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Setup reproducible bioinformatics environments for ENCODE
This skill provisions fully reproducible, version-pinned computational environments for diverse ENCODE assays, generating conda definitions, R/Bioconductor scripts, and Python requirements. It simplifies the setup of complex pipelines (e.g.…
Systematic ENCODE Experiment Batch Processing
Facilitates systematic batch operations across multiple ENCODE experiments, including quality control screening, bulk downloading, and comparative analysis. It provides workflows for managing large-scale data collections and generating summ…
Aggregate Chromatin Accessibility Peaks Across Studies
This skill generates a comprehensive union map of open chromatin by merging ATAC-seq and DNase-seq narrowPeak data from multiple ENCODE experiments. It handles cross-platform variation and applies rigorous filtering and confidence annotatio…
gnosis-mcp server connectivity and health check
Verifies gnosis-mcp server connectivity, schema integrity, and corpus health through detailed diagnostic reports. It identifies issues with embeddings, reranker configuration, and database consistency.
Optimize RAG chunk size and retrieval settings
This skill systematically sweeps various chunk sizes and retrieval modes (keyword, hybrid, rerank) to benchmark and determine the optimal configuration for your specific corpus. It reports standard metrics like nDCG and MRR against a golden…
Local Agentic Knowledge Base Setup and Indexing
This utility provides a comprehensive, step-by-step wizard for setting up a local, agentic knowledge base. It handles backend initialization, document ingestion (including web crawling and PDF support), and integrates the resulting index wi…
Alpha Arcade Prediction Market Trading
This toolset enables interaction with Alpha Arcade prediction markets on the Algorand blockchain, allowing users to browse markets, manage orders, and trade USDC-denominated shares. It supports limit and market orders, position management, …
Advanced knowledge base search and retrieval skill
This skill provides advanced retrieval across the knowledge base, supporting keyword, hybrid semantic, and category-filtered searches. It also allows querying the indexed git commit history to understand code provenance and document lineage…
Manage single documents in the knowledge graph
This skill provides granular CRUD operations for a knowledge base, allowing developers to index, delete, update metadata, and query relationships for individual documents. It is designed for point changes, complementing bulk ingestion proce…
Ingests local files, git history, and websites
This tool provides a unified pipeline for populating the gnosis-mcp knowledge base from local files, entire Git repositories, or remote websites. It supports advanced features like embedding, chunking, and pruning stale data chunks.
evaluate retrieval quality metrics and performance
This utility measures core retrieval metrics (Hit@5, MRR, nDCG@10) against a corpus of golden queries. It compares current performance against a saved baseline and provides actionable interpretation and tuning recommendations for diagnosing…
Load usage-weighted knowledge context summary
This tool retrieves a compact, usage-weighted context summary from the knowledge base. It surfaces the most relevant documentation, optimized for session startup or specific topic primers.
Real SIM SMS Verification for AI Agents
This tool facilitates reliable SMS and OTP verification for high-security services by utilizing real physical SIM cards, bypassing common carrier-lookup restrictions that affect VoIP numbers. It provides a comprehensive lifecycle of functio…
Advanced research access to arXiv papers
This server provides comprehensive, research-grade access to arXiv, allowing developers to search by topic or author, download full texts, traverse citation graphs, and perform local semantic searches over collected papers.
Algorand Haystack Router Swap Execution Tool
This tool facilitates complex, atomic token swaps on Algorand by interacting with the Haystack Router via the Algorand MCP. It allows developers to programmatically retrieve optimal swap quotes, check asset opt-in status, and execute swaps …
Algorand Blockchain Interaction and Wallet Management
This skill provides comprehensive interaction with the Algorand blockchain via the MCP server, enabling complex operations such as asset transfers, smart contract calls, and advanced DEX swaps. It manages secure wallet signing, multi-networ…
Running PinRAG Unit Tests
Executes the PinRAG pytest suite using uv while automatically loading required environment variables from the local MCP configuration. This skill enables local integration testing and CI-like workflows by synchronising dependencies and mana…
Local PinRAG Knowledge Base Management Tool
This tool suite allows developers to interact with a local PinRAG knowledge base by indexing documents (PDFs, URLs, files) and executing complex queries. It provides structured methods for listing, adding, and removing documents directly th…
Cost-Optimised LLM Task Router
Automates task routing to the most cost-effective model based on complexity and task type, ranging from local Ollama instances to high-end APIs. It supports specific workflows for research, coding, and analysis to maximise efficiency and tr…
LLM cost tracking and routing policy management
This skill manages and optimizes LLM usage costs by dynamically routing tasks to the most cost-effective models. It provides comprehensive reporting on savings, usage policies, and routing quality metrics.
Automates software release and package publishing
This tool automates the entire software release lifecycle, managing version bumping across configuration files and executing the full Git workflow. It handles creating GitHub Releases and publishing the package to PyPI, subsequently updatin…
LangChain/LangGraph Resource Access and Guidelines
Provides structured access to LangChain and LangGraph documentation via dedicated MCP servers, ensuring developers follow a defined search priority starting with canonical project overviews. It guides the use of specific queries and resourc…
FlowZap Diagram Generation Skill
Generate, validate and publish workflow, sequence and architecture diagrams using the FlowZap Code DSL. This skill provides the syntax rules and instructions for agents to produce shareable playground URLs via the companion MCP server.
Automatic LLM Task Classification and Routing
This skill automatically classifies incoming tasks using a multi-layer heuristic chain, falling back to local or commercial LLMs for robust intent detection. It then routes the task to the optimal specialized LLM and selects the appropriate…