synthetic_biology_design: Скилл проектирования и анализа

--- name: synthetic_biology_design description: "Synthetic Biology Design - Design synthetic biology construct: gene lookup, codon optimization, protein property prediction, and structure prediction. Use this skill for synthetic biology tasks involving get sequence id DegenerateCodonCalculatorbyAminoAcid calculate protein sequence properties pred protein structure esmfold. Combines 4 tools from 4 SCP server(s)." --- # Synthetic Biology Design **Discipline**: Synthetic Biology | **Tools Used**: 4 | **Servers**: 4 ## Description Design synthetic biology construct: gene lookup, codon optimization, protein property prediction, and structure prediction. ## Tools Used - **`get_sequence_id`** from `ensembl-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl` - **`DegenerateCodonCalculatorbyAminoAcid`** from `server-29` (sse) - `https://scp.intern-ai.org.cn/api/v1/mcp/29/SciToolAgent-Bio` - **`calculate_protein_sequence_properties`** from `server-2` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool` - **`pred_protein_structure_esmfold`** from `server-3` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model` ## Workflow 1. Get gene sequence 2. Design degenerate codons 3. Predict protein properties 4. Predict structure ## Test Case ### Input ```json { "gene_id": "ENSG00000141510", "amino_acids": "AVILM" } ``` ### Expected Steps 1. Get gene sequence 2. Design degenerate codons 3. Predict protein properties 4. Predict structure ## Usage Example > **Note:** Replace `sk-b04409a1-b32b-4511-9aeb-22980abdc05c` with your own SCP Hub API Key. You can obtain one from the [SCP Platform](https://scphub.intern-ai.org.cn). ```python import asyncio import json from contextlib import AsyncExitStack from mcp import ClientSession from mcp.client.streamable_http import streamablehttp_client from mcp.client.sse import sse_client SERVERS = { "ensembl-server": "https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl", "server-29": "https://scp.intern-ai.org.cn/api/v1/mcp/29/SciToolAgent-Bio", "server-2": "https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool", "server-3": "https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model" } async def connect(url, stack): transport = streamablehttp_client(url=url, headers={"SCP-HUB-API-KEY": "sk-b04409a1-b32b-4511-9aeb-22980abdc05c"}) read, write, _ = await stack.enter_async_context(transport) ctx = ClientSession(read, write) session = await stack.enter_async_context(ctx) await session.initialize() return session 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(): async with AsyncExitStack() as stack: # Connect to required servers sessions = {} sessions["ensembl-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl", stack) sessions["server-29"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/29/SciToolAgent-Bio", stack) sessions["server-2"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool", stack) sessions["server-3"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/3/DrugSDA-Model", stack) # Execute workflow steps # Step 1: Get gene sequence result_1 = await sessions["ensembl-server"].call_tool("get_sequence_id", arguments={}) data_1 = parse(result_1) print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}") # Step 2: Design degenerate codons result_2 = await sessions["server-29"].call_tool("DegenerateCodonCalculatorbyAminoAcid", arguments={}) data_2 = parse(result_2) print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}") # Step 3: Predict protein properties result_3 = await sessions["server-2"].call_tool("calculate_protein_sequence_properties", arguments={}) data_3 = parse(result_3) print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}") # Step 4: Predict structure result_4 = await sessions["server-3"].call_tool("pred_protein_structure_esmfold", arguments={}) data_4 = parse(result_4) print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}") # Cleanup print("Workflow complete!") if __name__ == "__main__": asyncio.run(main()) ```