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bio-instrument-data

Convert PDF, CSV, Excel, and TXT instrument files to ASM JSON or CSV.

114|13|Updated Jan 17, 2026
Search Tags:#bioinformatics#data conversion#LIMS#data standardization#allotrope#instrument data
One-click install
npx skills add https://github.com/frumu-ai/tandem --skill bio-instrument-data
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-instrument-data
Source: https://github.com/frumu-ai/tandem/tree/main/src-tauri/resources/skill-templates/bio-instrument-data
Command: npx skills add https://github.com/frumu-ai/tandem --skill bio-instrument-data

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires python, bash, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill standardizes diverse laboratory instrument output files into a unified, machine-readable format, streamlining data integration and analysis.

Core Features & Use Cases

  • Data Conversion: Converts PDF, CSV, Excel, and TXT instrument files to Allotrope Simple Model (ASM) JSON or flattened 2D CSV.
  • Auto-Detection: Automatically identifies instrument types for accurate parsing.
  • Multiple Outputs: Generates full ASM JSON, flattened CSV, and exportable Python parser code.
  • Use Case: Scientists can use this skill to prepare instrument data for LIMS systems, data lakes, or downstream analysis pipelines, ensuring data consistency and interoperability.

Quick Start

Use the bio-instrument-data skill to convert the file 'my_instrument_data.csv' into ASM JSON format.

Frequently Asked Questions about bio-instrument-data

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

FAQPage Schema
How do I convert laboratory instrument data from PDF or Excel into a standardized format for LIMS?▼

You can convert laboratory instrument data from PDF, Excel, CSV, and TXT files into the Allotrope Simple Model (ASM) JSON format or a flattened 2D CSV for LIMS integration. The tool auto-detects instrument types to accurately parse and standardize the output files.

What is the Allotrope Simple Model (ASM) JSON format used for in bioinformatics data standardization?▼

The Allotrope Simple Model (ASM) JSON format provides a unified, machine-readable structure for standardizing diverse scientific instrument data. It ensures data consistency and interoperability for downstream analytical pipelines and data lakes.

Can I automatically detect instrument types when parsing CSV or TXT output files?▼

Yes, auto-detection of instrument types is supported when parsing CSV, TXT, PDF, or Excel output files. This feature identifies the source instrument automatically to apply the correct parsing logic without manual configuration.

Do I need Python and Bash to generate parser code for scientific instrument data?▼

Yes, Python and Bash are required dependencies for this data conversion process. The tool generates exportable Python parser code that data engineers can use to process instrument files into ASM JSON or flattened CSV outputs.

What is the best way to prepare scientific instrument data for a data lake?▼

The best way to prepare scientific instrument data for a data lake is converting raw PDF, Excel, CSV, and TXT files into standardized ASM JSON or flattened 2D CSV. This ensures data consistency and interoperability across downstream analytical processes.

Are there limitations when converting PDF instrument output files to flattened 2D CSV?▼

Converting PDF instrument output files to flattened 2D CSV depends on the structure of the original document and the accuracy of auto-detection. Complex or non-tabular PDF layouts may limit the effectiveness of the data standardization parser.

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