pyopenms SKILL.md skillA
pyopenms from foryourhealth111-pixel/vibe-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add foryourhealth111-pixel/vibe-skills/pyopenms@git:20260226.1632f40Pins git:20260226.1632f40 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- foryourhealth111-pixel/vibe-skills
- Path
bundled/skills/pyopenms/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260226.1632f40, committed Feb 26, 2026
- Size
- 5,626 bytes
- Repository stars
- 3,805
- License
- Apache-2.0
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets.
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 for handling mass spectrometry file formats, processing spectral data, detecting features, identifying peptides/proteins, and performing quantitative analysis.
## Installation
Install using uv:
```bash
uv uv pip install pyopenms
```
Verify installation:
```python
import pyopenms
print(pyopenms.__version__)
```
## Core Capabilities
PyOpenMS organizes functionality into these domains:
### 1. File I/O and Data Formats
Handle mass spectrometry file formats and convert between representations.
**Supported formats**: mzML, mzXML, TraML, mzTab, FASTA, pepXML, protXML, mzIdentML, featureXML, consensusXML, idXML
Basic file reading:
```python
import pyopenms as ms
# Read mzML file
exp = ms.MSExperiment()
ms.MzMLFile().load("data.mzML", exp)
# Access spectra
for spectrum in exp:
mz, intensity = spectrum.get_peaks()
print(f"Spectrum: {len(mz)} peaks")
```
**For detailed file handling**: See `references/file_io.md`
### 2. Signal Processing
…Read the whole file at its exact version.
How to install
mdr add foryourhealth111-pixel/vibe-skills/pyopenms@sha256:04739ca058a3c56fThe line at the top of this page pins the label git:20260226.1632f40, 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_e5glkb4pa5rzd473)
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Versions
The registry has recorded 1 version of this file, committed on Feb 26, 2026.
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 (5626 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
foryourhealth111-pixel/vibe-skills · 3,805 stars · license Apache-2.0 · pushed 2026-11-07 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_e5glkb4pa5rzd473 GET https://markdownregistry.com/api/v1/resolve?ref=foryourhealth111-pixel/vibe-skills/pyopenms GET https://markdownregistry.com/api/v1/blob/04739ca058a3c56f8eed4a49df66eb3074b79275aab862619aca8dcc5953838e
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
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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