Instrument Data To Allotrope
Skill Verified ActiveConvert 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.
Standardize laboratory instrument data into compliant formats for LIMS systems, data lakes, or downstream analysis, improving data integrity and interoperability.
Features
- Convert instrument files to ASM JSON
- Generate flattened CSV output
- Export standalone Python parser code
- Support auto-detection of instrument types
- Handle PDF, CSV, Excel, and TXT input formats
Use Cases
- Standardizing raw lab data for LIMS upload
- Preparing instrument output for data lakes or analysis pipelines
- Generating parser code for data engineers to integrate into production workflows
- Ensuring data compliance with the Allotrope Simple Model standard
Non-Goals
- Replacing the instrument's native data export functionality
- Directly interfacing with LIMS systems (focus is on data format conversion)
- Performing complex scientific analysis on the data
- Handling proprietary data formats not parsable by allotropy or flexible CSV/Excel/TXT readers
Trust
- info:Issues AttentionThere are 29 open issues and 4 closed issues in the last 90 days, indicating active development but a slower closure rate for issues.
Execution
- info:Pinned dependenciesDependencies are listed, but specific version pinning is not explicitly shown in the README or scripts. Installation instructions use pip without lockfiles.
Installation
First, add the marketplace
/plugin marketplace add anthropics/knowledge-work-plugins/plugin install bio-research@knowledge-work-pluginsQuality Score
VerifiedTrust Signals
Similar Extensions
Chdb Sql
98In-process ClickHouse SQL engine for Python — run ClickHouse SQL queries directly on local files, remote databases, and cloud storage without a server. Use when the user wants to write SQL queries against Parquet/CSV/ JSON files, use ClickHouse table functions (mysql(), s3(), postgresql(), iceberg(), deltaLake() etc.), build stateful analytical pipelines with Session, use parametrized queries, window functions, or other advanced ClickHouse SQL features. Also use when the user explicitly mentions chdb.query(), ClickHouse SQL syntax, or wants cross-source SQL joins. Do NOT use for pandas-style DataFrame operations — use chdb-datastore instead.
Spreadsheet Generation API
100Generate CSV, Markdown, and XLSX spreadsheets from structured tabular data.
Geofeed Tuner
100Use this skill whenever the user mentions IP geolocation feeds, RFC 8805, geofeeds, or wants help creating, tuning, validating, or publishing a self-published IP geolocation feed in CSV format. Intended user audience is a network operator, ISP, mobile carrier, cloud provider, hosting company, IXP, or satellite provider asking about IP geolocation accuracy, or geofeed authoring best practices. Helps create, refine, and improve CSV-format IP geolocation feeds with opinionated recommendations beyond RFC 8805 compliance. Do NOT use for private or internal IP address management — applies only to publicly routable IP addresses.
Website Extraction Api
100Extract typed JSON from public website pages using a schema.
Extract Real Estate Listing
100Extract property address, price, room count, and features from a listing document into structured JSON for MLS and property platforms.
Extract Medical Record
100Extract patient details, diagnoses, and medications from a medical record into structured JSON for healthcare workflows.