instrument-data-to-allotrope

Name: instrument-data-to-allotrope
Availability: InStock
Author: openYak

Convert instrument outputs into Allotrope Simple Model JSON with flattened CSV.

704|58|Updated Mar 20, 2026

Search Tags:#validation #provenance #parsing #data-transformation #asm #lims #instrument-data

Ready to run

npx skills add https://github.com/openyak/desktop --skill instrument-data-to-allotrope-openyak

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: instrument-data-to-allotrope
Source: https://github.com/openyak/desktop/tree/main/backend/app/data/plugins/bio-research/skills/instrument-data-to-allotrope
Command: npx skills add https://github.com/openyak/desktop --skill instrument-data-to-allotrope-openyak

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires allotropy, pandas, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Convert laboratory instrument outputs into Allotrope Simple Model (ASM) JSON to enable standardized data exchange and easier downstream analysis.

Core Features & Use Cases

Auto-detect instrument type and parse common formats (CSV, XLSX, TSV, TXT, PDF) into ASM.
Output both ASM JSON and a flattened CSV for LIMS/import workflows, plus an exportable parser script for data engineers.
Preserve provenance and validation metadata, with optional customization via references/scripts.

Quick Start

Run the skill on a instrument data file to generate ASM JSON and an optional flattened CSV.

Frequently Asked Questions about instrument-data-to-allotrope

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I convert instrument data to Allotrope Simple Model JSON?▼

You can convert instrument data to Allotrope Simple Model (ASM) JSON by running this skill on raw instrument outputs. It auto-detects the instrument type and parses common formats like CSV, XLSX, and PDF into standardized ASM JSON.

Can I parse SoftMax Pro or Gen5 files into a flattened CSV for LIMS?▼

Yes, the skill outputs both ASM JSON and a flattened CSV specifically designed for LIMS and import workflows. It supports formats from SoftMax Pro, Gen5, NanoDrop, Beckman Vi-CELL, and QuantStudio.

Does the ASM conversion support provenance and validation metadata for auditability?▼

Yes, the skill preserves provenance and validation metadata during the conversion process to ensure auditability. It requires the allotropy library and pandas to parse files and maintain this metadata.

What do I need to parse instrument outputs into ASM if the file format is unrecognized?▼

If the instrument output format is unrecognized, the skill uses a robust fallback parser to attempt conversion to ASM. You need the allotropy library and pandas installed to enable this parsing functionality.

What is the best way to convert NanoDrop or QuantStudio datasets into ASM format?▼

The best way to convert NanoDrop or QuantStudio datasets into ASM format is using this skill, which auto-detects the instrument type and applies the appropriate parser. It generates ASM JSON and flattened CSV outputs automatically.