Research

--> --- name: bio-peer-review description: Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation. tool_type: mixed p...

--> --- name: bio-parallel-web description: Search the web, extract URL content, and run deep research using the Parallel Chat API and Extract API. Use for ALL web searches, research queries, and general information gathering. Provides synthesized summaries with citations. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---

--> --- name: bio-opentargets-database description: Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---

--> --- name: bio-openalex-database description: Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or conducting bibliometric analysis across 240M+ scholarly works. Use for literature searches, research output analysis, citation analysis, and academic database queries. tool_type: mixed pri...

--> --- name: bio-monarch-database description: Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene discovery, phenotype-to-gene mapping, cross-species disease modeling, and HPO term lookup. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file -...

--> --- name: bio-literature-review description: Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles...

--> --- name: bio-latex-posters description: Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. a...

--> --- name: bio-hypothesis-generation description: Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic. tool_type: mixed primary_tool: Unknown measurable_outcome: E...

--> --- name: bio-hypogenic description: Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute...

--> --- name: bio-hmdb-database description: Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---

--> --- name: bio-gwas-database description: Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---

--> --- name: bio-drugbank-database description: Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target...

--> --- name: bio-dhdna-profiler description: Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive style, profile writing or speech patterns, compare thinking styles between people, asks "what's my thinking style", "analyze how this person reasons", "cognitive profile", "thinking pattern", "DHDNA", "digital DNA", or wants to understand the mind behind any text. Also trigger when the user prov...

--> --- name: bio-denario description: Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration. tool_type: mixed primar...

--> --- name: bio-consciousness-council description: Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoints, needs help making a tough decision, asks for a council/panel/board discussion, wants to explore a problem from multiple angles, requests devil's advocate analysis, or says things like "what would different experts think about this", "help me think through this from all sides", "counci...

--> --- name: bio-clinical-reports description: 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. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 mi...

--> --- name: bio-clinical-decision-support description: Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs ...

--> --- name: bio-citation-management description: Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow succes...

--> --- name: bio-brenda-database description: Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---

--> --- name: bio-bgpt-paper-search description: Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with vali...

--> --- name: bio-metabolomics-pathway-enrichment description: Metabolomics pathway analysis using MetaboAnalystR (KEGG, Reactome), pathview visualization, MSEA, mummichog, and network-based topology analysis. tool_type: mixed primary_tool: metabolomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Map metabolites to biological pathways and perform enrichment, topology, and network analysis.

--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'pubmed-ncbi-mcp-server' description: 'Use the cyanheads PubMed MCP server to search PubMed, fetch metadata and full text, generate citations, inspect MeSH, and find related research.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---

--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'biocontext-ai-mcp-registry' description: 'Use the BioContextAI Registry to discover, compare, and select biomedical MCP servers for bioinformatics, systems biology, and biomedical AI workflows.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---

--> --- name: bio-literature description: Parse scholarly articles (PDF, DOI, URL) to extract metadata, GEO accessions, and acquisition links using OpenAlex + GROBID pipelines. tool_type: mixed primary_tool: literature measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---