pyopenms SKILL.md skillA
pyopenms from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/pyopenms@v3.0Pins v3.0 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/pyopenms/SKILL.md- Versions recorded
- 7
- Latest version
- v3.0, committed Oct 1, 2026
- First version recorded
- May 27, 2026
- Size
- 12,447 bytes
- Repository stars
- 56,497
- License
- MIT
Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# PyOpenMS ## Overview PyOpenMS provides Python bindings to the OpenMS library for computational mass spectrometry, enabling analysis of proteomics and metabolomics data. Use it to read/write MS file formats, process raw spectra, detect and quantify features, identify peptides and proteins, and run end-to-end LC-MS/MS pipelines. **This skill ships ready-to-run scripts in `scripts/`** covering the most common high-level workflows. Prefer running a script over writing new code—each is a parameterized CLI tool that handles loading, processing, and export. Drop into the Python API (and the `references/`) only when no script fits. ## Installation ```bash uv venv --python 3.13 uv pip install "pyopenms==3.6.0" pandas numpy matplotlib ``` Verify (note: `__version__` works, but the bundled binary prints a one-line memory-status notice on import that is harmless): ```python import pyopenms as ms print(ms.__version__) # 3.6.0 ``` ## Scripts (start here) Run with `python scripts/<name>.py --help` for full options. Input formats differ by script; inspect its help. Commands below run from the skill directory with the environment activated. Native regression tests use tiny synthetic …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/pyopenms@sha256:020e7392adbb000aThe line at the top of this page pins the label v3.0, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_veqkjddhxrlbln5e)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 7 versions of this file, between May 27, 2026 and Oct 1, 2026, about one every 21 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v3.0 latest | 2026-10-01 | a92663a | 12,447 B | A | view · diff |
| v2.2 | 2026-09-30 | ce9e6e9 | 9,743 B | A | view · diff |
| v2.1 | 2026-09-02 | 1e5eeff | 9,041 B | A | view · diff |
| v2.0 | 2026-07-26 | b085e11 | 8,083 B | A | view · diff |
| git:20260612.b8fea8f | 2026-06-12 | b8fea8f | 8,088 B | A | view · diff |
| git:20260611.1b8fae3 | 2026-06-11 | 1b8fae3 | 5,646 B | A | view · diff |
| v1.0 | 2026-05-27 | 0936740 | 5,641 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (12447 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_veqkjddhxrlbln5e GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/pyopenms GET https://markdownregistry.com/api/v1/blob/020e7392adbb000aaab4968ae9a803ca4bd97818ca35e9eebd3abc222766a48f
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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