IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB...

Area of Science:

• Structural Biology
• Biochemistry
• Crystallography

Background:

• Automated data collection at synchrotrons is increasing sample throughput.
• Efficient management of crystallization and diffraction data is crucial for protein structure determination.
• Current workflows require manual tracking of sample metadata, leading to potential inefficiencies.

Purpose of the Study:

• To introduce IceBear, a web-based software for monitoring crystallization experiments and managing associated data.
• To facilitate automated sample metadata uploading to synchrotron databases.
• To improve communication and data accessibility for protein crystallography research groups.

Main Methods:

• Development of the web-based IceBear software.
• Integration of a shipment module for direct metadata upload to ISPyB (Industrial Scientific Imaging and Protein Data Bank Information).
• Implementation of unique sample naming and crystal page generation within IceBear.
• Establishment of protocols for managing experimental resources like pins, pucks, and dewars.

Main Results:

• IceBear successfully records and tracks all information from crystallization setup to PDB deposition.
• Automated uploading of sample metadata to synchrotron databases (ISPyB) is achieved.
• A centralized database organizes project information, providing easy access to crystallization, diffraction, and structural data.
• Links between IceBear, ISPyB, and PDB facilitate comprehensive data traceability.

Conclusions:

• IceBear enhances efficiency and data management in protein crystallography research.
• The software improves communication and collaboration among researchers, supervisors, and institutions.
• Automated data handling streamlines the process from sample preparation to structure deposition.