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

被引:16
作者
Daniel, Ed [1 ,2 ]
Maksimainen, Mirko M. [1 ,2 ]
Smith, Neil [3 ]
Ratas, Ville [1 ]
Biterova, Ekaterina [2 ]
Murthy, Sudarshan N. [1 ,2 ]
Rahman, M. Tanvir [2 ]
Kiema, Tiila-Riikka [1 ]
Sridhar, Shruthi [1 ,2 ]
Cordara, Gabriele [1 ,2 ]
Dalwani, Subhadra [2 ]
Venkatesan, Rajaram [2 ]
Prilusky, Jaime [4 ]
Dym, Orly [5 ]
Lehtio, Lari [1 ,2 ]
Koski, M. Kristian [1 ]
Ashton, Alun W. [3 ,7 ]
Sussman, Joel L. [6 ]
Wierenga, Rik K. [1 ,2 ]
机构
[1] Univ Oulu, Bioctr Oulu, Oulu, Finland
[2] Univ Oulu, Fac Biochem & Mol Med, Oulu, Finland
[3] Diamond Light Source, Harwell Sci & Innovat Campus, Didcot, Oxon, England
[4] Weizmann Inst Sci, Bioinformat & Biol Comp Unit, Life Sci Core Facil, IL-7610001 Rehovot, Israel
[5] Weizmann Inst Sci, Israel Struct Prote Ctr, Life Sci Core Facil, IL-7610001 Rehovot, Israel
[6] Weizmann Inst Sci, Dept Struct Biol, IL-7610001 Rehovot, Israel
[7] Paul Scherrer Inst, Forsch Str, CH-5232 Villigen, Switzerland
来源
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2021年 / 77卷
基金
芬兰科学院; 欧盟地平线“2020”;
关键词
research-data management; crystallization; X-ray data collection; ISPyB; metadata; IceBear; MANAGEMENT; ISPYB; HELP;
D O I
10.1107/S2059798320015223
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:151 / 163
页数:13
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