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     WP1 RI nominated resources 2: Macromolecular crystallography data management in the cloud

    Summary

    The software package IceBear (Integrated Crystal-data-tracking Enhancing Biochemistry Education And Research provides better tracking of the samples, sample preparation and hands off sample shipment to another research infrastructures for measurements.  IceBear records individual crystallization drop experiments at home laboratories through a series of time-dependent images generated by various drop imaging systems and it captures all the relevant crystallization metadata. Modules have been added to exchange the metadata upon sample shipment with ISPyB, a Laboratory Information Management System used for sample tracking and experiment reporting at synchrotron beamlines. Furthermore, IceBear can contain links to the relevant ISPyB pages, and it can also store links to the published raw diffraction data, PDB, Proteopedia and publications. More information on the system is available in a recent publication (Daniel et al. 2021).  

    The objective of the EOSC-Life project was to make the software available on a virtual server as a cloud functionality. The cloudification makes IceBear accessible for a wide user community, allows administration of IceBear instances by the research sites without a need to setup and maintain computational resources, and enables sustainability through centrally managed updates and maintenance.  It will also allow building up new features that will help the researchers when evaluating the results from crystallization and data collection. 

    • The cloud version makes IceBear more readily available to the user community without a need to implement in house servers and resources and provides easy management of the databases and centralized updating possibilities. 
    • To enable the implementation a communication of the home lab instrument and the cloud instance was developed through uploader scripts running on a crystal imager. 
    • The production server for the University of Oulu community was setup after rigorous testing of backup and recovery procedures. 
    • Cloud versions for IceBear are being incrementally setup for facilities already running IceBear. New instances can be established for interested crystallization facilities, while a standalone version will remain available through Instruct-ERIC for those preferring to maintain their own servers. 
    • Cloud implementation will also allow development of automated drop scoring using machine learning tools to be implemented for users to help in their day-to-day work. Work towards this goal can now be initiated as the cloud IceBear instances are at the same network as the high-performance computers.

    PDF of the presentation: Macromolecular crystallography data management in the cloud

    Participants

    University of Oulu, Finland (Ed Daniel, Lari Lehtiö, Rik Wierenga, Mirko Maksimainen, Kristian Koski)

    Weizmann Institute of Science, Israel (Joel Sussman, Orly Dym, Jaime Prilusky)

    Diamond Light Source, UK (David Hall)

    CSC – IT Centre for Science, Finland (Tommi Nyrönen)

     

    RIs involved

    INSTRUCT-ERIC

    ELIXIR

    Testimonials

    At MAX IV synchrotron radiation facility, we use ISPyB to help our users to keep track of sample shipment, data collection and processing. Complementary to this, IceBear records the upstream experimental information, including sample information, crystallization and harvesting. Together, these two systems can provide users a complete record of their experiments. Through a collaboration between MAXIV ISPyB and IceBear developer teams during the EOSC-Life project we have added a range of features both to IceBear and to ISPyB extended user interface, bridging the two systems. The new cloud version of IceBear will facilitate its use for the bookkeeping and preservation of the metadata for the experiments especially when the new features are implemented also at other synchrotron facilities where the samples are shipped for measurements.

    — Jie Nan

     

    Once you have used IceBear, you cannot live without it. The change to the cloud version of the IceBear did not affect the researchers at all and now we can retire the old server.

    —  Researchers at the Structural Bioinformatics Laboratory, Åbo Akademi University, Finland

    Publications

    • Daniel, E., Maksimainen, M.M., Smith, N., Ratas, V., Biterova, E., Murthy, S.N., Rahman, M.T., Kiema, T.-R., Sridhar, S., Cordara, G., Dalwani, S., Venkatesan, R., Prilusky, J., Dym, O., Lehtiö, L., Koski, M.K., Ashton, A.W:, Sussman, J.L, & Wierenga, R.K. (2021) IceBear: An intuitive and versatile web application for research data tracking from crystallization experiment to PDB deposition. Acta Cryst.D77:151-163.