Can I use this for production data pipelines?

Yes, the skill can export standalone Python parser code using the allotropy library that data engineers can integrate directly into production workflows.

What instrument files does this skill support?

It supports common formats like PDF, CSV, Excel, and TXT from vendors including Agilent, Beckman, Molecular Devices, and Thermo Fisher.

Does it handle calculated data?

Yes, it distinguishes between raw measurements and calculated values, maintaining traceability via data-source-aggregate-document structures.

What is the Allotrope Simple Model (ASM)?

ASM is a standardized JSON-based format used in life sciences to ensure data interoperability and long-term archival across different laboratory instruments.

How does it handle unsupported instrument formats?

If a native parser isn't available, it employs a flexible fallback parser with fuzzy matching and metadata extraction to create a simplified ASM structure.

Allotrope Instrument Data Converter

Name: Allotrope Instrument Data Converter
Author: anthropics

byanthropics

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147

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Data Science & ML

Converts diverse laboratory instrument files into standardized Allotrope Simple Model (ASM) format for LIMS and data analysis.

This skill automates the transformation of raw laboratory instrument outputs—including PDF, CSV, Excel, and TXT files—into the industry-standard Allotrope Simple Model (ASM) JSON format. It supports auto-detection of common instrument types like plate readers, cell counters, and spectrophotometers, ensuring data integrity through built-in ASM validation. By providing both semantic JSON and flattened 2D CSV outputs, it bridges the gap between raw lab data and downstream systems like LIMS, data lakes, or analytical pipelines, even generating production-ready Python code for data engineering handoffs.

Key Features

01Creates flattened 2D CSV files for easy import into Excel or LIMS

02Auto-detects instrument types from common vendors like Beckman, Agilent, and Thermo Fisher

03147 GitHub stars

04Validates outputs against the latest Allotrope schemas to ensure compliance

05Generates full semantic ASM JSON with ontology URIs for long-term archival

06Produces exportable, production-ready Python parser code for data engineers

Use Cases

01Generating standalone Python parsing scripts for automated data engineering pipelines

02Standardizing disparate instrument outputs for ingestion into a centralized LIMS or ELN

03Converting complex hierarchical instrument data into flat CSVs for rapid statistical analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add anthropics/life-sciences instrument-data-to-allotrope

For use in Claude.ai and ChatGPT

Download Skill