University of Oulu

Daniel, E., Maksimainen, M., Smith, N., Ratas, V., Biterova, E., Murthy, S., Rahman, M., Kiema, T., Sridhar, S., Cordara, G., Dalwani, S., Venkatesan, R., Prilusky, J., Dym, O., Lehtiö, L., Koski, M., Ashton, A., Sussman, J., Wierenga, R. (2021) IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition. Acta Crystallographica Section D : structural biology, 77 (2), 151-163. http://doi.org/10.1107/S2059798320015223

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

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Author: Daniel, Ed1,2; Maksimainen, M. M.1,2; Smith, N.3;
Organizations: 1Biocenter Oulu, University of Oulu, Oulu, Finland
2Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
3Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
4Bioinformatics and Biological Computing Unit, Life Science Core Facility, Weizmann Institute of Science, Rehovot 7610001, Israel
5Israel Structural Proteomics Center, Life Science Core Facility, Weizmann Institute of Science, Rehovot 7610001, Israel
6Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.9 MB)
Persistent link: http://urn.fi/urn:nbn:fi-fe2021041310259
Language: English
Published: International Union of Crystallography, 2021
Publish Date: 2021-04-13
Description:

Abstract

The web-based IceBear software is a versatile tool to monitor the results of crystallization experiments and is designed to facilitate supervisor and student communications. It also records and tracks all relevant information from crystallization setup to PDB deposition in protein crystallography projects. Fully automated data collection is now possible at several synchrotrons, which means that the number of samples tested at the synchrotron is currently increasing rapidly. Therefore, the protein crystallography research communities at the University of Oulu, Weizmann Institute of Science and Diamond Light Source have joined forces to automate the uploading of sample metadata to the synchrotron. In IceBear, each crystal selected for data collection is given a unique sample name and a crystal page is generated. Subsequently, the metadata required for data collection are uploaded directly to the ISPyB synchrotron database by a shipment module, and for each sample a link to the relevant ISPyB page is stored. IceBear allows notes to be made for each sample during cryocooling treatment and during data collection, as well as in later steps of the structure determination. Protocols are also available to aid the recycling of pins, pucks and dewars when the dewar returns from the synchrotron. The IceBear database is organized around projects, and project members can easily access the crystallization and diffraction metadata for each sample, as well as any additional information that has been provided via the notes. The crystal page for each sample connects the crystallization, diffraction and structural information by providing links to the IceBear drop-viewer page and to the ISPyB data-collection page, as well as to the structure deposited in the Protein Data Bank.

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Series: Acta Crystallographica. Section D, Structural biology
ISSN: 2059-7983
ISSN-E: 2059-7983
ISSN-L: 2059-7983
Volume: 77
Pages: 151 - 163
DOI: 10.1107/S2059798320015223
OADOI: https://oadoi.org/10.1107/S2059798320015223
Type of Publication: A1 Journal article – refereed
Field of Science: 1182 Biochemistry, cell and molecular biology
Subjects:
Funding: This work was supported by Instruct-ULTRA, an EU H2020 project to further develop the services of Instruct-ERIC (Grant Agreement No. 731005 to RKW, JLS and AWA). This work was also funded by Diamond Light Source (RKW), by the Academy of Finland (grants No. 328117, 287063, 294085, 297875, 141487, 293369, 289024 and 319194 to LL, RKW and RV), by Biocenter Finland (RKW), by the Sigrid Juselius Foundation (MTR) and by Biocenter Oulu.
EU Grant Number: (731005) INSTRUCT-ULTRA - Releasing the full potential of Instruct to expand and consolidate infrastructure services for integrated structural life science research
Academy of Finland Grant Number: 328117
287063
294085
297875
141487
293369
289024
319194
Detailed Information: 328117 (Academy of Finland Funding decision)
287063 (Academy of Finland Funding decision)
294085 (Academy of Finland Funding decision)
297875 (Academy of Finland Funding decision)
141487 (Academy of Finland Funding decision)
293369 (Academy of Finland Funding decision)
289024 (Academy of Finland Funding decision)
319194 (Academy of Finland Funding decision)
Copyright information: © 2021 The Authors. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
  https://creativecommons.org/licenses/by/4.0/