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Persistent Memory and Knowledge Graph for Agents
This system provides persistent, structured memory for agents, allowing them to store, recall, and connect context across sessions. It utilizes a hybrid search mechanism combining vector, BM25, and graph traversal for robust knowledge compo…
Optimising Cursor AI Enterprise Spend
This skill provides a framework for identifying and reducing Cursor AI expenditure by analysing usage patterns, optimising model selection, and implementing spend limits. It leverages the cursor-usage MCP server to audit team-wide model dis…
Klever Blockchain Smart Contract Development Skill
This skill provides an expert framework for building, deploying, and interacting with smart contracts on the Klever blockchain. It covers the full development lifecycle, from writing secure Rust/WASM contracts to using koperator for deploym…
Interpreting Cursor Enterprise Usage Metrics
This skill provides deep context for interpreting raw Cursor Enterprise API data, enabling accurate analysis of AI spending, model adoption, and productivity metrics. It guides the user through complex data nuances, such as calculating over…
Multi-Platform Social Media Content Scheduler
This tool facilitates the creation, scheduling, and management of content across numerous social media platforms, including Facebook, Instagram, X, and LinkedIn. It supports batch posting, media uploads, and detailed platform-specific contr…
AI Agent Cost Optimizer
Optimises AI agent token and credit usage by classifying task complexity and routing requests to the most cost-efficient model tier. It reduces API expenses by up to 75% through prompt quality evaluation, task splitting, and context pruning…
Audit Agent Context Files Against Best Practices
This skill audits agent context files (e.g., AGENTS.md) against a comprehensive set of best practices. It identifies low-signal content, outdated documentation, and structural issues, providing concrete, actionable diffs for improvement.
Comprehensive Biomedical Data Retrieval and Analysis Tool
This CLI tool provides structured, multi-hop access to vast biomedical knowledge, enabling developers to query genes, drugs, diseases, and variants across multiple domains. It supports complex workflows for tasks such as adverse event check…
Annotating Genetic Variants with ENCODE Data
Annotate genetic variants with ENCODE functional genomics data to identify causal regulatory elements and link them to target genes. The skill supports the full post-GWAS workflow, including tissue-specific mapping, enrichment testing, and …
Visualizing ENCODE Genomic Data Workflows
This skill guides the creation of publication-quality visualizations for ENCODE data, covering deepTools heatmaps, profile plots, and correlation analysis. It also details using IGV for interactive genome browser viewing and web embedding v…
Query Genomic Annotations from UCSC Browser API
This tool provides programmatic access to the UCSC Genome Browser REST API, enabling the retrieval of comprehensive, cross-experiment genomic annotations. Developers can query regulatory elements, TF binding clusters, and DNA sequences for …
Manage and track ENCODE experiments locally
This skill enables local management of ENCODE experiments by tracking metadata, publications, and data provenance in a SQLite database. It supports experiment comparison, citation export in multiple formats, and the logging of derived files…
Analyzing ENCODE single-cell genomics data
This skill guides the retrieval and analysis of single-cell genomics data (scRNA-seq and scATAC-seq) from the ENCODE project. It provides detailed protocols for data structure, quality assessment, and integrating single-cell profiles with b…
ENCODE Toolkit Setup and Configuration
Provides instructions for installing, configuring, and verifying the ENCODE Toolkit MCP server. It covers installation via uvx or pip, managing credentials, and testing connections using metadata and search queries.
Search and explore ENCODE genomics data
This skill facilitates comprehensive querying and exploration of the ENCODE Project's vast genomics dataset. It guides users through a structured, multi-phase search process, allowing them to first explore available facets, validate metadat…
Cross-study scRNA-seq meta-analysis and integration
This skill integrates multiple single-cell RNA-seq datasets into a unified cell atlas. It performs rigorous meta-analysis, correcting for batch effects, technical dropout, and ambient contamination to assess reproducible cell type definitio…
generate scientific writing from provenance data
This skill auto-generates publication-ready scientific documentation, including methods sections and figure legends, directly from ENCODE analysis provenance records. It ensures rigorous reporting of all experimental and computational param…
Characterize Genomic Regulatory Elements Using ENCODE Data
This skill facilitates the discovery and classification of cis-regulatory elements (cCREs) by integrating ENCODE's comprehensive catalog with multi-omic data. It supports advanced analysis of chromatin states, identifying promoters, enhance…
Comprehensive ENCODE Data Quality Assessment Skill
This skill evaluates the reliability of ENCODE experiments by interpreting multiple orthogonal quality metrics, such as FRiP, NSC, and NRF, alongside official audit flags. It provides deep guidance for filtering and comparing data across va…
Publication Trust Assessment and Reliability Check
This skill systematically assesses the scientific reliability of academic publications by checking for formal retractions, errata, and expressions of concern. It critically searches for independent contradictions and replication failures ac…
WGBS Pipeline: FASTQ to Methylation Calling
This skill executes the full ENCODE WGBS pipeline, processing paired-end FASTQ reads through alignment, deduplication, and methylation extraction. It generates per-CpG methylation levels in the standardized bedMethyl format, suitable for do…
AI-First CMS for Structured Content Management
Contentrain is a Git-based, AI-first CMS designed for managing structured content using defined models. It provides a robust set of MCP tools for scaffolding, validation, and merging content across various formats, ensuring deterministic co…
ENCODE Hi-C Data Processing Pipeline
This Nextflow pipeline processes Hi-C FASTQ files to generate multi-resolution contact matrices and chromatin loop calls. It integrates BWA, pairtools, Juicer, and cooler for end-to-end chromatin conformation analysis.
ENCODE pipeline workflow generation and management
This skill facilitates the generation and execution of standardized ENCODE bioinformatics pipelines, supporting custom Nextflow or WDL workflows. It manages compute resource requirements and deployment across local, HPC, and major cloud pla…