[upstream-sync] plugin.json from K-Dense-AI/scientific-agent-skills@f6fcafeb [unknown]

upstream/K-Dense-AI-scientific-agent-skills/catalogue/README.md

@@ -2,9 +2,9 @@
 title: "Scientific Agent Skills"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/390f5146/README.md
-upstream_sha: 390f5146
-imported_at: 2026-08-20
+upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/f6fcafeb/README.md
+upstream_sha: f6fcafeb
+imported_at: 2026-08-29
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -14,7 +14,7 @@ validated: false
 # Scientific Agent Skills
 
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE.md)
-[![Version](https://img.shields.io/badge/Version-2.64.0-blue.svg)](pyproject.toml)
+[![Version](https://img.shields.io/badge/Version-2.65.0-blue.svg)](pyproject.toml)
 [![Skills](https://img.shields.io/badge/Skills-163-brightgreen.svg)](#-whats-included)
 [![Databases](https://img.shields.io/badge/Databases-100%2B-orange.svg)](#-whats-included)
 [![Agent Skills](https://img.shields.io/badge/Standard-Agent_Skills-blueviolet.svg)](https://agentskills.io/)
@@ -29,10 +29,10 @@ validated: false
 
 > **🔔 Claude Scientific Skills is now Scientific Agent Skills.** Same skills, broader compatibility — now works with any AI agent that supports the open [Agent Skills](https://agentskills.io/) standard, not just Claude.
 
-> **New: [K-Dense BYOK](https://github.com/K-Dense-AI/k-dense-byok)** — A free, open-source AI co-scientist that runs on your desktop, powered by Scientific Agent Skills. Bring your own API keys, pick from 40+ models, and get a full research workspace with web search, file handling, 100+ scientific databases, and access to all 161 skills in this repo. Your data stays on your computer, and you can optionally scale to cloud compute via [Modal](https://modal.com/) for heavy workloads. [Get started here.](https://github.com/K-Dense-AI/k-dense-byok)
+> **New: [K-Dense BYOK](https://github.com/K-Dense-AI/k-dense-byok)** — A free, open-source AI co-scientist that runs on your desktop, powered by Scientific Agent Skills. Bring your own API keys, pick from 40+ models, and get a full research workspace with web search, file handling, 100+ scientific databases, and access to all 163 skills in this repo. Your data stays on your computer, and you can optionally scale to cloud compute via [Modal](https://modal.com/) for heavy workloads. [Get started here.](https://github.com/K-Dense-AI/k-dense-byok)
 
-> **🎥 Live webinar — [Getting Started with K-Dense BYOK](https://luma.com/nucztxt5)** · Tuesday, August 25, 2026 · 2:00 PM PT / 5:00 PM ET · Online, free
-> Join us for a hands-on walkthrough of [K-Dense BYOK](https://github.com/K-Dense-AI/k-dense-byok), our free, open-source AI co-scientist that runs locally on your own machine and is powered by Scientific Agent Skills. We'll show you how to set it up, bring your own API keys, and run real research workflows with these skills. No prior technical experience needed, and questions are welcome throughout. **[Save your spot →](https://luma.com/nucztxt5)**
+> **🎥 Webinar recording — [Getting Started with K-Dense BYOK](https://youtu.be/Du3BIE48DKc?si=9dPpETKSc2PeQbvU)**
+> A hands-on walkthrough of [K-Dense BYOK](https://github.com/K-Dense-AI/k-dense-byok), our free, open-source AI co-scientist that runs locally on your own machine and is powered by Scientific Agent Skills. We cover how to set it up, bring your own API keys, and run real research workflows with these skills. No prior technical experience needed. **[Watch the recording →](https://youtu.be/Du3BIE48DKc?si=9dPpETKSc2PeQbvU)**
 
 > **Stay up to date:** Follow K-Dense on [X](https://x.com/k_dense_ai), [LinkedIn](https://www.linkedin.com/company/k-dense-inc), [YouTube](https://www.youtube.com/@K-Dense-Inc), and [Reddit](https://www.reddit.com/user/-k-dense-/) for new skills, release announcements, walkthroughs, research workflow demos, and examples you can use with your own AI agent.
 
@@ -48,6 +48,7 @@ These skills enable your AI agent to seamlessly work with specialized scientific
 - 🔬 Proteomics & Mass Spectrometry - LC-MS/MS processing, peptide identification, spectral matching, protein quantification
 - 🏥 Clinical Research & Evidence Workflows - Clinical trials, pharmacogenomics, variant evidence review, pharmacokinetic/pharmacodynamic modelling and dose-regimen evaluation, aggregate decision-support evaluation, source-bound draft report structures, and formatting of clinician-authored treatment decisions
 - 🧠 Healthcare AI & Biosignal Research - EHR and model research, physiological signal analysis, and retrospective validation—not patient-specific diagnosis, treatment, alarms, or deployment decisions
+- 🐭 Preclinical Research & Animal Welfare - Multivariate severity scoring and humane-endpoint forecasting for laboratory animal studies, for 3Rs/refinement analysis and EU Directive 2010/63/EU reporting—an aid to severity assessment, never a decision rule
 - 🖼️ Medical Imaging & Digital Pathology - Privacy-aware DICOM processing and research-only whole-slide image analysis, computational pathology, and radiology data workflows
 - 🤖 Machine Learning & AI - Deep learning, reinforcement learning, time series analysis, model interpretability, Bayesian methods
 - 🔮 Materials Science & Chemistry - Crystal structure analysis, phase diagrams, metabolic modeling, computational chemistry
@@ -130,7 +131,7 @@ Each skill includes:
 - **Multi-Step Workflows** - Execute complex pipelines with a single prompt
 
 ### 🎯 **Comprehensive Coverage**
-- **161 Skills** - Extensive coverage across all major scientific domains
+- **163 Skills** - Extensive coverage across all major scientific domains
 - **100+ Databases** - Unified access to 78+ databases via database-lookup, plus dedicated data access skills and multi-database packages like BioServices, BioPython, and gget
 - **70+ Optimized Python Package Skills** - Current, version-scoped guidance for packages including RDKit, Scanpy, PyTorch Lightning, scikit-learn, PyTDC, pydicom, PufferLib, QuTiP, GeoPandas, pymatgen, Qiskit, Molecular Dynamics (OpenMM/MDAnalysis), scVelo, and TimesFM (the agent can use any Python package; these are the pre-documented paths)
 
@@ -185,7 +186,7 @@ Pin to a specific release tag or commit SHA for reproducible installs:
 
 ```bash
 # Pin to a release tag
-gh skill install K-Dense-AI/scientific-agent-skills --pin v2.64.0
+gh skill install K-Dense-AI/scientific-agent-skills --pin v2.65.0
 
 # Pin to a commit SHA
 gh skill install K-Dense-AI/scientific-agent-skills --pin abc123def
@@ -237,7 +238,7 @@ For Hermes versions that support skill taps, add the repository as a tap:
 hermes skills tap add K-Dense-AI/scientific-agent-skills
 ```
 
-Every `SKILL.md` has YAML frontmatter, but legacy and community skills vary in `metadata` formatting (block or flow style) and optional extension fields. Repository updates must keep `metadata.version` as a quoted numeric string and pass canonical `skills-ref validate ./skills/<skill-name>` checks. Hosts may interpret optional metadata and credential prompts differently, so verify behavior on the target host. Because 161 skills add up to a lot of standing context, consider installing a topical subset rather than the whole collection.
+Every `SKILL.md` has YAML frontmatter, but legacy and community skills vary in `metadata` formatting (block or flow style) and optional extension fields. Repository updates must keep `metadata.version` as a quoted numeric string and pass canonical `skills-ref validate ./skills/<skill-name>` checks. Hosts may interpret optional metadata and credential prompts differently, so verify behavior on the target host. Because 163 skills add up to a lot of standing context, consider installing a topical subset rather than the whole collection.
 
 > **NemoClaw note:** NemoClaw runs agents inside NVIDIA OpenShell with default-deny outbound networking. Skills are discovered and loaded normally, but any skill that needs the network — package installs via `uv`, or API calls (Exa, Parallel, Benchling, NCBI, Materials Project, …) — only works once the operator pre-approves the relevant domains in the OpenShell TUI.
 
@@ -515,6 +516,9 @@ This repository contains **163 scientific and research skills** organized across
 - Decision-support research: local, aggregate or synthetic Clinical Decision Support evaluation and governance artifacts only
 - Clinical documentation: source-bound Clinical Reports drafts and formatting of verified clinician-authored decisions with Treatment Plans; neither skill diagnoses or recommends care
 
+#### 🐭 **Preclinical Research & Animal Welfare** (1 skill)
+- Severity assessment: RELSA Severity Assessment (multivariate RELSA scores from body weight, temperature, clinical/nesting scores, biomarkers, activity, heart rate, burrowing and wheel running; ARIMA humane-endpoint forecasting with 95% prediction intervals; KDE-derived attention and danger zones for 3Rs/refinement and EU Directive 2010/63/EU severity reporting) — an aid to severity assessment, never a decision rule
+
 #### 🖼️ **Medical Imaging & Digital Pathology** (4 skills)
 - DICOM processing: pydicom 3.0.2 with privacy-first local preflight and no diagnostic or de-identification-compliance claims
 - Whole slide imaging: histolab and research-only PathML 3.0.5
@@ -886,7 +890,7 @@ Recommended practice:
   title = {Scientific Agent Skills: A Comprehensive Collection of Scientific Tools for AI Agents},
   year = {2026},
   url = {https://github.com/K-Dense-AI/scientific-agent-skills},
-  note = {161 skills covering databases, packages, integrations, and analysis tools}
+  note = {163 skills covering databases, packages, integrations, and analysis tools}
 }
 ```
 

upstream/K-Dense-AI-scientific-agent-skills/catalogue/plugin.json

@@ -0,0 +1,36 @@
+---
+title: "Plugin"
+task: ""
+lineage_type: import
+upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/f6fcafeb/plugin.json
+upstream_sha: f6fcafeb
+imported_at: 2026-08-29
+prompt_class: unknown
+upstream_changes: accepted
+author: upstream
+validated: false
+---
+
+{
+  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
+  "name": "scientific-agent-skills",
+  "version": "2.65.0",
+  "description": "Ready-to-use scientific and research Agent Skills for biology, chemistry, medicine, and related workflows.",
+  "author": {
+    "name": "K-Dense Inc.",
+    "url": "https://k-dense.ai"
+  },
+  "homepage": "https://github.com/K-Dense-AI/scientific-agent-skills",
+  "repository": "https://github.com/K-Dense-AI/scientific-agent-skills",
+  "license": "MIT",
+  "keywords": [
+    "agent-skills",
+    "science",
+    "research",
+    "bioinformatics",
+    "cheminformatics",
+    "biology",
+    "chemistry",
+    "medicine"
+  ]
+}