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internscience/scp/ucsc-genome-exploration

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PublishedJune 14, 2026 at 12:58 AM

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version: "1.0.1" name: ucsc_genome_exploration description: "UCSC Genome Browser Exploration - Explore genome via UCSC: list genomes, list tracks, get sequence, get track data, and cytoband info. Use this skill for genomics tasks involving list genomes list tracks get sequence get track data get cytoband. Combines 5 tools from 1 SCP server(s)."

UCSC Genome Browser Exploration

Discipline: Genomics | Tools Used: 5 | Servers: 1

Description

Explore genome via UCSC: list genomes, list tracks, get sequence, get track data, and cytoband info.

Tools Used

`list_genomes` from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC
`list_tracks` from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC
`get_sequence` from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC
`get_track_data` from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC
`get_cytoband` from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC

Workflow

List available genomes
List tracks for hg38
Get DNA sequence for BRCA1 region
Get track data
Get cytoband info

Test Case

Input

json

{
    "genome": "hg38",
    "chrom": "chr17",
    "start": 43044295,
    "end": 43125370
}

Expected Steps

List available genomes
List tracks for hg38
Get DNA sequence for BRCA1 region
Get track data
Get cytoband info

Usage Example

Note: Replace <YOUR_SCP_HUB_API_KEY> with your own SCP Hub API Key. You can obtain one from the SCP Platform.

python

import asyncio
import json
from mcp import ClientSession
from mcp.client.streamable_http import streamablehttp_client
from mcp.client.sse import sse_client
SERVERS = {
    "ucsc-server": "https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC"
}
async def connect(url, transport_type):
    transport = streamablehttp_client(url=url, headers={"SCP-HUB-API-KEY": "<YOUR_SCP_HUB_API_KEY>"})
    read, write, _ = await transport.__aenter__()
    ctx = ClientSession(read, write)
    session = await ctx.__aenter__()
    await session.initialize()
    return session, ctx, transport
def parse(result):
    try:
        if hasattr(result, 'content') and result.content:
            c = result.content[0]
            if hasattr(c, 'text'):
                try: return json.loads(c.text)
                except: return c.text
        return str(result)
    except: return str(result)
async def main():
    # Connect to required servers
    sessions = {}
    sessions["ucsc-server"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC", "streamable-http")
    # Execute workflow steps
    # Step 1: List available genomes
    result_1 = await sessions["ucsc-server"].call_tool("list_genomes", arguments={})
    data_1 = parse(result_1)
    print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")
    # Step 2: List tracks for hg38
    result_2 = await sessions["ucsc-server"].call_tool("list_tracks", arguments={})
    data_2 = parse(result_2)
    print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")
    # Step 3: Get DNA sequence for BRCA1 region
    result_3 = await sessions["ucsc-server"].call_tool("get_sequence", arguments={})
    data_3 = parse(result_3)
    print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")
    # Step 4: Get track data
    result_4 = await sessions["ucsc-server"].call_tool("get_track_data", arguments={})
    data_4 = parse(result_4)
    print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}")
    # Step 5: Get cytoband info
    result_5 = await sessions["ucsc-server"].call_tool("get_cytoband", arguments={})
    data_5 = parse(result_5)
    print(f"Step 5 result: {json.dumps(data_5, indent=2, ensure_ascii=False)[:500]}")
    # Cleanup
    print("Workflow complete!")
if __name__ == "__main__":
    asyncio.run(main())

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