instrument-data-allotrope
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV for LIMS systems and data lakes.
Best use case
instrument-data-allotrope is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV for LIMS systems and data lakes.
Teams using instrument-data-allotrope should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/instrument-data-allotrope/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How instrument-data-allotrope Compares
| Feature / Agent | instrument-data-allotrope | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV for LIMS systems and data lakes.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# Instrument Data Allotrope
## Quick Start
```python
# Install requirements first
pip install allotropy pandas openpyxl pdfplumber --break-system-packages
# Core conversion
from allotropy.parser_factory import Vendor
from allotropy.to_allotrope import allotrope_from_file
# Convert with allotropy
asm = allotrope_from_file("instrument_data.csv", Vendor.BECKMAN_VI_CELL_BLU)
```
## Sub-Skills
- [Workflow Overview](workflow-overview/SKILL.md)
- [Output Format Selection](output-format-selection/SKILL.md)
- [Calculated Data Handling](calculated-data-handling/SKILL.md)
- [Validation](validation/SKILL.md)
- [Supported Instruments](supported-instruments/SKILL.md)
- [Tier 1: Native allotropy parsing (PREFERRED) (+2)](tier-1-native-allotropy-parsing-preferred/SKILL.md)
- [Pre-Parsing Checklist](pre-parsing-checklist/SKILL.md)
- [Common Mistakes to Avoid](common-mistakes-to-avoid/SKILL.md)
- [Code Export for Data Engineers](code-export-for-data-engineers/SKILL.md)
- [File Structure](file-structure/SKILL.md)
- [Example 1: Vi-CELL BLU file (+2)](example-1-vi-cell-blu-file/SKILL.md)
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