Results for “pre-tool-use”

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools; for the standard QC→cluster→UMAP→DE pipeline prefer alterlab-scanpy; for the AnnData data structure itself prefer alterlab-anndata; for protein language models prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

Search and deploy services from Railway's template marketplace. Use when user wants to add a service from a template, find templates for a specific use case, or deploy tools like Ghost, Strapi, n8n, Minio, Uptime Kuma, etc. For databases (Postgres, Redis, MySQL, MongoDB), prefer the railway-database skill.

Design and implement CI/CD pipelines and automation — fast checks on every PR, safe releases, and repeatable workflows. Load when setting up GitHub Actions (or similar), adding pre-merge gates, automating releases, or the user asks "add CI", "set up workflows", "automate checks", "CD pipeline". Not for one-off local scripts (use task-specific tooling).

Collects launch inputs and runs preflight checks before executing TAO workflows such as AutoML, training, evaluation, inference, export, TensorRT engine generation, or DEFT jobs on supported platforms.

Discovers, validates, or creates a SageMaker execution role before deploying or training, preventing IAM-related deployment failures.

Operate Firebase from the terminal with `firebase-tools`: install/auth the CLI, bootstrap `firebase.json` / `.firebaserc`, run the Emulator Suite, deploy Hosting / Functions / rules / App Hosting, manage preview channels, and handle Firebase admin tasks like auth import/export, Remote Config, App Distribution, and Extensions. Use when the job is Firebase platform/project operation through the CLI. Triggers on: firebase deploy, firebase init, firebase emulators, firebase hosting, firebase functions, firebase firestore, firebase database, firebase auth import, firebase remote config, firebase app distribution, firebase extensions, firebase apphosting, firebase dataconnect, firebase cli, firebase-tools, deploy firebase, firebase preview channel, firebase login, firebase use, firebase target apply. Route backend AI workflow orchestration to `genkit` and direct in-app SDK integration to `genkit` (`client-ai-logic` mode).

Post-exploitation workflow. Covers privilege escalation (Linux SUID/sudo/kernel, Windows UAC/service/token), persistence assessment, local enumeration, credential harvesting, and pivot preparation. Structured workflows for Linux and Windows targets using impacket, netexec, john, linpeas/winpeas, and standard Kali tools. Includes kernel exploit reference tables, GTFOBins exploitation chains, Potato attack selection, Docker/container escapes, DLL hijacking, SSH key harvesting, credential recovery from memory, and Windows token manipulation. Chains from /pentester or /credential-audit when access is obtained.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Azure Cosmos DB SDK best practices for .NET, Java, Python, Spring Boot, and LangChain: singleton client, async APIs, connection modes, retry handling, diagnostics, serialization, emulator configuration, ETags, and framework-specific patterns. USE FOR: CosmosClient singleton, async API, Direct vs Gateway mode, retry 429, preferred regions, excluded regions, availability strategy, circuit breaker, SDK diagnostics, serialization enums, emulator SSL, ETag concurrency, conditional create, patch increment, continuation token, content response, Spring Data Cosmos, Spring Boot versions, Newtonsoft dependency, namespace collision, Python async deps, local dev config, LangChain Cosmos DB saver, LangGraph checkpointer, MCP persistent session, tool content format, tool filtering, LangChain JS vectorstore, chat history, semantic cache. DO NOT USE FOR: data modeling (use cosmosdb-data-modeling), queries (use cosmosdb-query-optimization), partition keys (use cosmosdb-partition-key).

Audits and repairs Markdown link health across a skills repo via a four-tier pipeline (config hardening, intra-repo file-ref fixes, external URL substitutions, residual exclusions) and enforces a Tier 3 substitution guardrail that prevents regressions of previously-passing links; designed for lychee-based GitHub Actions link checkers but generalizes to markdown-link-check and similar tools. Use when the request mentions link audit, dead links, link health, lychee, broken links, link checker, markdown link audit, link-health audit, 404 audit, check-links failing, CI link-check, or 連結健檢, 死鏈, 失效連結, 斷鏈檢查. Part of the AlterLab Academic Skills suite.

Submits and tracks protein-testing experiments on the Adaptyv Bio Foundry cloud lab (wet-lab validation), and optimizes protein sequences before submission with computational tools (NetSolP, SoluProt, SolubleMPNN, ESM). Use when designing proteins that need wet-lab validation - binding/affinity screening, expression testing, thermostability, or fluorescence assays - or when submitting experiments to the Foundry API, browsing the target catalog, tracking experiment status, retrieving results, or pre-screening sequences for solubility/expression. Triggers on "Adaptyv", "Foundry API", "cloud lab", "biolayer interferometry / BLI", "wet-lab validation". Part of the AlterLab Academic Skills suite.