Localized reading guide
instrument-data-to-allotropePurpose, usage and source
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.
Source retrieved:
- Source repository
- anthropics/knowledge-work-plugins
- SKILL.md
bio-research/skills/instrument-data-to-allotrope/SKILL.md- Repository stars
- 34,049
- Repository updated
- 2026-10-30
- Categories
- Development
- Last collected
License: License file needs review
Workflow excerpts are reading aids, not executable instructions from Codez. No third-party Skill was run to produce this page.
The purpose and workflow passages below are upstream material, organized and translated for reading. They are distinct from the separately labeled Codez editorial analysis.
What this Skill does
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.
How the upstream workflow works
Workflow Overview
Detect instrument type from file contents (auto-detect or user-specified) Parse file using allotropy library (native) or flexible fallback parser ASM JSON (full semantic structure) Flattened CSV (2D tabular format)
Upstream passage · L21 ↗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.
Upstream passage · L6 ↗Output Format Selection
ASM JSON (default) - Full semantic structure with ontology URIs Best for: LIMS systems expecting ASM, data lakes, long-term archival
Upstream passage · L47 ↗# 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)Requirements and setup
No short requirements passage was selected from this file. This does not mean the Skill has no dependencies. Check the repository setup instructions and referenced files.
Limits and quality checks
No separate limits passage was selected from this file. This does not mean the Skill is safe for every input or environment. Review the complete source and validate your own result.
Start with a safe trial
- Check the supported host and the repository installation instructions. Keep the Skill directory and its referenced scripts, assets and documentation together; SKILL.md alone may omit dependencies.
- Give the agent your real input, desired output and acceptance criteria. Invocation syntax and available tools depend on the host; this site does not assume a universal install command.
- Try the source workflow in a disposable project or on a copy. Review operations that change files, remote services or billable resources before allowing them.
- Validate the output against the source quality checks and your own requirements. A successful trigger or a high repository Star count does not establish a correct result.
Read further in the source
- Instrument Data to Allotrope Converter
- Workflow Overview
- Output Format Selection
- Calculated Data Handling
- Validation
- Supported Instruments
- Tier 1: Native allotropy parsing (PREFERRED)
- Tier 2: Flexible fallback parsing
- Tier 3: PDF extraction
- Pre-Parsing Checklist
- Code Export for Data Engineers
- Handling parse failures
- ASM Schema Validation
Related Skills
Translation and scope
This reading guide selects passages from the pinned upstream SKILL.md. Translation is assisted. It is not a complete manual or a claim of tested compatibility. Read the original and its referenced files before use.
This introduction refers to the pinned version below; current repository activity and collection time are shown separately.
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- Source retrieved
- Source commit
2574e29377c7173d0cecffef29a6ecbd7f8ccb5d- Source SHA-256
6167bf1731e568b63110a8f27e987cfe386f44e64cd2d78d9080d5d7628a79c5