Individual skill
instrument-data-to-allotrope
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full ASM JSON, flattened CSV for easy import, and exportable Python code for data engineers. Common triggers include converting instrument files, standardizing lab data, preparing data for upload to LIMS/ELN systems, or generating parser code for production pipelines.
skills-imported/instrument-data-to-allotrope/SKILL.md
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- Last checked
- Nov 8, 2026
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- Repository last updated
- Oct 10, 2026
- License
- MIT
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CONNECTORS.mddoc · 1,409 bytesLICENSE.txtdoc · 10,254 bytesSKILL.mdcore · 11,140 bytesSKILL.mdcore · 11,140 bytesSKILL.mdcore · 11,140 bytesSKILL.mdcore · 11,140 bytesSKILL.mdcore · 11,140 bytesSKILL.mdcore · 11,140 bytesSKILL.mdcore · 11,140 bytesreferences/asm_schema_overview.mddoc · 6,110 bytesreferences/field_classification_guide.mddoc · 17,665 bytesreferences/flattening_guide.mddoc · 7,500 bytesreferences/supported_instruments.mddoc · 5,304 bytesrequirements.txtdoc · 811 bytesscripts/convert_to_asm.pyruns · 17,278 bytesscripts/export_parser.pyruns · 13,847 bytesscripts/flatten_asm.pyruns · 7,339 bytesscripts/validate_asm.pyruns · 36,719 bytes
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<!-- Provenance: adapted from anthropics/knowledge-work-plugins (Apache-2.0, (c) Anthropic).
Original skill: https://github.com/anthropics/knowledge-work-plugins/tree/main/bio-research/skills/instrument-data-to-allotrope. Changes for Muse AI: Claude/Cowork product refs -> Muse AI; MCP -> connector; CLAUDE.md -> MUSE.md; ${CLAUDE_PLUGIN_ROOT} -> this skill's directory; /plugin:command refs -> skill refs. -->
# Instrument Data to Allotrope Converter
Convert instrument files into standardized Allotrope Simple Model (ASM) format for LIMS upload, data lakes, or handoff to data engineering teams.
> **Note: This is an Example Skill**
>
> This skill demonstrates how skills can support your data engineering tasks—automating schema transformations, parsing instrument outputs, and generating production-ready code.
>
> **To customize for your organization:**
> - Modify the `references/` files to include your company's specific schemas or ontology mappings