query services non-interactively, or troubleshoot CLI auth issues. Trigger terms: render CLI, render login, render deploys, render logs, render ssh, render psql, render blueprints validate, render skills, RENDER_API_KEY, non-interactive, CI/CD deploy.

stanfish06 Bundle

First-time setup, environment configuration, and model-weight installation for Proteina-Complexa. Reach for this skill whenever the user says "set up complexa", "install complexa", "configure my environment file", "first-time setup", "what models do I have installed", "what's in my environment file", "download model weights", "download Complexa / AF2 / RF3 / ProteinMPNN / LigandMPNN / ESM2 / ESMFold checkpoints", "preflight my GPU", "verify environment", "complexa init", "complexa download", "complexa download --status", "complexa validate env", or any time a fresh checkout needs to be made runnable. This is the first skill to run on a new clone — it drives `complexa init`, `complexa download`, and `complexa validate env` end-to-end, edits the required `.env` keys, picks the right runtime (UV vs Docker), and emits a replayable setup artifact.

stanfish06 Bundle

Use this skill whenever the user wants to run a parameter sweep over a Proteina-Complexa design pipeline — cartesian-product hyperparameter scans, Pareto search over generation/reward/evaluation knobs, or any "compare configurations" workflow. Trigger phrases include "sweep beam width", "sweep nsteps", "hyperparameter sweep", "parameter scan", "scan beam_width and temperature", "compare configurations", "find the best generation params", "what's the optimal nsteps", "Pareto search for binder quality vs wall-clock", "complexa sweep", "tune Complexa", "ablate the reward weights", "configs/sweeps", "--sweeper", "run beam_width.yaml". This is the only skill that owns sweeper YAML authoring, cartesian-product expansion, and per-config result ranking.

stanfish06 Bundle

End-to-end Proteina-Complexa design pipeline driver. Use when the user wants to "design a binder", "design binders for X", "run complexa design", "de novo binder", "PDL1 binder", "TrkA binder", "design proteins for target", "protein binder design", "ligand binder", "design a small-molecule binder", "ATP-binding protein", "AME motif scaffolding", "scaffold a motif near a ligand", "motif + ligand design", "enzyme scaffolding", "flow matching protein design", "beam-search binder", "FK steering", "MCTS protein design", or "refold with AF2 / RF3 / ESMFold", or wants success rates, interface pAE, scRMSD, or FoldSeek diversity from one command. Drives the complexa design pipeline from target picking to manifest emission and reports how many designs passed.

stanfish06 Bundle

Use this skill whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder (default), ligand binder, or AME / enzyme scaffolding. Triggers include "add a target", "define a new target for binder design", "register a hotspot", "set up a PDL1 binder target", "ligand binder pocket", "SMILES target", "AME task", "enzyme motif", "M0024_1nzy", "complexa target add", "complexa target show", "configure target X", "what targets are available", "where do hotspots live", "what does target_input mean", "chain-spec syntax", "binder length range", or any question about `configs/targets/{,ligand_}targets_dict.yaml` and `configs/design_tasks/ame_dict_v2.yaml`. Also covers `complexa validate target`. This is the only skill that touches the three targets dict files.

stanfish06 Bundle

Check whether public NGS tools and packages already exist before downloading, installing, or running a sequencing pipeline.

stanfish06 Bundle

Generate and run MATLAB unit tests using matlab.unittest and matlab.uitest. Parameterized tests, fixtures, mocking, coverage analysis, CI/CD with buildtool, app testing with gestures. Use when creating tests, writing test classes, running test suites, checking coverage, testing apps, or validating MATLAB code.

stanfish06 Bundle

Validate and render Mermaid diagrams to SVG, PNG, or ASCII with bundled scripts (mermaid-cli, beautiful-mermaid, Puppeteer icon packs), plus styling rules for C4 and AWS architecture-beta diagrams. Use when a .mmd file needs a syntax check, a rendered image, batch rendering, ASCII output, an AWS icon diagram, a C4 diagram, or one of the 20 bundled themes. Do not use for choosing a diagram type or writing Mermaid inside markdown docs (use markdown-mermaid-writing or diagram-generator), or for previewing in the terminal (use mermaid-terminal).

stanfish06 Bundle

Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Use for ProteinMPNN, inverse folding, sequence design, backbone redesign, fixed chains/residues, omit_AAs, sampling temperature, soluble model, hosted NVIDIA API, local Docker, PDB input, and multi-FASTA output.

stanfish06 Bundle

Orchestrator for the full academic research pipeline: research -> write -> integrity check -> review -> revise -> re-review -> re-revise -> final integrity check -> finalize. Coordinates deep-research, academic-paper, and academic-paper-reviewer into a seamless 10-stage workflow with mandatory, coverage-bounded integrity checks, two-stage peer review, and auditable quality-assurance artifacts. Triggers on: academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, complete paper workflow, 연구부터 논문까지, 연구 주제 설정부터 논문 완성까지, 논문 전체 워크플로.

stanfish06 Bundle

Generate and normalize 2D sprite animations. Use when the user asks for full-strip generation from approved source frames, consistent anchor and scale normalization, or preview assets for browser-game animation.

stanfish06 Bundle

Step 6 of the bio-manuscript pipeline: design manuscript figures panel by panel. Use when planning figure logic, panel content, supplementary figures, and draft captions, keeping figure logic synchronized with manuscript claims.

stanfish06 Bundle

Step 4 of the bio-manuscript pipeline: design the evaluation-metric system. Use when extracting quantitative and qualitative metrics from literature or adjacent fields, organizing them into groups, and explaining what each metric measures and how to compute it.

stanfish06 Bundle

Design and run bounded chaos engineering experiments that test whether a system preserves measurable steady-state behavior during realistic faults. Use for resilience hypotheses, game days, fault injection, failover and recovery validation, or LitmusChaos and Chaos Mesh experiments involving pod, node, network, latency, resource, storage, DNS, time, or cloud failures. Require explicit authorization before mutating an environment, especially production; do not use as a substitute for load testing, disaster-recovery planning, penetration testing, or incident response. Pair with kubernetes-specialist when broader cluster design or workload remediation is required.

stanfish06 Bundle

Step 2 of the bio-manuscript pipeline: design the task system. Use when identifying the dominant task taxonomy in a field and organizing it into a staged Level 1-4 difficulty ladder to prepare for downstream dataset and metric design.

stanfish06 Skill

Authoring GitHub Actions CI/CD workflows — workflow/job/step structure, triggers, build-test matrices, dependency caching, secrets and least-privilege permissions, reusable workflows, and common Python/Node CI recipes. Use when creating or fixing .github/workflows/*.yml, setting up CI for tests/lint/build, adding a release or deploy pipeline, or speeding up/securing existing workflows. To audit agentic (AI-in-CI) workflows for injection, see agentic-actions-auditor.

stanfish06 Bundle

Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.

stanfish06 Bundle

Use when users want to run any workload on Hugging Face Jobs infrastructure. Covers UV scripts, Docker-based jobs, hardware selection, cost estimation, authentication with tokens, secrets management, timeout configuration, and result persistence. Designed for general-purpose compute workloads including data processing, inference, experiments, batch jobs, and any Python-based tasks. Use for tasks involving cloud compute, GPU workloads, or when users mention running jobs on Hugging Face infrastructure without local setup.

stanfish06 Bundle

Step 3 of the bio-manuscript pipeline: find and match public datasets to manuscript tasks. Use when extracting datasets from related papers or searching repositories (e.g. GEO), normalizing dataset metadata, and mapping datasets to the task system.

stanfish06 Bundle

Build GraphRAG retrieval pipelines on Neo4j using the neo4j-graphrag Python package (v1.16.0+). Covers retriever selection (VectorRetriever, HybridRetriever, VectorCypherRetriever, HybridCypherRetriever, Text2CypherRetriever, ToolsRetriever), external vector DB retrievers (Weaviate, Pinecone, Qdrant), retrieval_query Cypher fragments, query_params, filters, GraphRAG pipeline wiring (GraphRAG + LLM + prompt), all LLM providers (OpenAI, Anthropic, VertexAI, Bedrock, Cohere, Mistral, Ollama), embedder setup, index creation, token usage tracking, Cypher 25 SEARCH clause, and LangChain/LlamaIndex integration. Does NOT handle KG construction — use neo4j-document-import-skill. Does NOT handle plain vector search — use neo4j-vector-index-skill. Does NOT handle GDS analytics — use neo4j-gds-skill. Does NOT handle agent memory — use neo4j-agent-memory-skill.

stanfish06 Bundle

Phase 2.6 of the bio-manuscript pipeline: human review checkpoint. Use when presenting a refined proposal to a human reviewer, collecting explicit feedback, recording approval or requested changes, and routing the workflow back to the correct phase.

stanfish06 Bundle

Generates and writes new unit tests for any programming language — scaffolds test projects and configures coverage tooling (coverlet, pytest-cov, @vitest/coverage-v8) as part of test generation. Use when asked to generate tests, generate pytest tests, generate Vitest tests, write unit tests, add tests, improve coverage, comprehensive tests, or scaffold a new test project or suite for an app, service, library, REST API, blueprint, or package — including project-wide, multi-file test generation across services, repositories, routes, and modules. Supports C#/.NET, Python (pytest, Flask/Django), TypeScript/JavaScript (Vitest, Jest, Mocha), Go, Rust, Java (JUnit). Runs a research, planning, and implementation pipeline so tests compile and pass. DO NOT USE FOR: running existing tests (use run-tests); analyzing existing coverage reports (use coverage-analysis or crap-score); writing, fixing, or modernizing MSTest-specific tests, assertions, attributes, or lifecycle (use writing-mstest-tests).

stanfish06 Bundle

Data validation using Great Expectations. Expectation suites, checkpoints, and data docs for pipeline monitoring.

stanfish06 Bundle

Refinement loop for the bio-manuscript pipeline: three-reviewer iterative optimization (editor, computational, biological). Use when reviewing a manuscript plan, producing structured review comments, revising round by round, and tracking score and revision history toward a target journal.

stanfish06 Skill

Prepares production launches. Use when preparing to deploy to production. Use when you need a pre-launch checklist, when setting up monitoring, when planning a staged rollout, or when you need a rollback strategy.

stanfish06 Bundle

Quick install and deploy vLLM, start serving with a simple LLM, and test OpenAI API.

stanfish06 Bundle

Step 1 of the bio-manuscript pipeline: assess research-idea novelty. Use when expanding a topic into variants/synonyms, searching PubMed/bioRxiv/arXiv q-bio, de-duplicating related papers, assigning a novelty level, and suggesting how to sharpen or reposition the idea.

stanfish06 Skill

Automates CI/CD pipeline setup. Use when setting up or modifying build and deployment pipelines. Use when you need to automate quality gates, configure test runners in CI, or establish deployment strategies.

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Step 5 of the bio-manuscript pipeline: design the analysis-method system. Use when planning which analyses, tools, and biological validations support each figure and task, mapping analyses to BioClaw-compatible tools or fallbacks, and connecting analyses to figure panels.

stanfish06 Bundle

Step 7 of the bio-manuscript pipeline: draft the main manuscript text. Use when writing the Introduction, Results (around the figure logic), Discussion, and a Methods skeleton from the figure plan, metric system, and analysis system.

stanfish06 Skill

Migrates .NET test projects from VSTest to Microsoft.Testing.Platform (MTP). Use when user asks to "migrate to MTP", "switch from VSTest", "enable Microsoft.Testing.Platform", "use MTP runner", set OutputType=Exe only for test projects in Directory.Build.props, or mentions EnableMSTestRunner, EnableNUnitRunner, or UseMicrosoftTestingPlatformRunner. USE FOR: MTP behavioral differences vs VSTest (exit code 8, zero tests discovered, --ignore-exit-code, TESTINGPLATFORM_EXITCODE_IGNORE); centralizing MTP properties and OutputType=Exe on test projects via MSBuildProjectName, not IsTestProject. Supports MSTest, NUnit, xUnit.net v2 (via YTest.MTP.XUnit2), and xUnit.net v3. Covers runner enablement, CLI argument and filter translation (--filter-class/--filter-trait/--filter-query), global.json config, CI/CD updates, and extension packages. DO NOT USE FOR: migrating between test frameworks (MSTest/xUnit/NUnit), xUnit.net v2 to v3 API migration, MSTest version upgrades, TFM upgrades, or UWP/WinUI test projects.

stanfish06 Bundle

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.

stanfish06 Bundle

Use for software supply-chain security assessment covering SBOM, SCA, CI/CD pipelines, container images, build integrity, dependency provenance, and vulnerability reachability.

stanfish06 Bundle

Prepare and optimize browser-game 3D assets. Use when the user asks for GLB or glTF shipping work, including Blender cleanup and export, collision or LOD setup, compression, texture packaging, and runtime validation.