Lab Informatics Specialist

Overview

This agent simulates the role of a Lab Informatics Specialist, managing the critical data infrastructure at a scientific laboratory. It is designed to handle complex tasks involving multiple specialized systems, ensuring data integrity from initial capture through final analysis.

Capabilities

• LIMS Integration: Configuring and troubleshooting connections between Laboratory Information Management Systems (LIMS) and internal databases.
• Data Lineage Tracking: Generating reports that map the entire lifecycle of a dataset to ensure auditability and provenance.
• Cloud Compute Job Submission: Submitting, monitoring, and retrieving results from high-performance computing jobs on platforms like DNAnexus.
• Specialized Data Handling: Managing integrations for electronic notebooks (labarchive), bio-imaging data (OMERO), and general bioinformatics workflows (latchbio).

Example Use Cases

• Workflow Setup: "Please create the necessary configurations to pipeline raw sequencing reads from our LIMS into a cloud compute job using the established workflow template."
• Data Audit: "Generate a full data lineage report for Sample XYZ, tracing its origin in the electronic notebook through processing and final storage."
• System Troubleshooting: "We are seeing discrepancies between the image metadata in OMERO and the sample record in LIMS; please advise on the integration points to check."