From 61e0b7bc40c4cad3b38793a8563fc340f31c539a Mon Sep 17 00:00:00 2001 From: GAP Promoter Date: Tue, 26 May 2026 07:25:02 +0000 Subject: [PATCH 1/2] Add ziatdinovmax/SciLink to the registry --- agents/ziatdinovmax__scilink/README.md | 85 ++++++++++++++++++++++ agents/ziatdinovmax__scilink/metadata.json | 14 ++++ 2 files changed, 99 insertions(+) create mode 100644 agents/ziatdinovmax__scilink/README.md create mode 100644 agents/ziatdinovmax__scilink/metadata.json diff --git a/agents/ziatdinovmax__scilink/README.md b/agents/ziatdinovmax__scilink/README.md new file mode 100644 index 0000000..13c9ae8 --- /dev/null +++ b/agents/ziatdinovmax__scilink/README.md @@ -0,0 +1,85 @@ +# SciLink + +**LLM-powered agents for scientific research automation** — an AI research partner for +materials science, chemistry, physics, and adjacent experimental disciplines. + +SciLink deploys a system of intelligent orchestrator agents that cover the full scientific +research cycle: plan experiments, analyze multi-modal instrument data, and run +computational simulations — all within a single, coherent session. + +--- + +## Run + +```bash +npx @open-gitagent/gitagent run -r https://github.com/ziatdinovmax/SciLink +``` + +--- + +## What It Can Do + +SciLink provides three complementary orchestrator modes: + +### 🔬 Analyze Mode +Multi-modal experimental data analysis powered by domain-specific skill bundles: +- **Microscopy & Image Analysis** — particle segmentation, grain mapping, SAM-powered feature extraction +- **Spectroscopy** — curve fitting, peak identification, XRD, Raman, EELS +- **Hyperspectral Datacubes** — 3D datacube analysis, dimensionality reduction, component mapping +- Generates and executes verified Python analysis code in a sandboxed environment +- Produces reproducible session artefacts (code, plots, structured findings) + +### 📋 Plan Mode +Literature-grounded experimental campaign design: +- **Hypothesis Generation** — RAG over your papers, project notes, and prior results +- **Bayesian Optimization** — sequential single-objective and multi-objective BO for optimal next-experiment selection +- **Agentic Knowledge Query** — dynamically queries tabular databases and structured records without upfront schema definition +- Knowledge-only skill bundles (no runnable code) keep planning focused on reasoning and synthesis + +### ⚛️ Simulate Mode +Computational modeling with iterative structure refinement: +- **DFT Workflows** — structure generation, VASP input preparation, INCAR validation against literature, post-run output analysis +- **Classical MD** — LAMMPS input generation, force-field selection, trajectory analysis +- **Structure Validation** — 3-axis visualizations, structure comparison, automated fix suggestions +- HPC job submission and result download via SSH/SLURM backend + +### 🤖 Meta Orchestrator +A top-level router that delegates to the right specialist automatically — users interact with a single interface and never switch modes manually. Context and findings flow between specialists via a delegation ledger. + +--- + +## Autonomy Levels + +| Level | Behavior | +|---|---| +| **Co-Pilot** | Human reviews every step before the agent commits | +| **Autopilot** | Agent leads; human reviews major decisions and generated outputs | +| **Autonomous** | End-to-end execution, no human review — for headless/HPC pipelines | + +--- + +## Skill Subsystem + +Domain experts extend SciLink without touching core agent code by contributing self-contained +skill bundles: a `.md` narrative file organized around a fixed section vocabulary +(`Overview → Planning → Implementation → Interpretation → Validation`) plus optional +Python helpers registered as tools. Skill-gated tool visibility keeps per-call context +focused on the active technique. + +--- + +## Install + +```bash +pip install scilink # core (analysis + planning) +pip install scilink[ui] # + Streamlit web UI +pip install scilink[sim] # + simulation dependencies (ASE, atomate2, etc.) +pip install scilink[all] # everything +``` + +Also available as an MCP server (`scilink mcp`) for integration with Claude Code and other MCP-compatible clients. + +--- + +## Built with +[gitagent](https://github.com/open-gitagent/gitagent) — a git-native, framework-agnostic open standard for AI agents. diff --git a/agents/ziatdinovmax__scilink/metadata.json b/agents/ziatdinovmax__scilink/metadata.json new file mode 100644 index 0000000..48bad84 --- /dev/null +++ b/agents/ziatdinovmax__scilink/metadata.json @@ -0,0 +1,14 @@ +{ + "name": "scilink", + "author": "ziatdinovmax", + "description": "LLM-powered scientific research automation: multi-modal data analysis, Bayesian experiment planning, and DFT/MD simulation via three orchestrator agents.", + "repository": "https://github.com/ziatdinovmax/SciLink", + "version": "0.0.30", + "category": "research", + "tags": ["science", "materials-science", "spectroscopy", "microscopy", "dft", "bayesian-optimization", "llm-agents", "automation"], + "license": "MIT", + "model": "anthropic:claude-sonnet-4-6", + "adapters": ["claude-code", "system-prompt"], + "icon": false, + "banner": false +} From 2b4e5d3c4c0485cfe95fddb64080e5ec37e1be4d Mon Sep 17 00:00:00 2001 From: GAP Promoter Date: Tue, 26 May 2026 07:25:56 +0000 Subject: [PATCH 2/2] Update repository URL to fork with GAP files --- agents/ziatdinovmax__scilink/metadata.json | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/agents/ziatdinovmax__scilink/metadata.json b/agents/ziatdinovmax__scilink/metadata.json index 48bad84..dc8ac2d 100644 --- a/agents/ziatdinovmax__scilink/metadata.json +++ b/agents/ziatdinovmax__scilink/metadata.json @@ -2,13 +2,25 @@ "name": "scilink", "author": "ziatdinovmax", "description": "LLM-powered scientific research automation: multi-modal data analysis, Bayesian experiment planning, and DFT/MD simulation via three orchestrator agents.", - "repository": "https://github.com/ziatdinovmax/SciLink", + "repository": "https://github.com/shreyas-lyzr/SciLink", "version": "0.0.30", "category": "research", - "tags": ["science", "materials-science", "spectroscopy", "microscopy", "dft", "bayesian-optimization", "llm-agents", "automation"], + "tags": [ + "science", + "materials-science", + "spectroscopy", + "microscopy", + "dft", + "bayesian-optimization", + "llm-agents", + "automation" + ], "license": "MIT", "model": "anthropic:claude-sonnet-4-6", - "adapters": ["claude-code", "system-prompt"], + "adapters": [ + "claude-code", + "system-prompt" + ], "icon": false, "banner": false }