Merge branch 'main' into feat/datalad-skill

Resolve the README badge conflict by keeping upstream's 2.65.0 version and
the 164 skill count this branch adds, and bring the four prose skill counts
added upstream since the branch started to the same number.

Author: dylanpulver

AGENTS.md

@@ -52,9 +52,9 @@ tests/<skill-name>/          # same name as the skill directory
 └── fixtures/                # optional test data
 ```
 
-**Diagrams never live under `skills/` either.** Every skill has one generated workflow diagram at
-`docs/images/<skill-name>.png`, produced by `scripts/generate_skill_image.py` and kept in step with
-the skill's documentation — see [Skill diagrams](#skill-diagrams).
+**Diagrams never live under `skills/` either.** A skill may have a generated workflow diagram at
+`docs/images/<skill-name>.png`, produced by `scripts/generate_skill_image.py`. Diagrams are optional
+— see [Skill diagrams](#skill-diagrams).
 
 Tests reach their skill through an explicit anchor, never a relative walk:
 
@@ -73,11 +73,6 @@ SKILL_ROOT = Path(__file__).resolve().parents[2] / "skills" / "<skill-name>"
 5. If the skill ships `scripts/`, put their tests in **`tests/<name>/`** — never in the skill
    directory. Fixtures go in `tests/<name>/fixtures/`.
 6. Validate and scan (below).
-7. Generate the skill's diagram — a new skill without `docs/images/<name>.png` is incomplete:
-
-   ```bash
-   uv run python scripts/generate_skill_image.py --skill <name>
-   ```
 
 ```markdown
 ---
@@ -115,16 +110,6 @@ Use this skill when...
 5. Re-run any example, command, or script you touched, plus `tests/<name>/` if that suite exists.
    Suites check that `metadata.version` is present and quoted, not what it equals, so a version bump
    never needs a matching test edit.
-6. **Regenerate the diagram in the same change** whenever the edit changes what the skill does or
-   how its workflow runs — the picture is generated from `SKILL.md` and `references/`, so it goes
-   stale silently. The command overwrites `docs/images/<name>.png` in place:
-
-   ```bash
-   uv run python scripts/generate_skill_image.py --skill <name>
-   ```
-
-   A typo fix, a link repair, or a version bump alone does not need a new image.
-
 ## Frontmatter
 
 `SKILL.md` starts with YAML frontmatter. **Only these six fields are allowed** — the spec defines a
@@ -331,10 +316,11 @@ touch the shared contract.
 
 ## Skill diagrams
 
-Every skill carries one generated workflow diagram at `docs/images/<skill-name>.png`. Creating a
-skill means creating its image; changing what a skill does means regenerating it. The image is not
-optional decoration — it is derived from the documentation, so an out-of-date one misrepresents the
-skill.
+A skill may carry a generated workflow diagram at `docs/images/<skill-name>.png`. Diagrams are
+optional: neither a new skill nor a change to an existing one is blocked on having or refreshing an
+image, and no CI check enforces them. If you do ship one, note that it is derived from the
+documentation, so regenerate it when the skill's workflow changes rather than leaving a picture that
+misrepresents the skill.
 
 `scripts/generate_skill_image.py` is local repository tooling, standard library only, and runs in
 two stages on one `OPENROUTER_API_KEY` (environment variable, repository `.env`, or `--api-key`):
@@ -380,7 +366,7 @@ hand-tuning one skill's prompt, so the set stays visually consistent.
   leaked local path, and a drifted Agent Plugins manifest.
 - If the skill ships `scripts/`: a suite exists at `tests/<name>/`, a `[skills.<name>]` entry exists
   in `tests/skill-requirements.toml`, and `python tests/run_all.py --isolated <name>` passes.
-- `docs/images/<name>.png` exists, and was regenerated if the change altered what the skill does.
-  Its labels are spelled correctly and its arrows point where they should.
+- If the skill ships `docs/images/<name>.png`, its labels are spelled correctly and its arrows point
+  where they should. The image itself is optional.
 - Examples and scripts are tested, or clearly marked illustrative.
 - No secrets or private data; scan results clean or explained in the PR.

README.md

@@ -1,7 +1,7 @@
 # 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-164-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/)
@@ -16,7 +16,10 @@
 
 > **🔔 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 164 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)
+
+> **🎥 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.
 
@@ -32,6 +35,7 @@ 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
@@ -114,7 +118,7 @@ Each skill includes:
 - **Multi-Step Workflows** - Execute complex pipelines with a single prompt
 
 ### 🎯 **Comprehensive Coverage**
-- **161 Skills** - Extensive coverage across all major scientific domains
+- **164 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)
 
@@ -169,7 +173,7 @@ 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
@@ -221,7 +225,7 @@ 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 164 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.
 
@@ -499,6 +503,9 @@ This repository contains **164 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
@@ -871,7 +878,7 @@ 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 = {164 skills covering databases, packages, integrations, and analysis tools}
 }
 ```