IceBear

IceBear manages research data for protein crystallography by tracking crystallization experiments and associated metadata from crystallization and cryocooling through diffraction data collection and PDB deposition.

Key Features:

• Automated Data Collection and Tracking: Automates collection and recording of metadata across stages from crystallization setup to PDB deposition.
• Enhanced Communication: Records and centralizes experiment status and notes to support communication between project members.
• Integration with Synchrotron Facilities: Supports automated data collection at synchrotrons and integrates with the ISPyB synchrotron database via a shipment module for direct upload of sample metadata.
• Unique Sample Identification: Assigns a unique sample name to each selected crystal and generates a dedicated crystal page consolidating related information.
• Comprehensive Metadata Management: Records notes at stages including cryocooling treatment, data collection, and subsequent steps in structure determination to maintain experimental provenance.
• Resource Recycling Protocols: Includes protocols for tracking recycling of pins, pucks, and dewars returned from synchrotron facilities.
• Project-Centric Organization: Organizes data around projects to provide access to crystallization and diffraction metadata for project members.
• Interconnected Data Links: Links each crystal page to crystallization drop views, ISPyB data-collection pages, and PDB-deposited structures.

Scientific Applications:

• Protein Crystallography Project Management: Centralizes experimental and metadata tracking across crystallization, diffraction, and structure-determination workflows.
• Synchrotron Sample and Data Coordination: Coordinates sample metadata and automated data collection workflows between laboratories and synchrotron facilities via ISPyB integration.
• Structure Determination Recordkeeping: Maintains detailed records of cryocooling, data-collection conditions, and downstream structure-determination notes for reproducibility and provenance.
• PDB Deposition Support: Tracks metadata and links required for deposition of structures to the Protein Data Bank (PDB).

Methodology:

Integrates automated data collection at synchrotrons with the ISPyB database via a shipment module, assigns unique sample names and generates crystal pages that link crystallization, diffraction, and PDB data, and records experimental metadata including cryocooling and data-collection notes; includes protocols for tracking recycling of pins, pucks, and dewars.