scilink 0.0.20

LLM-powered agents for scientific research automation

SciLink

AI-Powered Scientific Research Automation Platform

SciLink employs a system of intelligent agents to automate experimental design, data analysis, and iterative optimization workflows. Built around large language models with domain-specific tools, these agents act as AI research partners that can plan experiments, analyze results across multiple modalities, and suggest optimal next steps.

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Overview

SciLink provides three complementary agent systems that cover the full scientific research cycle:

System	Purpose	Key Capabilities
Planning Agents	Experimental design & optimization	Hypothesis generation, Bayesian optimization, literature-aware planning
Analysis Agents	Multi-modal data analysis	Microscopy, spectroscopy, particle segmentation, curve fitting
Simulation Agents	Computational modeling	DFT calculations, classical MD (LAMMPS), structure recommendations

All systems support three autonomy levels:

• Co-Pilot (default) — Human leads, AI assists. Reviews every step.
• Supervised — AI leads, human reviews major decisions.
• Autonomous — Full autonomy, no human review.

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Installation

pip install scilink

# With web UI
pip install scilink[ui]

# With simulation dependencies (ASE, atomate2, etc.)
pip install scilink[sim]

Environment Variables

Set API keys for your preferred LLM provider:

# Google Gemini (default)
export GEMINI_API_KEY="your-key"

# OpenAI
export OPENAI_API_KEY="your-key"

# Anthropic
export ANTHROPIC_API_KEY="your-key"

# OpenAI-compatible proxy (if applicable)
export SCILINK_API_KEY="your-key"

When using SCILINK_API_KEY, also provide a --base-url pointing to your OpenAI-compatible endpoint.

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Quick Start

SciLink can be used via the CLI, web UI, MCP server, or Python API.

CLI

# Planning session
scilink plan
scilink plan --autonomy supervised --data-dir ./results --knowledge-dir ./papers

# Analysis session
scilink analyze
scilink analyze --data ./sample.tif --metadata ./metadata.json

Web UI

scilink ui

Requires pip install scilink[ui].

MCP Server

scilink serve --model gemini-3.1-pro-preview

See MCP Integration for details.

Python API

from scilink.agents.planning_agents import PlanningAgent
from scilink.agents.exp_agents import AnalysisOrchestratorAgent, AnalysisMode

# Generate an experimental plan
planner = PlanningAgent(model_name="gemini-3.1-pro-preview")
plan = planner.propose_experiments(
    objective="Optimize lithium extraction yield",
    knowledge_paths=["./literature/"],
    primary_data_set={"file_path": "./composition_data.xlsx"}
)

# Analyze microscopy data
analyzer = AnalysisOrchestratorAgent(analysis_mode=AnalysisMode.SUPERVISED)
result = analyzer.chat("Analyze ./stem_image.tif and generate scientific claims")

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MCP Integration

SciLink supports the Model Context Protocol (MCP) as both a server (exposing its tools/agents to external clients like Claude Code) and a client (connecting to external MCP servers for additional capabilities).

As an MCP Server

Expose SciLink's analysis and planning tools to any MCP-compatible client:

# Default (stdio transport, autonomous mode)
scilink serve --model gemini-3.1-pro-preview

# Analysis only, with human approval for major actions
scilink serve --mode analyze --autonomy co-pilot

# HTTP transport (SSE)
scilink serve --transport sse --host 127.0.0.1 --port 8000

The server exposes all orchestrator tools (prefixed scilink_ for analysis, scilink_plan_ for planning), plus job management tools for long-running operations. Autonomy modes control which tools require human approval before execution. See docs/claude_code_integration.md for the full MCP server guide.

As an MCP Client

Connect external MCP servers to extend SciLink with additional tools:

# Python MCP server (e.g., arXiv paper search)
scilink analyze --mcp stdio:arxiv:python,-m,arxiv_mcp_server,--storage-path,/tmp/papers

Programmatically:

orchestrator = AnalysisOrchestratorAgent()
tool_count = orchestrator.connect_mcp_server(
    server_name="arxiv",
    command=["python", "-m", "arxiv_mcp_server", "--storage-path", "/tmp/papers"]
)

In the web UI, go to the Tools tab > MCP Servers section, select a transport (stdio/SSE), enter the server name and command, and click Connect.

See docs/mcp_client_integration.md for the full MCP guide.

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Extensibility

SciLink supports custom tools, skills, and agents that can be added via CLI flags, the web UI, or programmatically.

Custom Tools

Provide a Python file with tool_schemas (list of OpenAI-format tool dicts) and a create_tool_functions(data) factory:

scilink analyze --tools ./my_image_tools.py

Custom Skills

Add domain-specific analysis guidance via Markdown skill files:

scilink analyze --skills ./raman_skill.md ./ftir_skill.md

Built-in skills are available for curve fitting (XPS, Raman, etc.) and hyperspectral analysis (EELS, etc.).

Custom Agents

Register additional BaseAnalysisAgent subclasses:

scilink analyze --agents ./my_xrd_agent.py

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Planning Agents

The Planning Agents module automates experimental design, data analysis, and iterative optimization workflows.

Architecture

PlanningOrchestratorAgent (main coordinator)
├── PlanningAgent (scientific strategy)
│   ├── Dual KnowledgeBase (Docs KB + Code KB)
│   ├── RAG Engine (retrieval-augmented generation)
│   └── Literature Agent (external search)
├── ScalarizerAgent (raw data → scalar metrics)
└── BOAgent (Bayesian optimization)

Agent	Purpose
PlanningOrchestratorAgent	Coordinates the full experimental workflow via natural language
PlanningAgent	Generates experimental strategies using dual knowledge bases
ScalarizerAgent	Converts raw data (CSV, Excel) into optimization-ready metrics
BOAgent	Suggests optimal parameters via Bayesian Optimization

CLI Usage

scilink plan
scilink plan --autonomy supervised --data-dir ./results --knowledge-dir ./papers
scilink plan --model claude-opus-4-5

Interactive Session Example

$ scilink plan

📋 What's your research objective?
Your objective: Optimize lithium extraction from brine

👤 You: Generate a plan using papers in ./literature/

🤖 Agent: ⚡ Generating Initial Plan...
    📚 Retrieved 8 document chunks.

🔬 EXPERIMENT 1: pH-Controlled Selective Precipitation
> 🎯 Hypothesis: Adjusting pH to 10-11 will selectively precipitate Mg(OH)₂ while retaining Li⁺

👤 You: Analyze ./results/batch_001.csv and run optimization

🤖 Agent: [calls analyze_file → {"metrics": {"yield": 78.5}}]
  [calls run_optimization → {"recommended_parameters": {"temp": 85.2, "pH": 6.8}}]

CLI Commands

Command	Description
/help	Show available commands
/tools	List all available agent tools
/files	List files in workspace
/state	Show current agent state
/autonomy [level]	Show or change autonomy level
/checkpoint	Save session checkpoint
/quit	Exit session

Python API

from scilink.agents.planning_agents.planning_orchestrator import (
    PlanningOrchestratorAgent, AutonomyLevel
)
from scilink.agents.planning_agents import PlanningAgent, ScalarizerAgent, BOAgent

# Using the orchestrator
orchestrator = PlanningOrchestratorAgent(
    objective="Optimize reaction yield",
    autonomy_level=AutonomyLevel.SUPERVISED,
    data_dir="./experimental_results",
    knowledge_dir="./papers"
)
response = orchestrator.chat("Generate initial plan and analyze batch_001.csv")

# Direct agent usage
agent = PlanningAgent(model_name="gemini-3.1-pro-preview")
plan = agent.propose_experiments(
    objective="Screen precipitation conditions",
    knowledge_paths=["./literature/"],
    primary_data_set={"file_path": "./composition_data.xlsx"}
)

# Bayesian optimization
bo = BOAgent(model_name="gemini-3.1-pro-preview")
result = bo.run_optimization_loop(
    data_path="./optimization_data.csv",
    objective_text="Maximize yield while minimizing cost",
    input_cols=["Temperature", "pH", "Concentration"],
    input_bounds=[[20, 80], [6, 10], [0.1, 2.0]],
    target_cols=["Yield"],
    batch_size=1
)

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Experimental Analysis Agents

The Analysis Agents module provides automated scientific data analysis across multiple modalities.

Architecture

AnalysisOrchestratorAgent (main coordinator)
├── FFTMicroscopyAnalysisAgent (ID: 0)
├── SAMMicroscopyAnalysisAgent (ID: 1)
├── HyperspectralAnalysisAgent (ID: 2)
└── CurveFittingAgent (ID: 3)

ID	Agent	Use Case
0	FFTMicroscopyAnalysisAgent	Microstructure via FFT/NMF — grains, phases, atomic-resolution
1	SAMMicroscopyAnalysisAgent	Particle segmentation — counting, size distributions
2	HyperspectralAnalysisAgent	Spectroscopic datacubes — EELS-SI, EDS, Raman imaging
3	CurveFittingAgent	1D fitting — XRD, UV-Vis, PL, DSC, kinetics

CLI Usage

scilink analyze
scilink analyze --data ./sample.tif --metadata ./metadata.json
scilink analyze --mode autonomous --data ./spectrum.npy

Interactive Session Example

$ scilink analyze --data ./stem_image.tif

👤 You: Examine my data and suggest an analysis approach

🤖 Agent: ⚡ Examining data at ./stem_image.tif...
  • Type: microscopy, Shape: 2048 x 2048
  • Suggested agents: FFTMicroscopyAnalysisAgent (0) or SAMMicroscopyAnalysisAgent (1)

👤 You: Run the analysis

🤖 Agent: ⚡ Running analysis...
  The HAADF-STEM image reveals MoS2 with predominantly 2H phase structure.
  FFT analysis identified four distinct spatial frequency patterns...
  **Scientific Claims Generated:** 3

CLI Commands

Command	Description
/help	Show available commands
/tools	List orchestrator tools
/agents	List analysis agents with descriptions
/status	Show session state
/mode [level]	Show or change analysis mode
/schema	Show metadata JSON schema
/quit	Exit session

Python API

from scilink.agents.exp_agents import (
    AnalysisOrchestratorAgent, AnalysisMode,
    FFTMicroscopyAnalysisAgent, SAMMicroscopyAnalysisAgent,
    HyperspectralAnalysisAgent, CurveFittingAgent
)

# Using the orchestrator
orchestrator = AnalysisOrchestratorAgent(
    base_dir="./my_analysis",
    analysis_mode=AnalysisMode.SUPERVISED
)
response = orchestrator.chat("Examine ./data/sample.tif")

# Direct agent usage
agent = CurveFittingAgent(output_dir="./curve_output", use_literature=True)
result = agent.analyze(
    "pl_spectrum.csv",
    system_info={"experiment": {"technique": "Photoluminescence"}},
    hints="Focus on band-edge emission"
)

# Series with trend analysis
result = agent.analyze(
    ["pl_300K.csv", "pl_350K.csv", "pl_400K.csv"],
    series_metadata={"variable": "temperature", "values": [300, 350, 400], "unit": "K"}
)

Metadata Conversion

from scilink.agents.exp_agents import generate_metadata_json_from_text

# "HAADF-STEM of MoS2 monolayer, 50nm FOV, 300kV"
# → {"experiment_type": "Microscopy", "experiment": {"technique": "HAADF-STEM"}, ...}
metadata = generate_metadata_json_from_text("./experiment_notes.txt")

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Novelty Assessment

SciLink can automatically check experimental findings against the scientific literature to identify what's genuinely new. This is powered by integration with FutureHouse AI agents.

👤 You: Assess novelty of these claims

🤖 Agent: ⚡ Searching literature via FutureHouse...

  📚 [Score 2/5] Mixed 2H/1T phase coexistence → Well-documented
  🤔 [Score 3/5] Sulfur vacancy density of 3.2 × 10¹³ cm⁻² → Similar measurements exist
  🌟 [Score 4/5] 1T phase localized within 5nm of grain boundaries → Limited prior reports

  Summary: 1 HIGH-NOVELTY finding identified

The discovery loop: Analysis generates scientific claims → Novelty Assessment scores each against literature → Recommendations prioritize validation experiments for novel findings.

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Output Structure

Planning Session

campaign_session/
├── optimization_data.csv      # Accumulated experimental data
├── plan.json                  # Current experimental plan
├── plan.html                  # Rendered plan visualization
├── checkpoint.json            # Session state for restoration
└── output_scripts/            # Generated automation code

Analysis Session

analysis_session/
├── results/
│   └── analysis_{dataset}_{agent}_{timestamp}/
│       ├── metadata_used.json
│       ├── analysis_results.json
│       ├── visualizations/
│       └── report.html
├── chat_history.json
└── checkpoint.json

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Simulation Agents (Coming Soon)

The Simulation Agents module will provide AI-powered computational modeling, bridging experimental observations with atomistic simulations.

Agent	Purpose
DFTAgent	Density Functional Theory workflow automation
MDAgent	Classical molecular dynamics simulations via LAMMPS
SimulationRecommendationAgent	Recommends structures and simulation objectives based on experimental analysis

Key planned features include experiment-to-simulation pipelines, defect modeling, and direct integration with the Analysis Agents.

Note: This module is currently being refactored. Check back for updates.