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

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 pr...

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Autores principales: Daniel, Ed, Maksimainen, Mirko M., Smith, Neil, Ratas, Ville, Biterova, Ekaterina, Murthy, Sudarshan N., Rahman, M. Tanvir, Kiema, Tiila-Riikka, Sridhar, Shruthi, Cordara, Gabriele, Dalwani, Subhadra, Venkatesan, Rajaram, Prilusky, Jaime, Dym, Orly, Lehtiö, Lari, Koski, M. Kristian, Ashton, Alun W., Sussman, Joel L., Wierenga, Rik K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7869904/
https://www.ncbi.nlm.nih.gov/pubmed/33559605
http://dx.doi.org/10.1107/S2059798320015223
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author Daniel, Ed
Maksimainen, Mirko M.
Smith, Neil
Ratas, Ville
Biterova, Ekaterina
Murthy, Sudarshan N.
Rahman, M. Tanvir
Kiema, Tiila-Riikka
Sridhar, Shruthi
Cordara, Gabriele
Dalwani, Subhadra
Venkatesan, Rajaram
Prilusky, Jaime
Dym, Orly
Lehtiö, Lari
Koski, M. Kristian
Ashton, Alun W.
Sussman, Joel L.
Wierenga, Rik K.
author_facet Daniel, Ed
Maksimainen, Mirko M.
Smith, Neil
Ratas, Ville
Biterova, Ekaterina
Murthy, Sudarshan N.
Rahman, M. Tanvir
Kiema, Tiila-Riikka
Sridhar, Shruthi
Cordara, Gabriele
Dalwani, Subhadra
Venkatesan, Rajaram
Prilusky, Jaime
Dym, Orly
Lehtiö, Lari
Koski, M. Kristian
Ashton, Alun W.
Sussman, Joel L.
Wierenga, Rik K.
author_sort Daniel, Ed
collection PubMed
description 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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spelling pubmed-78699042021-02-19 IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition Daniel, Ed Maksimainen, Mirko M. Smith, Neil Ratas, Ville Biterova, Ekaterina Murthy, Sudarshan N. Rahman, M. Tanvir Kiema, Tiila-Riikka Sridhar, Shruthi Cordara, Gabriele Dalwani, Subhadra Venkatesan, Rajaram Prilusky, Jaime Dym, Orly Lehtiö, Lari Koski, M. Kristian Ashton, Alun W. Sussman, Joel L. Wierenga, Rik K. Acta Crystallogr D Struct Biol Research Papers 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. International Union of Crystallography 2021-01-26 /pmc/articles/PMC7869904/ /pubmed/33559605 http://dx.doi.org/10.1107/S2059798320015223 Text en © Daniel et al. 2021 http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/4.0/
spellingShingle Research Papers
Daniel, Ed
Maksimainen, Mirko M.
Smith, Neil
Ratas, Ville
Biterova, Ekaterina
Murthy, Sudarshan N.
Rahman, M. Tanvir
Kiema, Tiila-Riikka
Sridhar, Shruthi
Cordara, Gabriele
Dalwani, Subhadra
Venkatesan, Rajaram
Prilusky, Jaime
Dym, Orly
Lehtiö, Lari
Koski, M. Kristian
Ashton, Alun W.
Sussman, Joel L.
Wierenga, Rik K.
IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition
title IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition
title_full IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition
title_fullStr IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition
title_full_unstemmed IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition
title_short IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition
title_sort icebear: an intuitive and versatile web application for research-data tracking from crystallization experiment to pdb deposition
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7869904/
https://www.ncbi.nlm.nih.gov/pubmed/33559605
http://dx.doi.org/10.1107/S2059798320015223
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