Integrating 3D biological data on scales from molecules to cells
Lead Research Organisation:
European Bioinformatics Institute
Department Name: Protein Data Bank in Europe
Abstract
At the highest level of detail biology becomes a study of molecular machines. This is a truly complex and fascinating world; for instance, molecular machines generate forces, assemble or disassemble other molecules, function like channels, and store or transport energy.
Well established techniques such as X-ray crystallography, nuclear magnetic resonance spectroscopy (NMR) and electron microscopy (EM) are capable of visualizing the three-dimensional (3D) structures of these machines at the molecular level, but usually do so at the cost of studying them in isolation and in a state frozen in time. As with everyday machines, molecular machines may need to change state, change shape or move parts in order to perform their function. In analogy with an assembly line in a factory, many biological processes involve a multitude of molecular machines and a frozen glimpse of isolated machines is therefore insufficient for understanding the "big picture".
The emergence of new microscopy techniques such electron tomography (ET), soft X-ray tomography (SXT) and 3D scanning electron microscopy (3DSEM) now makes it possible to visualise molecular machinery in the context of cells, and even larger structures in 3D, albeit not yet at the level of detail afforded by the established techniques mentioned above. The challenge now is to integrate imagery at different microscopic scales to gain a broader perspective on the 3D micro-cosmos of biology.
In this project, we will take crucial steps in tackling this challenge by developing added-value services for the EMDB archive - the definitive archive for the 3DEM field managed by the Protein Data Bank in Europe (PDBe, located in Cambridge) and its international partners. We will achieve this by developing:
a) A web-based visualisation tool (volume browser) that provides a user with an easily accessible integrated view of 3D biological data at the cellular and molecular scales derived from the EMDB and PDB (the definitive archive for atomic coordinate models of biological macromolecules) archives, the means to navigate seamlessly between them and to link to other relevant bioinformatics resources;
b) A web-based tool for adding biological annotations to the archived data in EMDB, which is vital to achieve the integration described in (a);
c) A pilot image archive for "raw" experimental data that could be used for developing new EM methodology as well as for checking the validity of 3D structures archived in EMDB.
The web-based volume browser and the new archive will make a variety of 3D structural information vastly more accessible to the wider biomedical science community. The context and perspective gained by linking cellular and molecular structure data will provide unique insights that cannot be gained from the individual structures alone. Moreover, often these data sets contain much more information than what was exploited in the original publication. Therefore, the volume browser will become a vital instrument for knowledge discovery.
Well established techniques such as X-ray crystallography, nuclear magnetic resonance spectroscopy (NMR) and electron microscopy (EM) are capable of visualizing the three-dimensional (3D) structures of these machines at the molecular level, but usually do so at the cost of studying them in isolation and in a state frozen in time. As with everyday machines, molecular machines may need to change state, change shape or move parts in order to perform their function. In analogy with an assembly line in a factory, many biological processes involve a multitude of molecular machines and a frozen glimpse of isolated machines is therefore insufficient for understanding the "big picture".
The emergence of new microscopy techniques such electron tomography (ET), soft X-ray tomography (SXT) and 3D scanning electron microscopy (3DSEM) now makes it possible to visualise molecular machinery in the context of cells, and even larger structures in 3D, albeit not yet at the level of detail afforded by the established techniques mentioned above. The challenge now is to integrate imagery at different microscopic scales to gain a broader perspective on the 3D micro-cosmos of biology.
In this project, we will take crucial steps in tackling this challenge by developing added-value services for the EMDB archive - the definitive archive for the 3DEM field managed by the Protein Data Bank in Europe (PDBe, located in Cambridge) and its international partners. We will achieve this by developing:
a) A web-based visualisation tool (volume browser) that provides a user with an easily accessible integrated view of 3D biological data at the cellular and molecular scales derived from the EMDB and PDB (the definitive archive for atomic coordinate models of biological macromolecules) archives, the means to navigate seamlessly between them and to link to other relevant bioinformatics resources;
b) A web-based tool for adding biological annotations to the archived data in EMDB, which is vital to achieve the integration described in (a);
c) A pilot image archive for "raw" experimental data that could be used for developing new EM methodology as well as for checking the validity of 3D structures archived in EMDB.
The web-based volume browser and the new archive will make a variety of 3D structural information vastly more accessible to the wider biomedical science community. The context and perspective gained by linking cellular and molecular structure data will provide unique insights that cannot be gained from the individual structures alone. Moreover, often these data sets contain much more information than what was exploited in the original publication. Therefore, the volume browser will become a vital instrument for knowledge discovery.
Technical Summary
In this project we will develop two tools and a new archive that will add considerable value to EMDB data and enable its integration with other structural and bioinformatics resources:
a) Volume browser: We will develop a web-accessible tool to provide an integrated view of 3D biological data at the cellular and molecular scales derived from the EMDB and PDB archives, the means to navigate seamlessly between them and to navigate to related bioinformatics resources.
b) Segmentation-annotation tool: PDBe has developed a draft EMDB segmentation-file format (EMDB-SFF) that accommodates a range of segmentation representations used in the field as well as the requisite annotation. We will develop a web-based tool that will allow users to fully exploit the capabilities of this format by uploading segmentations in any common format, overlaying segmentations on the 3D volume, adding biological annotation, and then writing out the segmentations in the EMDB-SFF so that it can be included in an EMDB deposition.
c) Pilot image archive: Raw image data cannot be deposited in EMDB for a number of practical reasons - the size of single-particle datasets can exceed that of the deposited reconstructions by orders of magnitude, and there is no consensus as to what constitutes "raw" data. We will develop a pilot image archive for 2D image data related to EMDB entries, which will allow us to comprehensively address these issues in consultation with the EM community, provide public access to this data, and consider options for the future integration of the archive with other resources.
a) Volume browser: We will develop a web-accessible tool to provide an integrated view of 3D biological data at the cellular and molecular scales derived from the EMDB and PDB archives, the means to navigate seamlessly between them and to navigate to related bioinformatics resources.
b) Segmentation-annotation tool: PDBe has developed a draft EMDB segmentation-file format (EMDB-SFF) that accommodates a range of segmentation representations used in the field as well as the requisite annotation. We will develop a web-based tool that will allow users to fully exploit the capabilities of this format by uploading segmentations in any common format, overlaying segmentations on the 3D volume, adding biological annotation, and then writing out the segmentations in the EMDB-SFF so that it can be included in an EMDB deposition.
c) Pilot image archive: Raw image data cannot be deposited in EMDB for a number of practical reasons - the size of single-particle datasets can exceed that of the deposited reconstructions by orders of magnitude, and there is no consensus as to what constitutes "raw" data. We will develop a pilot image archive for 2D image data related to EMDB entries, which will allow us to comprehensively address these issues in consultation with the EM community, provide public access to this data, and consider options for the future integration of the archive with other resources.
Planned Impact
The pilot image archive will mainly impact the EM community. It will a) lessen the burden of image archiving for individual labs, b) be a valuable source of well-annotated data for methods development and testing, c) be a valuable resource for data that can be used for the validation of 3D reconstructions archived in EMDB, and d) will provide a rich source of well-documented test cases that can be used in teaching and training of researchers entering the EM and ET fields. Resulting improvements in the quality of EMDB data will promote its wider use in biomedical research.
The Segmentation-annotation tool will enable the deposition of biologically annotated segmentations to EMDB, thereby substantially enhancing the potential for integration of EMDB data with data from the PDB and other bioinformatics resources. In addition to benefitting the EM community, this web service may also be used by related imaging fields that use segmentations to interpret 3D volumes, such as the biological soft X-ray tomography and 3D scanning EM communities. Improved integration between EMDB and other bioinformatics resources will also stimulate use of or reference to EMDB data by these and other resources. As many biomedical researchers will be more familiar using these resources, this will substantially increase the exposure of EMDB data to a wider biomedical audience.
The Volume browser tool will be a unique publicly accessible resource providing an integrated view of 3D data from EMDB and PDB -as well as data from relevant bioinformatics resources- spanning scales from cells to atoms. For example, tomographic reconstructions with overlaid segmentations will provide the 3D cellular context for biomacromolecules to molecularly oriented biologists, whereas scientists approaching their problems at the cellular level will be able to find high-resolution structures of molecules associated with segmented regions of tomograms. The presentation of data in an easily accessible manner and the enhanced integration of data will create opportunities for the discovery of new knowledge by the wider biomedical community. For teachers and students of biology and biochemistry, the resource will provide an evidence-based visual exposition of many key biological systems and processes. For the pharmaceutical industry the resource will open new avenues to a visual understanding of how potential drug targets behave in the context of their cellular environment. Reciprocal links from bioinformatics resources to the volume browser will improve its ranking in common search engines such as Google when searching for general biological and medical terms used by the public. It will thus provide a valuable entry point for general users to develop a better visual appreciation for the basis of biology and medicine on the microscale.
The Segmentation-annotation tool will enable the deposition of biologically annotated segmentations to EMDB, thereby substantially enhancing the potential for integration of EMDB data with data from the PDB and other bioinformatics resources. In addition to benefitting the EM community, this web service may also be used by related imaging fields that use segmentations to interpret 3D volumes, such as the biological soft X-ray tomography and 3D scanning EM communities. Improved integration between EMDB and other bioinformatics resources will also stimulate use of or reference to EMDB data by these and other resources. As many biomedical researchers will be more familiar using these resources, this will substantially increase the exposure of EMDB data to a wider biomedical audience.
The Volume browser tool will be a unique publicly accessible resource providing an integrated view of 3D data from EMDB and PDB -as well as data from relevant bioinformatics resources- spanning scales from cells to atoms. For example, tomographic reconstructions with overlaid segmentations will provide the 3D cellular context for biomacromolecules to molecularly oriented biologists, whereas scientists approaching their problems at the cellular level will be able to find high-resolution structures of molecules associated with segmented regions of tomograms. The presentation of data in an easily accessible manner and the enhanced integration of data will create opportunities for the discovery of new knowledge by the wider biomedical community. For teachers and students of biology and biochemistry, the resource will provide an evidence-based visual exposition of many key biological systems and processes. For the pharmaceutical industry the resource will open new avenues to a visual understanding of how potential drug targets behave in the context of their cellular environment. Reciprocal links from bioinformatics resources to the volume browser will improve its ranking in common search engines such as Google when searching for general biological and medical terms used by the public. It will thus provide a valuable entry point for general users to develop a better visual appreciation for the basis of biology and medicine on the microscale.
Publications
Berman H
(2014)
The Protein Data Bank archive as an open data resource
in Journal of Computer-Aided Molecular Design
Berman HM
(2016)
The archiving and dissemination of biological structure data.
in Current opinion in structural biology
Bárcena M
(2021)
Structural biology in the fight against COVID-19.
in Nature structural & molecular biology
Collinson LM
(2023)
Volume EM: a quiet revolution takes shape.
in Nature methods
Hartley M
(2022)
The BioImage Archive - Building a Home for Life-Sciences Microscopy Data.
in Journal of molecular biology
Hartley M
(2023)
Providing open imaging data at scale: An EMBL-EBI perspective.
in Histochemistry and cell biology
Iudin A
(2023)
EMPIAR: the Electron Microscopy Public Image Archive.
in Nucleic acids research
Iudin A
(2023)
Methods in Cell Biology
Iudin A
(2023)
Volume Electron Microscopy
Iudin A
(2016)
EMPIAR: a public archive for raw electron microscopy image data.
in Nature methods
Kleywegt G
(2021)
Image archiving at EMBL-EBI - EMPIAR and the BioImage Archive
in Microscopy and Microanalysis
Kleywegt GJ
(2018)
Structural biology data archiving - where we are and what lies ahead.
in FEBS letters
Korir P
(2024)
Ten recommendations for organising bioimaging data for archival
in F1000Research
Lawson CL
(2016)
EMDataBank unified data resource for 3DEM.
in Nucleic acids research
Marabini R
(2016)
The Electron Microscopy eXchange (EMX) initiative.
in Journal of structural biology
Patwardhan A
(2017)
Trends in the Electron Microscopy Data Bank (EMDB).
in Acta crystallographica. Section D, Structural biology
Patwardhan A
(2016)
Databases and Archiving for CryoEM.
in Methods in enzymology
Patwardhan A
(2014)
A 3D cellular context for the macromolecular world.
in Nature structural & molecular biology
Patwardhan A
(2017)
Building bridges between cellular and molecular structural biology.
in eLife
Salavert-Torres J
(2016)
Web-based volume slicer for 3D electron-microscopy data from EMDB.
in Journal of structural biology
Sarkans U
(2021)
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.
in Nature methods
Thakur M
(2023)
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.
in Nucleic acids research
Velankar S
(2016)
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.
in Nucleic acids research
Walter A
(2021)
Correlative multimodal imaging: Building a community.
in Methods in cell biology
Description | Research Grant |
Amount | £931,495 (GBP) |
Funding ID | MR/P019544/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2017 |
End | 09/2020 |
Title | EMPIAR - Electron Microscopy Public Image Archive |
Description | Raw image data related to EMDB structures and also to volume EM and X-ray imaging studies |
Type Of Material | Database/Collection of data |
Year Produced | 2014 |
Provided To Others? | Yes |
Impact | EMPIAR is being used regularly for validation, methods development, teaching and training. In early 2024, there were almost 900 papers mentioning EMPIAR (https://europepmc.org/betaSearch?query=empiar&page=1). A full paper describing the resource was published in 2023 (https://academic.oup.com/nar/article/51/D1/D1503/6849493). |
URL | http://empiar.org/ |
Title | SPW - Sample-Preparation Widget |
Description | SPW is an easy-to-use and re-usable web component that allows for the detailed and structured description of sample preparation (SP) protocols used for volume EM (vEM) experiments. SPW was designed in collaboration with Kedar Narayan, Michele Darrow and Carles Bosch Pinol of the Sample Preparation Working Group which is part of the vEM Community Initiative. It allows for easy to use point-and-click functionality, using controlled vocabularies where possible and allowing free-text information only if absolutely required. The tool was primarily designed to produce protocols that can accompany vEM datasets deposited to EMPIAR, but it can also be used to upload, view, edit, copy, and download entries for use at the bench. From 2024, further development of SPW will take place at the RFI in Michele Darrow's team, funded by a CZI grant to the vEM Community Initiative. |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | SPW was developed in close collaboration with vEM experts so that it would address the community's needs. We are currently still testing with real users and will also make it possible to publish submitted protocols on the EMPIAR website. |
URL | https://empiar.org/spw |
Title | EMDB-SFF Toolkit (sfftk) |
Description | Translators to/from EMDB segmentation file format (EMDB-SFF) |
Type Of Technology | Software |
Year Produced | 2016 |
Open Source License? | Yes |
Impact | Users can convert proprietary segmentation file formats then annotate them against public archives and ontologies. Users can also integrate the toolkit into their applications and pipelines directly to generate EMDB-SFF files. Downloads from https://github.com/emdb-empiar/sfftk-rw and https://github.com/emdb-empiar/sfftk |
URL | https://emdb-empiar.github.io/EMDB-SFF/ |
Title | EMPIAR deposition system |
Description | Web based deposition system to deposit data and meta data to EMPIAR |
Type Of Technology | Webtool/Application |
Year Produced | 2015 |
Impact | This tool makes it easier to deposit data to EMPIAR |
URL | https://empiar.org/deposition |
Title | EMPIAR website |
Description | Website providing access for downloading and viewing EMPIAR data |
Type Of Technology | Webtool/Application |
Year Produced | 2015 |
Impact | The amount of data downloaded from EMPIAR has grown to over 150TB on average per month and over 100TB of data gets submitted per month |
URL | https://empiar.org/ |
Title | Volume Browser |
Description | A web-based slice viewer for EMDB and EMPIAR 3DEM and volume EM entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and rapidly switch between them and navigate through the volume. Supersedes the Volume Slicer. The software is used on our public website, e.g. https://www.ebi.ac.uk/emdb/EMD-1234?tab=volume |
Type Of Technology | Webtool/Application |
Year Produced | 2018 |
Impact | The general public has direct access to slice views of EMDB reconstructions and EMPIAR 3DEM volumes. |
URL | https://www.ebi.ac.uk/empiar/volume-browser/ |
Title | Volume slicer |
Description | 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. |
Type Of Technology | Webtool/Application |
Year Produced | 2015 |
Impact | The general public has direct access to slice views of EMDB reconstructions. |
URL | http://www.ebi.ac.uk/pdbe/emdb/3dslice/EMD-2363 |
Title | bandbox |
Description | bandbox is a CLI tool to quickly evaluate how organised your dataset is. You can use
bandbox on any directory and it will recursively descend through to all subdirectories to assess whether the structure and names are easy to use.
bandbox reads in a set of configs a config file (
bandbox.cfg ), which it uses to assess your dataset. Once complete,
bandbox displays various assessments and whether they are
ok or
nok , together with details about which paths from the specified directory have failed that assessment. The user may also display the directory tree using the
--show-tree option as well as summarise the output using the
--summarise option which may be modified using the
--summarise-size option. |
Type Of Technology | Software |
Year Produced | 2022 |
Impact | None recorded yet. |
URL | https://zenodo.org/record/7807540 |
Description | "Bioimage data archiving at EMBL-EBI", invited talk, "Exascale challenges for ML in multiscale life sciences" workshop, virtual, January 2021 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Bioimage data archiving at EMBL-EBI", invited talk, "Exascale challenges for ML in multiscale life sciences" workshop, virtual, January 2021 |
Year(s) Of Engagement Activity | 2021 |
Description | "EM Validation by wwPDB & EMDB", presentation at the EMBO Course "Cryo-Electron Microscopy and 3D Image Processing", EMBL Heidelberg, virtual, September 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | "EM Validation by wwPDB & EMDB", presentation at the EMBO Course "Cryo-Electron Microscopy and 3D Image Processing", EMBL Heidelberg, virtual, September 2020 |
Year(s) Of Engagement Activity | 2020 |
Description | "EM data archiving", lecture Gerard Kleywegt and lectures and practical Osman Salih in the EM EMBO Course, Birkbeck, London, UK, September 2019 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Contributed to this course for young EM practitioners. |
Year(s) Of Engagement Activity | 2019 |
Description | "EMDB and EMPIAR" by Ardan Patwardhan at EMBO Practical Course: Cryo-Electron Microscopy and 3D Image Processing (virtual), April 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | Course presentation on EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2020 |
Description | "EMDB and EMPIAR"; S2C2 CryoEM CCP-EM Modeling Workshop presentation, November 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Workshop presentation on EMDB and EMPIAR which generated interest and questions from the audience as well as potential collaborations. |
Year(s) Of Engagement Activity | 2020 |
Description | "EMPIAR: recent developments and outlook", presentation Andrii Iudin at the 2nd CryoNet Annual Symposium, Stockholm, Sweden, October 2019 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presented recent developments and plans for EMPIAR, Volume Browser, Segmentation Annotation Tool, BioImage Archive Glue project |
Year(s) Of Engagement Activity | 2019 |
Description | "Image Archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk, Global Bioimaging workshop ""Image Data: data management, cloud-based sharing, and image data repositories", virtual, January 2021 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Image Archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk, Global Bioimaging workshop ""Image Data: data management, cloud-based sharing, and image data repositories", virtual, January 2021 |
Year(s) Of Engagement Activity | 2021 |
Description | "Introduction to structural biology data", lecture Gerard Kleywegt, "Computational Structural Biology" course, EMBL-EBI, Cambridge, UK, September 2019 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Taught in this course for young scientists with an interest in using structural biology data. |
Year(s) Of Engagement Activity | 2019 |
Description | "Introduction to structural biology data", lecture, "Structural Bioinformatics" course, EMBL-EBI, virtual, November 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | "Introduction to structural biology data", lecture, "Structural Bioinformatics" course, EMBL-EBI, virtual, November 2020 |
Year(s) Of Engagement Activity | 2020 |
Description | "Open EM Data (BIG and small)", invited talk Gerard Kleywegt at the EM-UK Meeting, Plymouth (UK), January 2020. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | "Open EM Data (BIG and small)", invited talk Gerard Kleywegt at the EM-UK Meeting, Plymouth (UK), January 2020. |
Year(s) Of Engagement Activity | 2020 |
Description | "What's new at EMDB and EMPIAR?", lecture Gerard Kleywegt at the CCP-EM Spring Symposium, Nottingham, UK, April 2019 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Gave an overview of new developments and plans concerning cryo-EM data archiving in PDB, EMDB and EMPIAR. |
Year(s) Of Engagement Activity | 2019 |
Description | "What's new in EMDB and EMPIAR" by Ardan Patwardhan at the CCP-EM Spring Symposium (virtual), April 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation of new developments in EMDB and EMPIAR including uses cases of validation resources applied to SARS-CoV-2 |
Year(s) Of Engagement Activity | 2020 |
Description | 1st Cryo Electron Microscopy and 3D Image Processing of Macromolecular Assemblies and Cellular Tomography (CEM3DIP), Thiruvananthapuram, India |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Talk on EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2016 |
URL | http://workshop.iisertvm.ac.in/cem3dip/index.php/welcome |
Description | 2018 International Conference of the Korean Society for Structural Biology |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation on EMDB and EMPIAR and discussions on collaborations with the South Korean community |
Year(s) Of Engagement Activity | 2018 |
Description | 220821-29 EMBO Practical Course on Cryo-Electron Microscopy and 3D Image Processing, EMBL Heidelberg Talk on EMDB and EMPIAR by Ardan Patwardhan |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | 220821-29 EMBO Practical Course on Cryo-Electron Microscopy and 3D Image Processing, EMBL Heidelberg Talk on EMDB and EMPIAR by Ardan Patwardhan |
Year(s) Of Engagement Activity | 2022 |
Description | 221213 MicroED course at UCLA Jack Turner (EMDB) gave a (remote) presentation about EM archiving in EMDB and EMPIAR |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | 221213 MicroED course at UCLA Jack Turner (EMDB) gave a (remote) presentation about EM archiving in EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2022 |
Description | 230323-0405 - CSHL course Cryo-Electron Microscopy, Cold Spring Harbor - presentation |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | Presentation by J. Turner (EMDB) about EMDB and EMPIAR and validation of cryo-EM data |
Year(s) Of Engagement Activity | 2023 |
URL | https://meetings.cshl.edu/courses.aspx?course=C-cryoem&year=23 |
Description | 230328 Presentation at "Guide to FAIR bioimage data" workshop run by Euro-BioImaging |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | M. Hartley gave a presentation entitled "EMPIAR - The Electron Microscopy Public Image Archive". |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.eurobioimaging.eu/news/euro-bioimagings-guide-to-fair-bioimage-data/ |
Description | 230410-14 Presentation at NCCAT-NCITU 2023 CryoET short course, New York |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | J. Turner gave a presentation about EMDB and EMPIAR and validation of cryo-EM data |
Year(s) Of Engagement Activity | 2023 |
URL | https://nccat.nysbc.org/activities/courses/tomography-short-course-2023/ |
Description | 230425-27 Presentation at CCP-EM Spring Symposium, Nottingham |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk to give an update to the community about EMPIAR and EMDB. Also a poster about EMPIAR. |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php |
Description | 230522-26 EMPIAR teaching in "Microscopy data analysis & image archiving" course, EMBL-EBI |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | S. Weyand, O. Salih, with help from the rest of the EMPIAR team and external collaborators, taught a module about the use of machine learning in volume EM |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.ebi.ac.uk/training/events/microscopy-data-analysis-0/ |
Description | 230605-09 Presentation at the cryoNET advanced image processing course, Århus |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | J. Turner gave a presentation on EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.scilifelab.se/event/1stfirst-cryonet-course-on-advanced-single-particle-cryo-em-analysis... |
Description | 230710-21 Presentation at São Paulo School of Advanced Science in CryoEM |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | J. Turner gave a presentation about EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2023 |
URL | https://sites.usp.br/cryoemschool2023/home/ |
Description | 230716-21 Presentation at First GRC on volume EM in Ventura, California |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | M. Hartley gave an invited talk about archiving of volume EM and correlative imaging at EMPIAR and BIA |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.grc.org/volume-electron-microscopy-conference/2023/ |
Description | 230905-12 Presentation at EMBO Practical Course on CryoEM, Birkbeck |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | J. Turner gave a presentation on EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2023 |
URL | https://meetings.embo.org/event/23-cryo-em-image-processing |
Description | 231009-12 Presentation at CCP-EM Icknield workshop, Harwell |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | J. Turner gave a presentation on EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2023 |
URL | https://instruct-eric.org/events/ccp-em-icknield-workshop-2023 |
Description | 240311-15 Presentation at NYSBC-NCCAT SPA short course (New York; virtual) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | J. Turner gave a presentation about EMDB and EMPIAR and validation of cryo-EM data |
Year(s) Of Engagement Activity | 2024 |
URL | https://nccat.nysbc.org/activities/courses/nccat-spa-short-course-2024/ |
Description | 240313-27 Presentation at CSHL course Cryo-Electron Microscopy, Cold Spring Harbor |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | J. Turner gave a presentation about EMDB and EMPIAR and validation of cryo-EM data |
Year(s) Of Engagement Activity | 2024 |
URL | https://meetings.cshl.edu/courses.aspx?course=C-CRYOEM&year=24 |
Description | 3DEM Gordon Research Conference, Rhode Island USA |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Poster presentation on EMDB and EMPIAR activities |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.grc.org/three-dimensional-electron-microscopy-conference/2018/ |
Description | CCP-EM Developers' Workshop |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Discussions involving compression for EMPIAR |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.ccpem.ac.uk/courses.php |
Description | CCP-EM Icknield Model Building Workshop |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk focusing on validation for cryo EM but also highlighting other resources for EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2018 |
Description | CCP-EM Spring Symposium 2015 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talk on EMDB and EMPIAR and plans |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.ccpem.ac.uk/courses.php |
Description | CCP-EM Spring Symposium 2016 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | EMDB and EMPIAR presentation |
Year(s) Of Engagement Activity | 2016 |
Description | CCP-EM Spring Symposium, Keele University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Talk and poster presentations on various aspects of the activities and plans relating to EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2018 |
URL | http://www.ccpem.ac.uk/training/spring_symposium_2018/spring_symposium.php |
Description | CEITEC Winter School |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Two invited lectures: • "The wonderful world of structure archiving - What's happening and what's next?", invited lecture, CEITEC Winter School on Structural Cell Biology, Brno, Czech Republic, February 2015. • "Applied common sense - The why, what and how of validation", invited lecture, CEITEC Winter School on Structural Cell Biology, Brno, Czech Republic, February 2015. |
Year(s) Of Engagement Activity | 2015 |
Description | CSHL course: X-Ray Methods in Structural Biology |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Invited lecture as well as two practicals and discussions with students in the course and fellow course instructors. |
Year(s) Of Engagement Activity | 2016 |
URL | http://meetings.cshl.edu/courses.aspx?course=c-crys&year=16 |
Description | Community workshop on Volume EM, Wellcome Trust, October 2019 - organised jointly with Ardan Patwardhan, Lucy Collinson and Paul Verkade |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We organised a workshop for the Volume EM community to discuss needs and opportunities with members of the community and funder representatives. Main outcome was agreement to work on a roadmap for Volume EM in the UK. |
Year(s) Of Engagement Activity | 2019 |
Description | Cryo EM and 3D Image Processing (CEM3DIP) course New Delhi 2018 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Presentation on EMDB and EMPIAR to make audience aware of activities and resources available, plans for the future and how they could enhance their research by interacting with us. |
Year(s) Of Engagement Activity | 2018 |
URL | http://meetings.embo.org/event/18-cem3dip |
Description | Cryo-EM 3D Image Analysis Symposium 2016: Data storage round-table, Tahoe, USA |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Discussion session on data storage: EMPIAR used as an example |
Year(s) Of Engagement Activity | 2016 |
Description | Dynamo (subtomogram averaging software) Workshop, Basel 2018 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Workshop attended by Sanja Abbott. Important to understand needs of tomography community with regards to archiving |
Year(s) Of Engagement Activity | 2018 |
URL | https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Basel_Dynamo_Workshop_2018 |
Description | EMBO Practical Course: Cryo-Electron Microscopy and 3D Image Processing 2016 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talk on EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.embl.de/training/events/2016/CRY16-01/index.html |
Description | EMBO Practical Course: Image processing for cryo-electron microscopy |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk on EMDB and EMPIAR and engagement with students |
Year(s) Of Engagement Activity | 2015 |
URL | http://events.embo.org/15-cryo-em/ |
Description | Expert workshop on "3D segmentations and transformations - building bridges between cellular and molecular structural biology" |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Workshop to discuss segmentation/transformation formats and biological annotation |
Year(s) Of Engagement Activity | 2015 |
Description | From 2D images to 3D structures: A practical course on Electron Microscopy Single Particle Analysis, I2PC, Madrid, Spain |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talks on EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2016 |
Description | G.J. Kleywegt - "EMPIAR - update & plans", talk at the Third Annual Volume EM Community Town Hall Meeting, virtual, October 2021. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "EMPIAR - update & plans", talk at the Third Annual Volume EM Community Town Hall Meeting, virtual, October 2021. |
Year(s) Of Engagement Activity | 2021 |
URL | https://drive.google.com/file/d/1_lUuuSgP2rRqLooa3ArIqm7f7xt6tgB7/view?usp=sharing |
Description | G.J. Kleywegt - "Electron Microscopy Public Image Archive (EMPIAR)", invited webinar for Global BioImaging, virtual, January 2022. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Electron Microscopy Public Image Archive (EMPIAR)", invited webinar for Global BioImaging, virtual, January 2022. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.youtube.com/watch?v=z8yPcO-MR5I |
Description | G.J. Kleywegt - "Electron Microscopy Public Image Archive (EMPIAR)", invited webinar for Microscopy Australia, virtual, June 2021. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Electron Microscopy Public Image Archive (EMPIAR)", invited webinar for Microscopy Australia, virtual, June 2021. |
Year(s) Of Engagement Activity | 2021 |
Description | G.J. Kleywegt - "Image Archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk in PETRA IV workshop, DESY Hamburg, Germany, virtual (presented by Ardan Patwardhan), March 2021. |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Image Archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk in PETRA IV workshop, DESY Hamburg, Germany, virtual (presented by Ardan Patwardhan), March 2021. |
Year(s) Of Engagement Activity | 2021 |
Description | G.J. Kleywegt - "Image archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk at Microscopy & Microanalysis 2021 (session "From Images to Insights: Working with Large Multi-modal Data in Cell Biological Imaging"), Pittsburgh, USA, virtual, August 2021. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Image archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk at Microscopy & Microanalysis 2021 (session "From Images to Insights: Working with Large Multi-modal Data in Cell Biological Imaging"), Pittsburgh, USA, virtual, August 2021. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.youtube.com/watch?v=NR1Kxauukjo |
Description | GRC: Three-Dimensional Electron Microscopy |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Discussion on use of EMPIAR for storage of primary data |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.grc.org/programs.aspx?id=10864 |
Description | Instruct Biennial Meeting |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | INSTRUCT biennial meeting with networking |
Year(s) Of Engagement Activity | 2015 |
URL | https://www.structuralbiology.eu/update/biennial/ |
Description | Invited speaker talk on Structural Biology Data Archiving at FEBS Congress 2018 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Structural biology data archiving - where are we and what lies ahead?", invited lecture, FEBS Congress, Prague, Czech Republic, July 2018. |
Year(s) Of Engagement Activity | 2018 |
Description | Invited talk at 2022 CCP-EM Spring Symposium |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "What's new in public EM data archiving at EMBL-EBI?", invited talk at the CCP-EM Spring Symposium, Nottingham, UK, May 2022. |
Year(s) Of Engagement Activity | 2022 |
Description | Invited webinar for Global Bioimaging, January 2022 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Electron Microscopy Public Image Archive (EMPIAR)", invited webinar for Global BioImaging, virtual, January 2022. (youtu.be/watch?v=z8yPcO-MR5I) |
Year(s) Of Engagement Activity | 2022 |
URL | http://youtu.be/watch?v=z8yPcO-MR5I |
Description | J. Turner, G.J. Kleywegt - Talks & Practical: "EMDB & EMPIAR: Public Archiving of Cryo-EM Data"; Event - Structural Bioinformatics 2022 (EMBL-EBI), Virtual, October 2022 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | J. Turner, G.J. Kleywegt - Talks & Practical: "EMDB & EMPIAR: Public Archiving of Cryo-EM Data"; Event - Structural Bioinformatics 2022 (EMBL-EBI), Virtual, October 2022 |
Year(s) Of Engagement Activity | 2022 |
Description | Keynote lecture titled Supporting the bioimaging revolution |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Supporting the bio imaging revolution was presented as a keynote lecture at SCANDEM 2017 (68th Annual Conference of the Nordic Microscopy Society), Reykjavik, Iceland. |
Year(s) Of Engagement Activity | 2017 |
Description | Lecture on Introduction to Structural Biology Data |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | A lecture on the Introduction to structural biology data, was presented as part of the Computational Structural Biology course at EMBL-EBI in Cambridge, UK. |
Year(s) Of Engagement Activity | 2017 |
Description | Lecture on Structural Biology Data Archiving |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Structural biology data archiving - where are we and what lies ahead?", seminar, EMBL, Heidelberg, Germany, September 2018. |
Year(s) Of Engagement Activity | 2018 |
Description | Lecture titled Structural Biology Data Archiving |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | A lecture titled Structural biology data archiving was presented as during a course on X-ray Methods in Structural Biology at the Cold Spring Habor Laboratory, Cold Spring Harbor, NY, USA. |
Year(s) Of Engagement Activity | 2017 |
Description | O. Salih - Talk & Practical: "EMDB & EMPIAR: Public Archiving of Cryo-EM Data"; Event - Bioinformatics Resources for Protein Biology 2022 (EMBL-EBI), Virtual, 22 February 2022 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | O. Salih - Talk & Practical: "EMDB & EMPIAR: Public Archiving of Cryo-EM Data"; Event - Bioinformatics Resources for Protein Biology 2022 (EMBL-EBI), Virtual, 22 February 2022 |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.ebi.ac.uk/training/events/bioinformatics-resources-protein-biology-2022/#vf-tabs__sectio... |
Description | O. Salih, J. Turner, G.J. Kleywegt - Talks & Practical: "EMDB & EMPIAR: Public Archiving of Cryo-EM Data"; Event - Structural Bioinformatics 2021 (EMBL-EBI), Virtual, 13 October 2021 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | O. Salih, J. Turner, G.J. Kleywegt - Talks & Practical: "EMDB & EMPIAR: Public Archiving of Cryo-EM Data"; Event - Structural Bioinformatics 2021 (EMBL-EBI), Virtual, 13 October 2021 |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.ebi.ac.uk/training/materials/structural-bioinformatics-materials/day-3/emdb-and-empiar/ |
Description | O. Salih, S. Weyand, A. Iudin, G.J. Kleywegt - Talks & Practical: "EMPIAR: Depositing & Accessing Data"; Event - Microscopy Data Analysis: Machine learning and the BioImage Archive (EMBL-EBI), Virtual, 14 July 2021 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | O. Salih, S. Weyand, A. Iudin, G.J. Kleywegt - Talks & Practical: "EMPIAR: Depositing & Accessing Data"; Event - Microscopy Data Analysis: Machine learning and the BioImage Archive (EMBL-EBI), Virtual, 14 July 2021 |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.ebi.ac.uk/training/materials/microscopy-image-analysis-materials/bioimage-databases-reso... |
Description | Organised "expert workshop on Frontiers in Cryo-EM Validation" with the Wellcome Trust-funded UK EM Validation Network partners, EMBL-EBI, Cambridge, UK, January 2019 |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We organised this expert workshop to explore frontiers and community needs w.r.t. cryo-EM validation. |
Year(s) Of Engagement Activity | 2019 |
Description | Organised expert virtual workshop on "Public archiving of volume-EM data: needs, opportunities and challenges", 6-8 December 2021, with 46 community experts participating |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Organised expert virtual workshop on "Public archiving of volume-EM data: needs, opportunities and challenges", 6-8 December 2021, with 46 community experts participating. Topics discussed: - Data-model and deposition - Dissemination (formats, APIs, data-streaming) - Segmentation This will inform our future work on fully supporting vEM data in the resource. |
Year(s) Of Engagement Activity | 2021 |
Description | S. Somasundharam, "Specimen Preparation Workflow Widget - Demo", virtual, October 2021 |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | S. Somasundharam, "Specimen Preparation Workflow Widget - Demo", virtual, October 2021 Relevant Sandbox URL: https://wwwdev.ebi.ac.uk/emdb/spw/empiar/widget |
Year(s) Of Engagement Activity | 2021 |
URL | https://wwwdev.ebi.ac.uk/emdb/spw/empiar/widget |
Description | S. Weyand, O. Salih, A. Iudin, G.J. Kleywegt - Talks & Practical: "EMPIAR: Depositing & Accessing Data"; Event - Microscopy Data Analysis: Machine learning and the BioImage Archive (EMBL-EBI), Virtual, May 2022 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | S. Weyand, O. Salih, A. Iudin, G.J. Kleywegt - Talks & Practical: "EMPIAR: Depositing & Accessing Data"; Event - Microscopy Data Analysis: Machine learning and the BioImage Archive (EMBL-EBI), Virtual, May 2022 |
Year(s) Of Engagement Activity | 2022 |
Description | School visit and presentation at Bar Hill School |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Public engagement presentation on microscopy to primary school students |
Year(s) Of Engagement Activity | 2018 |
Description | Scipion Facilities Meeting 2018 |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Discussions on how to interface Scipion which is now being used by a number of cryo-EM centers with EMPIAR to enable data pipelining |
Year(s) Of Engagement Activity | 2018 |
URL | http://i2pc.es/2nd-i2pc-cryoem-facilities-meeting-madrid-june-26-27-2018/ |
Description | Seminar at EMBL Hamburg |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | EMDB and EMPIAR - status, plans and challenges |
Year(s) Of Engagement Activity | 2016 |
Description | Seminar at EMBL Heidelberg |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | Public archiving of EM and bioimaging data: EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2016 |
Description | Seminar in Uppsala |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | Invited lecture and follow-up discussion with local scientists and students. |
Year(s) Of Engagement Activity | 2016 |
Description | Seminar in Vienna |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | Invited lecture on "The wonderful world of structure archiving - what's happening and what's next?" as well as discussions with various local scientists and students. |
Year(s) Of Engagement Activity | 2016 |
Description | Structural bioinformatics training course |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Co-organiser of and lecturer in this practical course, interacting with students and fellow instructors. |
Year(s) Of Engagement Activity | 2016,2017,2018 |
URL | http://www.ebi.ac.uk/training/events/2016/structural-bioinformatics-2016 |
Description | Talk & Practical Session on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for Bioinformatics Resources for Protein Biology Course (Cambridge University) - April 2019 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Undergraduate students |
Results and Impact | Talk: Gave an overiview of the Cryo-EM field and the "resolution revolution", then showed statistics concerning EM Data coming into the PDB, EMDB & EMPIAR archives. Gave overviews of the resources we provide, and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. Practical: Investigative Question & Answer session on using EMDB and EMPIAR resources, downloading data, visualising data & assessing the data quality. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk & Practical Session on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for Bioinformatics Resources for Protein Biology Course (EMBL-EBI) - February 2019 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | Talk: Gave an overiview of the Cryo-EM field and the "resolution revolution", then showed statistics concerning EM Data coming into the PDB, EMDB & EMPIAR archives. Gave overviews of the resources we provide, and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. Practical: Investigative Question & Answer session on using EMDB and EMPIAR resources, downloading data, visualising data & assessing the data quality. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for CCP-EM Icknield Model Building Workshop (RAL/DLS, Oxford) - April 2019 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk: Gave an overiview of the Cryo-EM field and the "resolution revolution", then showed statistics concerning EM Data coming into the PDB, EMDB & EMPIAR archives. Gave overviews of the resources we provide, and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for EMBO Practical Course CEM3DIP 2020 (IISER-Kolkata, India) - January 2020 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk: Gave an overview of the Cryo-EM field and the "resolution revolution", then showed statistics concerning EM Data coming into the PDB, EMDB & EMPIAR archives. Gave overviews of the resources we provide, and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. |
Year(s) Of Engagement Activity | 2020 |
Description | Talk on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for EMBO Practical Course for Cryo-EM Image Processing (Birkbeck) - September 2019 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk: Gave overviews of the resources we provide (PDBe, EMDB, EMPIAR), and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for Structural Bioinformatics Course (EMBL-EBI) - September 2019 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk: Gave an overiview of the Cryo-EM field and the "resolution revolution", then showed statistics concerning EM Data coming into the PDB, EMDB & EMPIAR archives. Gave overviews of the resources we provide, and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. |
Year(s) Of Engagement Activity | 2019 |
Description | UK Structural Biology Forum meeting |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Meeting to discuss national initiatives to deal with the surge in cryo-EM |
Year(s) Of Engagement Activity | 2015 |
URL | https://www.structuralbiology.eu/networks/instruct-uk-network?tab=about |
Description | Univ of Copenhagen PhD Day (keynote speaker) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | Keynote speaker at the PhD Day of the Dept of Biology of the Univ of Copenhagen. Also interacted with students who presented posters as well as the PhD students who organised the PhD Day. |
Year(s) Of Engagement Activity | 2016 |
URL | http://phdday.wixsite.com/2016 |
Description | Wellcome Trust Cryo EM User Meeting |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Discussion on needs of the UK cryo EM community where the role of EMDB and EMPIAR were also highlighted and discussed. |
Year(s) Of Engagement Activity | 2018 |
Description | Workshop on 3D solutions in Cryo-Electron Microscopy 2015 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk on EMDB and EMPIAR and engagement with students |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.maastrichtuniversity.nl/web/Institutes/MaastrichtMultiModalMolecularImagingInstitute/Work... |
Description | Workshop on Computational Methods in Bio-imaging Sciences, National University of Singapore, Institute of Mathematical Sciences |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Introduction to EM and EM databases to a wider scientific post-grad audience |
Year(s) Of Engagement Activity | 2018 |
URL | https://ims.nus.edu.sg/events/2017/data/wk3.php |
Description | Workshop on bioimaging and data annotation |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Discuss imaging formats |
Year(s) Of Engagement Activity | 2015 |
Description | Workshop on metadata standards and data formats |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Discuss metadata standards for imaging data |
Year(s) Of Engagement Activity | 2015 |