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Web-based volume slicer for 3D electron-microscopy data from EMDB

José Salavert-Torres, Andrii Iudin, Ingvar Lagerstedt, Eduardo Sanz-García, Gerard J. Kleywegt, Ardan Patwardhan
2016 Journal of Structural Biology  
We describe the functionality and design of the Volume slicer -a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to
more » ... elop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale.
doi:10.1016/j.jsb.2016.02.012 pmid:26876163 pmcid:PMC4819904 fatcat:e3qbyk3gengxvlkafxleq3kiwi

Data-deposition protocols for correlative soft X-ray tomography and super-resolution structured illumination microscopy applications

Andrii Iudin, Ugis Sarkans, Mohamed A. Koronfel, Tom Fish, Ian Dobbie, Maria Harkiolaki, Ardan Patwardhan, Gerard J. Kleywegt
2021 STAR Protocols  
EMBL-EBI builds and maintains EMPIAR (Iudin et al., 2016) for storing 2D and 3D electron and X-ray microscopy/tomography data, and BioStudies for storing bio-imaging data from all other modalities including  ... 
doi:10.1016/j.xpro.2020.100253 pmid:33490973 pmcid:PMC7811169 fatcat:s24bsszilnao3bda5rgidddxnq

Building bridges between cellular and molecular structural biology

Ardan Patwardhan, Robert Brandt, Sarah J Butcher, Lucy Collinson, David Gault, Kay Grünewald, Corey Hecksel, Juha T Huiskonen, Andrii Iudin, Martin L Jones, Paul K Korir, Abraham J Koster (+15 others)
2017 eLife  
., 2002) , the Electron Microscopy Public Image Archive (EMPIAR; empiar.org; Iudin et al., 2016) , and the Protein Data Bank (PDB; wwpdb. org; Bernstein et al., 1977) Integration between PDB and EMDB  ... 
doi:10.7554/elife.25835 pmid:28682240 pmcid:PMC5524535 fatcat:aknpnuuiyfcx3h4xau6ffhiu6u

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

Sameer Velankar, Glen van Ginkel, Younes Alhroub, Gary M. Battle, John M. Berrisford, Matthew J. Conroy, Jose M. Dana, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Pieter M. S. Hendrickx, Ingvar Lagerstedt (+21 others)
2015 Nucleic Acids Research  
The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite
more » ... or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and upto-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and sup-port expert users in analysing macromolecular structure data.
doi:10.1093/nar/gkv1047 pmid:26476444 pmcid:PMC4702783 fatcat:sqjtb2p3drbjncdycqrfr3m2lm

REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology

Ugis Sarkans, Wah Chiu, Lucy Collinson, Michele C Darrow, Jan Ellenberg, David Grunwald, Jean-Karim Hériché, Andrii Iudin, Gabriel G Martins, Terry Meehan, Kedar Narayan, Ardan Patwardhan (+34 others)
2021 Nature Methods  
Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.
doi:10.1038/s41592-021-01166-8 pmid:34021280 pmcid:PMC8606015 fatcat:cfzzyhd34jdhfa6r3xroeoxgo4

Measurement of isolated photons with and without accompanying jets at HERA

Andriy Iudin
2013 Proceedings of XXI International Workshop on Deep-Inelastic Scattering and Related Subjects — PoS(DIS 2013)   unpublished
doi:10.22323/1.191.0148 fatcat:byy7shzq6jgqdi5ekfnpns4zoy

Isolated photon production at HERA

Andriy Iudin
2014 Proceedings of International Conference on the Structure and the Interactions of the Photon including the 20th International Workshop on Photon-Photon Collisions and the International Workshop on High Energy Photon Linear Colliders — PoS(Photon 2013)   unpublished
doi:10.22323/1.192.0008 fatcat:iy3klhoyvzgpzpgvgdvopufhzm

Analysis of Isolated Photons in Photoproduction in PYTHIA

2019 East European Journal of Physics  
This EEJP. 3 (2019) Andrii Iudin, Sergey Voronov allows general code guidance. The second part of the user code is called in three stages.  ...  Experiment ZEUS published results of first observations of isolated photons with accompanying jets at high transverse momenta EEJP. 3 (2019) Andrii Iudin, Sergey Voronov conducted at luminosity of 6.4  ...  20 EEJP. 3 (2019) Andrii Iudin, Sergey Voronov АНАЛІЗ ІЗОЛЬОВАНИХ ФОТОНІВ У ФОТОНАРОДЖЕННІ В PYTHIA А.С. Юдін 1 , С.О.  ... 
doi:10.26565/2312-4334-2019-3-02 fatcat:wa4in5acdbgstmr3vejbzhqfsm

A collection of yeast cellular electron cryotomography data

Lu Gan, Cai Tong Ng, Chen Chen, Shujun Cai
2019 GigaScience  
Acknowledgments We thank Gemma An and Chithran VM for help with some reconstructions; Uttam Surana and Mohan Balasubramanian for the yeast strains; Ardan Patwardhan and Andrii Iudin for feedback on data  ... 
doi:10.1093/gigascience/giz077 pmid:31247098 pmcid:PMC6596884 fatcat:xyynqlthyfaqzoe7soavyxhuae

A collection of yeast cellular electron cryotomography data [article]

Lu Gan, Cai Tong Ng, Chen Chen, Shujun Cai
2019 bioRxiv   pre-print
Iudin for feedback on data organization; Christoph Baranec for discussion on 331 astronomy data-sharing practices; Paul Matsudaira, Jian Shi, Ann Tran, and Ping Lee 332 Chong for setting up and operating  ...  resources may use this data to develop annotation Gemma An and Chithran VM for help with some reconstructions; Uttam 329 Surana and Mohan Balasubramanian for the yeast strains; Ardan Patwardhan and 330 Andrii  ... 
doi:10.1101/594432 fatcat:3o5qgft7tnhyxe5hnf2effdwie

Physical Culture and the Embodied Soviet Subject, 1921-1939: Surveillance, Aesthetics, Spectatorship

Samuel Alec Goff, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Emma Widdis
2018
Andrii the physical specimen (Schastlivyi finish) In character, Andrii is the inverse of Marko: physically strong, egotistical, individualistic.  ...  It is Lukich who instructs Marko that he must discard his cane and perform against Andrii.  ... 
doi:10.17863/cam.20371 fatcat:yxjhzf76jba5vbe2tfha63msey

Penance and Punishment: Monastic Incarceration in Imperial Russia

A. Joy Demoskoff
2016
John-Paul Himka and Andriy Zayarnyuk (Toronto: University of Toronto Press, 2006), 226; Roy R. Robson, Old Believers in Modern Russia (DeKalb: Northern Illinois University Press, 1995) ; Robert H.  ...  Iudin wrote that "As late as 1719 monasteries still sought special permission to employ prison-like techniques for subduing the dangerously mad." 663 Clearly, the insane did not "suddenly" become subjects  ... 
doi:10.7939/r3x921p9t fatcat:66qmg3aemjeyva652idkfebecm