A side-by-side look at the AllMCPs Server and Encode Toolkit MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose AllMCPs Server for aggregators work over a hosted endpoint; choose Encode Toolkit for biology, medicine and bioinformatics as a local process. You can also run both side by side in one block.
mcpServersALLMCPS_MCP_URL.search_mcp_servers, get_mcp_install_config, recommend_mcp_stack.encode_search_experiments, encode_get_experiment, encode_list_files.Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Aggregators | Biology, Medicine and Bioinformatics |
| Quality signal | 85/100 · Excellent | 61/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Remote HTTP/SSE | Local subprocess (stdio) |
| Auth | No auth required | No auth required |
| Pricing | Free | Free |
| Required env vars | ALLMCPS_MCP_URL | None listed |
| Verified owner | Verified | Community listing |
| GitHub stars | 4 | 21 |
| Directory activity | 59 views 20 installs 1 upvotes | 3 views 0 installs 0 upvotes |
| Tools | 11 | 20 |
| Full listing | View AllMCPs Server | View Encode Toolkit |
search_mcp_serversSearch the AllMCPs directory for Model Context Protocol (MCP) servers by keyword or category.get_mcp_install_configGet the exact claude_desktop_config.json setup snippet and documentation for a specific MCP server by ID.recommend_mcp_stackRecommend a curated multi-tool MCP server stack for a specific developer role or workflow (e.g. "fullstack", "data science", "devops").list_mcp_categoriesList all categories available in the AllMCPs directory along with server counts.get_boost_pricingGet pricing and features for boosting / featuring an MCP server on AllMCPs.com.boost_mcp_serverInitiate a sponsorship / boost order for an MCP server by ID, returning a Stripe checkout session URL and x402 invoice.get_boost_statusCheck current boost status, verified badge level, and sponsorship expiration for an MCP server by ID.submit_mcp_serverProgrammatically submit a new MCP server repository to AllMCPs.com for indexing and review. Supports the same optional enrichment fields as the human submission form — fill in whichever you can confidently determine from the repository (README, package.json, code) to produce a fully flushed-out listing. Omit anything you are not confident about rather than guessing; all enrichment fields are optional and unrecognized enum values are simply dropped, not rejected.verify_mcp_claimVerify ownership and claim an MCP server listing by checking GitHub README badge, website badge, or DNS TXT record. Works two ways: (1) fully unattended — pass `agentToken` from confirm_mcp_agent (or set an `Authorization: Bearer <token>` header if your client supports it), no human sign-in needed; or (2) if called with neither, requires the caller to already have an active AllMCPs browser session. Unattended agents should use register_mcp_agent + confirm_mcp_agent first.register_mcp_agentStart unattended-agent registration: emails a 6-digit confirmation code to the given address. Follow up with confirm_mcp_agent to exchange the code for a bearer token, which unlocks verify_mcp_claim (and future privileged tools) without ever needing a human to sign in via browser.confirm_mcp_agentExchange the 6-digit code emailed by register_mcp_agent for a durable bearer token (90-day TTL). Pass the returned token as `agentToken` on verify_mcp_claim, or set it as an `Authorization: Bearer <token>` header on subsequent MCP requests if your client supports that.encode_search_experimentsSearch ENCODE experiments with comprehensive filters.
Examples:
- Find all Histone ChIP-seq on human pancreas tissue:
assay_title="Histone ChIP-seq", organ="pancreas", biosample_type="tissue"
- Find ATAC-seq on human brain:
assay_title="ATAC-seq", organ="brain"
- Find RNA-seq on GM12878 cell line:
assay_title="total RNA-seq", biosample_term_name="GM12878"
- Find ChIP-seq targeting H3K27me3:
assay_title="Histone ChIP-seq", target="H3K27me3"
- Find all mouse liver experiments:
organism="Mus musculus", organ="liver"
- Free text search:
search_term="CRISPR screen pancreatic"
Common assay_title values: "Histone ChIP-seq", "TF ChIP-seq", "ATAC-seq",
"DNase-seq", "total RNA-seq", "polyA plus RNA-seq", "WGBS", "intact Hi-C",
"CUT&RUN", "CUT&Tag", "STARR-seq", "MPRA", "eCLIP", "CRISPR screen"
Common organ values: "pancreas", "liver", "brain", "heart", "kidney",
"lung", "intestine", "skin of body", "blood", "spleen", "thymus"
biosample_type values: "tissue", "cell line", "primary cell",
"in vitro differentiated cells", "organoid"
WHEN TO USE: Use as the primary entry point when users want to find experiments.
Start with encode_get_facets if unsure what filters to use.
RELATED TOOLS: encode_get_facets, encode_get_metadata, encode_search_files
Args:
assay_title: Assay type (e.g., "Histone ChIP-seq", "ATAC-seq", "total RNA-seq")
organism: Species (default: "Homo sapiens"). Also: "Mus musculus"
organ: Organ/tissue system (e.g., "pancreas", "brain", "liver")
biosample_type: Sample classification ("tissue", "cell line", "primary cell", "organoid")
biosample_term_name: Specific cell/tissue name (e.g., "GM12878", "HepG2", "pancreas")
target: ChIP/CUT&RUN target (e.g., "H3K27me3", "CTCF", "p300")
status: Data status (default: "released"). Also: "archived", "revoked"
lab: Submitting lab name
award: Funding project
assembly: Genome assembly (e.g., "GRCh38", "mm10")
replication_type: "isogenic", "anisogenic", or "unreplicated"
life_stage: "embryonic", "postnatal", "child", "adult"
sex: "male", "female", "mixed"
treatment: Treatment name if perturbation experiment
genetic_modification: Modification type ("CRISPR", "RNAi")
perturbed: True for perturbation experiments only
search_term: Free text search across all fields
date_released_from: Start date (YYYY-MM-DD) for date range filter
date_released_to: End date (YYYY-MM-DD) for date range filter
limit: Max results to return (default 25, use larger for comprehensive searches)
offset: Skip first N results (for pagination)
Returns:
JSON with experiment results, total count, and pagination info.
Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
{
"mcpServers": {
"allmcps-server": {
"command": "npx",
"args": [
"-y",
"allmcps-server"
],
"env": {
"ALLMCPS_MCP_URL": "YOUR_ALLMCPS_MCP_URL_HERE"
}
}
}
}
{
"mcpServers": {
"ammawla-encode-toolkit": {
"command": "uvx",
"args": [
"encode-toolkit"
]
}
}
}
encode_get_experimentencode_list_filesList all files for a specific ENCODE experiment, with optional filters.
Examples:
- All BED files: experiment_accession="ENCSR133RZO", file_format="bed"
- FASTQs only: experiment_accession="ENCSR133RZO", file_format="fastq"
- Signal tracks: experiment_accession="ENCSR133RZO", output_category="signal"
- Default/recommended files: preferred_default=True
- Peaks from GRCh38: file_format="bed", output_type="IDR thresholded peaks", assembly="GRCh38"
Common file_format values: "fastq", "bam", "bed", "bigWig", "bigBed", "tsv", "hic"
Common output_type values: "reads", "alignments", "signal of unique reads",
"signal of all reads", "fold change over control", "IDR thresholded peaks",
"pseudoreplicated peaks", "replicated peaks", "gene quantifications",
"transcript quantifications", "contact matrix"
WHEN TO USE: Use to browse files within a known experiment. Use encode_search_files
instead to find files across experiments.
RELATED TOOLS: encode_search_files, encode_get_file_info, encode_download_files
Args:
experiment_accession: ENCODE experiment accession (e.g., "ENCSR133RZO")
file_format: Filter by format ("fastq", "bam", "bed", "bigWig", "bigBed", etc.)
file_type: Filter by specific type ("bed narrowPeak", "bed broadPeak", etc.)
output_type: Filter by output type ("reads", "peaks", "signal", etc.)
output_category: Filter by category ("raw data", "alignment", "signal", "annotation")
assembly: Filter by genome assembly ("GRCh38", "hg19", "mm10")
status: Filter by status ("released", "archived", "in progress")
preferred_default: If True, return only default/recommended files
limit: Max files to return (default 200)
Returns:
JSON list of files with accession, format, size, download URL, and metadata.
encode_search_filesSearch files across ALL experiments with combined experiment + file filters.
This is powerful for finding specific file types across many experiments.
Examples:
- All BED files from human pancreas ChIP-seq:
file_format="bed", assay_title="Histone ChIP-seq", organ="pancreas"
- FASTQs from mouse liver RNA-seq:
file_format="fastq", assay_title="total RNA-seq", organ="liver", organism="Mus musculus"
- All IDR peak files for H3K27me3:
output_type="IDR thresholded peaks", target="H3K27me3"
- BigWig signal tracks from ATAC-seq on brain tissue:
file_format="bigWig", assay_title="ATAC-seq", organ="brain", biosample_type="tissue"
WHEN TO USE: Use to find specific file types across ALL experiments. More powerful
than encode_list_files for cross-experiment file discovery.
RELATED TOOLS: encode_list_files, encode_batch_download, encode_get_file_info
Args:
file_format: File format ("fastq", "bam", "bed", "bigWig", etc.)
file_type: Specific file type ("bed narrowPeak", "bed broadPeak", etc.)
output_type: Output type ("reads", "peaks", "signal", etc.)
output_category: Output category ("raw data", "alignment", "signal", "annotation")
assembly: Genome assembly ("GRCh38", "hg19", "mm10")
assay_title: Filter by assay type of parent experiment
organism: Filter by organism of parent experiment
organ: Filter by organ of parent experiment
biosample_type: Filter by biosample type ("tissue", "cell line", etc.)
target: Filter by ChIP/CUT&RUN target
status: File status (default: "released")
preferred_default: If True, only default/recommended files
search_term: Free text search
limit: Max results (default 25)
offset: Skip first N results (pagination)
Returns:
JSON with file results, total count, and pagination info.
encode_download_filesDownload specific ENCODE files by accession to a local directory.
Downloads files from ENCODE to your local machine. Supports MD5 verification,
concurrent downloads, and skip-if-already-downloaded.
WHEN TO USE: Use for downloading specific files by accession. For bulk downloads,
prefer encode_batch_download.
RELATED TOOLS: encode_batch_download, encode_search_files, encode_log_derived_file
Args:
file_accessions: List of file accessions to download (e.g., ["ENCFF635JIA", "ENCFF388RZD"])
download_dir: Local directory path to save files (e.g., "./data/encode")
organize_by: How to organize downloaded files:
- "flat": All files in download_dir (default)
- "experiment": download_dir/ENCSR.../filename
- "format": download_dir/bed/filename
- "experiment_format": download_dir/ENCSR.../bed/filename
verify_md5: Verify file integrity with MD5 checksum (default True)
Returns:
JSON with download results for each file (path, size, success/error, MD5 status).
encode_get_metadataGet available filter values for ENCODE searches.
Use this to discover valid values for search parameters.
WHEN TO USE: Use to discover valid filter values before searching. Helps prevent
typos in assay_title, organ, biosample_type etc.
RELATED TOOLS: encode_get_facets, encode_search_experiments
Args:
metadata_type: Type of metadata to retrieve. Options:
- "assays": Available assay types (Histone ChIP-seq, ATAC-seq, total RNA-seq, etc.)
- "organisms": Available organisms (Homo sapiens, Mus musculus, etc.)
- "organs": Available organ/tissue systems (pancreas, brain, liver, etc.)
- "biosample_types": Biosample classifications (tissue, cell line, primary cell, etc.)
- "file_formats": File format types (fastq, bam, bed, bigWig, etc.)
- "output_types": Output data types (reads, peaks, signal, etc.)
- "output_categories": Output categories (raw data, alignment, signal, etc.)
- "assemblies": Genome assemblies (GRCh38, hg19, mm10, etc.)
- "life_stages": Life stages (embryonic, adult, child, etc.)
- "replication_types": Replication types (isogenic, anisogenic, unreplicated)
- "statuses": Experiment statuses (released, archived, etc.)
- "file_statuses": File statuses (released, archived, in progress, etc.)
Returns:
JSON list of valid values for the specified metadata type.
encode_batch_downloadSearch for files and download them all in batch.
First searches for files matching the criteria, then downloads them.
By default runs in dry_run mode to preview what would be downloaded.
Set dry_run=False to actually download.
WHEN TO USE: Use for searching and downloading files in one step. Always use
dry_run=True first to preview. For specific file accessions, use encode_download_files.
RELATED TOOLS: encode_download_files, encode_search_files
Examples:
- Download all BED files from human pancreas ChIP-seq:
file_format="bed", assay_title="Histone ChIP-seq", organ="pancreas",
download_dir="/data/encode", dry_run=False
- Preview FASTQ downloads for mouse brain RNA-seq:
file_format="fastq", assay_title="total RNA-seq", organ="brain",
organism="Mus musculus", download_dir="/data/encode"
- Download IDR peaks for H3K27me3 in GRCh38:
output_type="IDR thresholded peaks", target="H3K27me3", assembly="GRCh38",
download_dir="/data/encode", dry_run=False
Args:
download_dir: Local directory to save files
file_format: File format filter ("fastq", "bam", "bed", "bigWig", etc.)
output_type: Output type filter ("reads", "peaks", "signal", etc.)
output_category: Output category ("raw data", "alignment", "annotation", etc.)
assembly: Genome assembly ("GRCh38", "mm10", etc.)
assay_title: Assay type ("Histone ChIP-seq", "ATAC-seq", "total RNA-seq", etc.)
organism: Organism (default: "Homo sapiens")
organ: Organ/tissue ("pancreas", "brain", "liver", etc.)
biosample_type: Biosample type ("tissue", "cell line", "primary cell", etc.)
target: ChIP/CUT&RUN target ("H3K27me3", "CTCF", etc.)
preferred_default: If True, only download default/recommended files
organize_by: File organization ("flat", "experiment", "format", "experiment_format")
verify_md5: Verify downloads with MD5 checksums (default True)
limit: Max files to download (default 100, safety limit)
dry_run: If True (default), only preview what would be downloaded. Set False to download.
offset: Skip the first N matching files; pass the next_offset of the previous reply to
continue a search that has more files than limit
Returns:
JSON with download preview (dry_run=True) or download results (dry_run=False).
encode_manage_credentialsManage ENCODE API credentials for accessing restricted/unreleased data.
Most ENCODE data is public and requires no authentication.
Credentials are only needed for unreleased or restricted datasets.
Credentials are stored securely in your OS keyring (macOS Keychain,
Linux Secret Service, Windows Credential Locker) and never in plaintext.
WHEN TO USE: Use only for accessing unreleased/restricted ENCODE data.
Public data requires no authentication.
RELATED TOOLS: encode_search_experiments
Args:
action: What to do:
- "store": Save new credentials (requires access_key and secret_key)
- "check": Check if credentials are configured
- "clear": Remove stored credentials
access_key: Your ENCODE access key (only for action="store")
secret_key: Your ENCODE secret key (only for action="store")
Returns:
JSON with action result.
encode_get_facetsGet live filter counts from ENCODE to discover what data is available.
Returns faceted counts showing how many experiments/files exist for each
filter value. Useful for exploring what's available before searching.
WHEN TO USE: Use to explore what data exists before searching. Shows counts
per filter value. Best first step for unknown datasets.
RELATED TOOLS: encode_get_metadata, encode_search_experiments
Examples:
- What assays are available for pancreas?
organ="pancreas"
- What organs have Histone ChIP-seq data?
assay_title="Histone ChIP-seq"
- What targets are available for mouse brain ChIP-seq?
assay_title="Histone ChIP-seq", organism="Mus musculus", organ="brain"
Args:
search_type: Object type ("Experiment" or "File")
assay_title: Pre-filter by assay type
organism: Pre-filter by organism
organ: Pre-filter by organ
biosample_type: Pre-filter by biosample type
Returns:
JSON with facet names and their term counts.
encode_get_file_infoGet detailed information about a specific ENCODE file.
WHEN TO USE: Use when you need detailed metadata for a specific file
(size, md5, assembly, biological replicate info).
RELATED TOOLS: encode_download_files, encode_list_files
Args:
accession: File accession ID (e.g., "ENCFF635JIA")
Returns:
JSON with file metadata including format, size, download URL, MD5, assembly, etc.
encode_track_experimentTrack an ENCODE experiment locally with its publications, methods, and pipeline info.
Fetches full experiment metadata from ENCODE and stores it in a local SQLite
database along with any associated publications (PMIDs, DOIs, authors, journal)
and pipeline/analysis information (software versions, methods).
This is like adding an experiment to your "library" - similar to Endnote for papers.
WHEN TO USE: Use to save an experiment to your local library with publications
and pipeline info. Required before compare or citations.
RELATED TOOLS: encode_compare_experiments, encode_get_citations, encode_export_data
Args:
accession: ENCODE experiment accession (e.g., "ENCSR133RZO")
fetch_publications: Also fetch and store publications/citations (default True)
fetch_pipelines: Also fetch and store pipeline/analysis info (default True)
notes: Optional notes to attach to this experiment
Returns:
JSON with tracking result including publications and pipeline info found.
encode_list_trackedList all experiments you've tracked locally, with optional filters.
Shows your local library of tracked ENCODE experiments, their metadata,
publication counts, and derived file counts.
WHEN TO USE: Use to see all experiments in your local library. Filter by assay,
organism, or organ.
RELATED TOOLS: encode_summarize_collection, encode_export_data
Args:
assay_title: Filter by assay type (partial match)
organism: Filter by organism (partial match)
organ: Filter by organ (partial match)
Returns:
JSON with tracked experiments metadata table and tracker stats.