MCP Servers Reference

This document provides a detailed reference for the Model Context Protocol (MCP) servers integrated into the OmicFabric system.

OmicFabric Core `(omicfabric-core)`

The main server consolidating genomic and nutrigenomic research tools.

What it is for

This server is the primary analytical engine for research-level data analysis, including high-throughput sequencing pipelines and specialized nutrigenomics workflows.

How to use it: High-Level Workflows

Available Pipelines

variant_dietary_association_pipeline

Identifies associations between genotypes and dietary variables.

Parameters

{
  "genotype_vcf": "path/to/vcf/file",     // Required
  "dietary_data_csv": "path/to/intake",   // Required
  "covariates": ["Age", "BMI"]            // Optional
}

microbiome_nutrient_metabolism_workflow

Profiles metagenomic data for nutrient degradation pathways.

Parameters

{
  "metagenomic_data": "path/to/sequences", // Required
  "nutrient_focus": ["Fiber", "Lipids"]   // Optional
}

metabolomic_pathway_enrichment_analysis

Identifies enriched pathways in metabolic datasets.

Parameters

{
  "metabolite_list": "path/to/csv",       // Required
  "experimental_condition": "string_label" // Required
}

genomics_variant_analysis_workflow

Best-practices variant calling.

Parameters

{
  "sample_id": "string",                  // Required
  "reference_genome": "GRCh38"           // Optional, default: GRCh38
}

How to use it: Granular Research Tools

calculate_genotype_diet_interaction: Statistical modeling of GxI interaction. (Params: variant_ids, dietary_variable)
query_nutrigenetics_db: Search research databases for gene-nutrient interaction evidence. (Params: query_term)
profile_microbial_abundance_by_nutrient: Correlate microbial taxa with intake. (Params: taxonomy_table, dietary_index)
quantify_metabolic_flux_index: Estimate metabolic flux markers. (Params: metabolite_data, enzymatic_data)
get_gene_info: Fetch detailed information from NCBI/Ensembl. (Params: gene_symbol, organism)
run_blast: Similarity search against sequence databases. (Params: sequence, database, program)
run_msa: Multiple Sequence Alignment. (Params: sequences, tool)

What it is NOT for

⚠️ This is NOT a diagnostic tool. All outputs are for research analysis; interpretation belongs to the scientist.

⚠️ It does not provide medical advice or personalized clinical nutrition plans.

Genomics Visualization `(genomics-viz)`

What it is for

Specialized in generating data structures and configurations for visualizing genomic data.

How to use it

create_phylo_tree: Generate a phylogenetic tree from an MSA file.
Params: msa_path (required), method (optional)
generate_browser_track: Configure a track for genome browser visualization.
Params: data_path, track_name, format (all required)

Galaxy Integration `(galaxy-integration)`

What it is for

Provides a bridge to the Galaxy Project’s workflow management system for complex multi-step pipelines.

How to use it

run_galaxy_workflow: Trigger an existing Galaxy workflow on a specific dataset ID.
Params: workflow_id, dataset_id (required), parameters (optional)
get_galaxy_dataset: Retrieve metadata and access URLs for datasets in Galaxy histories.
Params: history_id, dataset_name (required)