SCP: Science Context Protocol

Science Context Protocol — Building a Global Collaboration Network for Autonomous Scientific Agents

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🎯 Vision

SCP is dedicated to breaking down tool barriers in scientific research, enabling researchers to focus on the science itself, and empowering AI agents to become true "experiment designers."

SCP (Science Context Protocol) is an open-source standard protocol designed to accelerate scientific discovery by building a global collaboration network for autonomous scientific agents, connecting heterogeneous scientific resources (software tools, AI models, datasets, workflow engines, lab instruments, etc.).

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📑 Table of Contents

• 🎯 Vision
• ✨ Core Capabilities
• 🏗️ Architecture
• 🚀 Quick Start
• 🛠️ Tool Ecosystem
• 🎓 Scientific Skills
  • What Are Scientific Skills?
  • Skill Catalog by Domain
  • Skill Highlights
  • How to use SCP skills
• 📊 Use Cases
• 🔬 SCP vs MCP
• 🌐 Resources
• 📄 License
• 🙏 Acknowledgments

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✨ Core Capabilities

Capability	Description
🔗 Protocol-Level Connectivity	Unified description and invocation of 2,200+ scientific resources (tools, models, instruments, etc.)
🧠 Intelligent Orchestration	SCP Hub supports automated planning, execution, and monitoring of multi-step workflows
🧪 Dry-Wet Lab Integration	Seamless integration of computational tools and lab equipment for closed-loop validation
🤖 Multi-Agent Collaboration	Supports multiple AI agents working collaboratively within a unified context
📋 Full Lifecycle Management	End-to-end traceability from registration, planning, and execution to archiving
🔐 Security & Access Control	Fine-grained authentication and authorization mechanisms based on experiments

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🏗️ Architecture

SCP adopts a Hub-Spoke Architecture:

┌─────────────────────────────────────────────────────────────┐
│                    SCP Client                               │
│            (Researchers / AI Scientists)                     │
└───────────────────────┬─────────────────────────────────────┘
                        │
                        ▼
┌─────────────────────────────────────────────────────────────┐
│               SCP Hub (Central Orchestrator)                 │
│     Intent Parsing · Workflow Generation · Task Scheduling   │
│                  · Permission Management                     │
└───────────────────────┬─────────────────────────────────────┘
                        │
        ┌───────────────┼───────────────┐
        ▼               ▼               ▼
┌──────────────┐ ┌──────────────┐ ┌──────────────┐
│  SCP Server  │ │  SCP Server  │ │  SCP Server  │
│ (Edge Node)  │ │ (Edge Node)  │ │ (Edge Node)  │
└──────┬───────┘ └──────┬───────┘ └──────┬───────┘
       │                │                │
  Tools/Models     Databases/       Compute
                   Instruments      Resources

• SCP Hub: Central orchestrator responsible for task scheduling and permission management
• SCP Server: Edge node interfacing with local resources
• SCP Client: User interface for researchers or AI scientists

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🚀 Quick Start

Installation

# Clone the repository
git clone https://github.com/InternScience/scp.git
cd scp

# Install dependencies
pip install -e .

Usage

Option 1: Self-Hosted Deployment

Set up your own SCP Server and Hub for full control over deployment and management.

Option 2: Intern-Discovery Platform (Recommended)

Visit SCP Square — we provide a managed SCP Hub where you can submit your own SCP Server to the square for cross-platform discovery and access.

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🛠️ Tool Ecosystem

SCP has integrated 2,200+ scientific tools spanning multiple disciplines:

Domain	Share	Representative Tool Types
🧬 Biology & Related Technologies	45.9%	Genome analysis, protein structure prediction
⚛️ Physics	21.1%	Quantum computing, materials simulation
🧪 Chemistry	11.6%	Molecular docking, reaction prediction
🔧 Mechanics & Materials Science	8.7%	Finite element analysis, molecular dynamics
📐 Mathematics	8.0%	Symbolic computation, optimization algorithms
💻 Information Science & Computing	4.6%	Machine learning, data mining

🔗 View Complete Tool List

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🎓 Scientific Skills

Building upon tool standardization, SCP further introduces the concept of "Scientific Skills (SCP Skills)" — the first batch of 206 scientific skills is now available in the skills/ directory.

What Are Scientific Skills?

Each Skill is an independently callable, freely composable "research instruction" that orchestrates multiple databases, computational models, and even device drivers behind the scenes, forming a reusable, standardized experiment template.

For Researchers: No need to deal with complex tool manuals and code debugging — focus your energy on the scientific questions themselves For AI Agents: Skills become freely stackable "LEGO bricks," enabling agents to evolve from "tool users" to "experiment designers"

Skill Catalog by Domain

All 206 skills are organized into 8 major scientific domains:

Domain	Skills	Representative Examples
💊 Drug Discovery & Pharmacology	71	Target identification, ADMET prediction, virtual screening, molecular docking, drug safety & repurposing, clinical pharmacology
🧬 Genomics & Genetic Analysis	41	Variant pathogenicity, cancer genomics, population genetics, rare disease, virus genomics, epigenomics
🧬 Protein Science & Engineering	38	Structure prediction (ESMFold/AlphaFold), binding sites, mutation analysis, antibody & peptide design, enzyme engineering
🧪 Chemistry & Molecular Science	24	Structure analysis, molecular fingerprints, SAR, material composition, natural products, metabolomics
⚙️ Physics & Engineering Computing	18	Circuit analysis, thermodynamics, optics, electromagnetics, crystallography, unit conversion
🔬 Lab Automation & Literature Mining	7	Protocol generation, PDF extraction, PubMed search, scientific literature mining, meta-analysis
🌍 Earth & Environmental Science	5	Atmospheric science, wind energy assessment, seawater properties, oceanographic calculations
📊 Biomedical Database Integration	2	OpenTargets disease-target queries, experimental data processing

💊 Drug Discovery & Pharmacology — 71 Skills (click to expand)

admet_druglikeness_report · affinity_maturation · alanine_scanning_pipeline · antibody_drug_development · atc_drug_classification · boltz2-binding-affinity · cancer_therapy_design · chemical_safety_assessment · clinical_pharmacology_report · clinical_trial_drug_profile · combinatorial_chemistry · comparative_drug_analysis · compound_to_drug_pipeline · disease-reversal-prediction · disease_compound_pipeline · disease_drug_landscape · disease_knowledge_graph · drug-screening-docking · drug_indication_mapping · drug_interaction_checker · drug_metabolism_study · drug_repurposing_screen · drug_safety_profile · drug_target_identification · drug_target_structure · drug_warning_report · drugsda-admet · drugsda-compound-retrieve · drugsda-data-valid · drugsda-denovo-sampling · drugsda-dleps · drugsda-drug-likeness · drugsda-esmfold · drugsda-file-transfer · drugsda-linker-sampling · drugsda-mol-properties · drugsda-mol-similarity · drugsda-mol2mol-sampling · drugsda-p2rank · drugsda-peptide-sampling · drugsda-prosst · drugsda-rgroup-sampling · drugsda-target-retrieve · enzyme_inhibitor_design · epigenetics_drug · fda-drug-risk-assessment · gene_to_drug_pipeline · gene_variant_drug_nexus · infectious_disease_analysis · lead_compound_optimization · molecular_docking_pipeline · one_health_analysis · opentargets-disease-target · orphan_drug_analysis · pandemic_preparedness · pediatric_drug_safety · personalized_medicine · pharmacogenomics_analysis · pharmacokinetics_profile · polypharmacology_analysis · precision_oncology · protein_drug_interaction · smiles_comprehensive_analysis · structural_pharmacogenomics · substance_toxicology · systems_pharmacology · toxicity_assessment · variant-pharmacogenomics · virtual_screening · gene-knowledge-integration · molecular-property-profiling

🧬 Genomics & Genetic Analysis — 41 Skills (click to expand)

biomarker_discovery · biosample_genomics · chromosome_analysis · comprehensive-variant-annotation · cross_species_genomics · epigenomic_landscape · gene_disease_association · gene_expression_atlas · gene_family_evolution · genetic_counseling_report · genome_annotation · go_term_analysis · microbiome_genomics · mouse_model_analysis · multispecies_gene_analysis · ncbi-gene-retrieval · ncbi_gene_deep_dive · organism_classification · phenotype-by-hpo-id · population_genetics · rare_disease_genetics · region-gene-elements · regulatory_region_analysis · snp_functional_analysis · tcga-gene-expression · tissue_specific_analysis · transcriptome_analysis · ucsc_genome_exploration · variant-clinical-significance · variant-cross-database-ids · variant-functional-prediction · variant-genomic-location · variant-gwas-associations · variant-population-frequency · variant_pathogenicity · virus_genomics · gene_comprehensive_lookup · gene_therapy_target · ensembl-sequence-retrieval · kegg-gene-search · multiomics_integration

🧬 Protein Science & Engineering — 38 Skills (click to expand)

alphafold_structure_pipeline · antibody_target_analysis · binding_site_characterization · blast_protein_analysis · comprehensive-protein-analysis · disease_protein_profiling · dna-rna-sequence-analysis · enzyme_engineering · full_protein_analysis · interproscan-domain-analysis · interproscan_pipeline · metabolomics_pathway · molecular_visualization_suite · mutation_impact_analysis · peptide-properties-calculation · protein-blast-search · protein-properties-calculation · protein_classification_analysis · protein_complex_analysis · protein_database_crossref · protein_engineering · protein_function_annotation · protein_interaction_network · protein_property_comparison · protein_quality_assessment · protein_similarity_search · protein_solubility_optimization · protein_structure_analysis · proteome_analysis · string-ppi-enrichment · structural_homology_modeling · synthetic_biology_design · uniprot-protein-retrieval · uniprot_deep_analysis · lab_protocol_from_literature · code_execution_analysis · molecular-descriptors-calculation · web_literature_mining

🧪 Chemistry & Molecular Science — 24 Skills (click to expand)

aliphatic_ring_analysis · bioassay_analysis · cas_compound_lookup · cell_line_assay_analysis · chembl-molecule-search · chemical-mass-percent-calculation · chemical-structure-analysis · chemical_patent_analysis · chemical_property_profiling · chemical_structure_comparison · compound-name-retrieval · compound_database_crossref · functional_group_profiling · molecular-format-conversion · molecular-properties-calculation · molecular-similarity-search · molecular_fingerprint_analysis · natural_product_analysis · polymer_property_analysis · pubchem-smiles-search · pubchem_deep_dive · smiles-to-cas-conversion · substructure_activity_search · material-density-volume-calculation

⚙️ Physics & Engineering Computing — 18 Skills (click to expand)

buoyancy-acceleration-calculation · capacitance-calculation · electrical_circuit_analysis · electromagnetic_analysis · energy_conversion · experimental_data_processing · geometric-volume-calculation · geometry_trigonometry · length_measurement · measurement-error-analysis · mobility_analysis · nuclear_physics · optical-frequency-calculation · optics_analysis · signal_processing · statistical_error_analysis · thermal_analysis · unit_conversion_suite

🔬 Lab Automation & Literature Mining — 7 Skills (click to expand)

biomedical-web-search · meta-analysis-execution · protocol-extraction-from-pdf · protocol-generation · protocol-to-executable-json · pubmed-article-search · scientific-literature-search

🌍 Earth & Environmental Science — 5 Skills (click to expand)

atmospheric-science-calculations · oceanographic-seawater-properties · seawater-freezing-temperature · seawater-sound-speed-calculation · wind-site-assessment

📊 Other — 2 Skills

seismic-waveform-processing · unit-conversion-nanoscale

Skill Highlights

• 📦 206 Skills in total, each containing a complete SKILL.md with documentation, test cases, and runnable Python code
• ✅ All skills have been tested against live SCP endpoints and verified to work
• 🔧 250+ distinct tools orchestrated across 31 SCP Servers
• 🌍 Covering 8 major scientific domains and 112+ sub-disciplines
• 🔑 Each skill includes authentication setup — just replace <YOUR_SCP_HUB_API_KEY> with your own key applied and generated in each SCP server page listed in SCP Square

💡 Want more? If you'd like any useful models or tools to be available as 24/7 accessible APIs, just let us know by submitting an issue, and we'll deploy them for you.

How to use SCP skills

Please refer to the SCP Skills Tutorial.

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📊 Use Cases

Scenario	Description
📝 Automated Experiment Protocol Design	Generate executable experiment protocols from natural language objectives
📄 PDF Protocol Auto-Reproduction	Extract experiment steps from PDFs and execute them automatically
💊 AI-Driven Molecular Screening	Integrated QED scoring, ADMET prediction, and molecular docking
🧪 Dry-Wet Integrated Protein Engineering	Closed-loop workflow from sequence design to experimental validation

📖 For detailed case studies, please refer to our Technical Report or User Cases

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🔬 SCP vs MCP

Feature	MCP	SCP
Protocol Standardization	General tool invocation	Structured, complete scientific experiment workflows
High-Throughput Experiment Support	No built-in experiment management	Supports batch experiments and context management
Multi-Agent Collaboration	Point-to-point communication	Centralized orchestration and task distribution
Wet-Lab Equipment Integration	Requires custom adapters	Standardized device drivers and interfaces

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🌐 Resources

Resource	Link
🛠️ SCP Tool Square	Explore 2,200+ integrated tools
🚀 SCP Skills Tutorial	Docker setup, model switching & skills usage guide
📖 Documentation (Chinese)	Detailed user guide
📄 Technical Report	SCP design and experiment details
💬 Community	Discussions and Q&A

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📄 License

This project is open-sourced under the Apache License 2.0.

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🙏 Acknowledgments

SCP is developed by Shanghai AI Laboratory. We thank the open-source community for their support.

If you use SCP in your research, please cite our technical report:

@article{jiang2025scp,
  title={SCP: Accelerating Discovery with a Global Web of Autonomous Scientific Agents},
  author={Jiang, Yankai and Lou, Wenjie and Wang, Lilong and Tang, Zhenyu and Feng, Shiyang and Lu, Jiaxuan and Sun, Haoran and Pan, Yaning and Gu, Shuang and Su, Haoyang and others},
  journal={arXiv preprint arXiv:2512.24189},
  year={2025}
}

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Made with ❤️ by Shanghai AI Laboratory