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Resource type: slides 

Computational Reproducibility with the shell, Git and Docker

This workshop provides an overview over tools for computational reproducibility in research. At the end of this workshop participants will be able to navigate via the shell and use it for version control with Git. They will know what types of projects require which forms of computing environments...

Keywords: scientific software, reproducibility, docker container, version control, shell

Resource type: slides

Computational Reproducibility with the shell, Git and Docker https://pan-training.eu/materials/computational-reproducibility-with-the-shell-git-and-docker This workshop provides an overview over tools for computational reproducibility in research. At the end of this workshop participants will be able to navigate via the shell and use it for version control with Git. They will know what types of projects require which forms of computing environments and be able to set up a Docker container to run computations in a reproducible way. scientific software, reproducibility, docker container, version control, shell research data scientist PhD students researchers scientists
ExPaNDS Workshop - Follow a user story! A journey through the PaN data services.

The ExPaNDS Workshop "Follow a user story", which took place on the 24th of January in Hamburg, Germany (hybrid), aimed to provide a "User Journey", taking the audience on the road of the "European Open Science Cloud Photon and Neutron Data Services". The objective was to demonstrate how as...

Keywords: expands, EOSC, data services, FAIR, VISA, PaN portal

Resource type: slides, video

ExPaNDS Workshop - Follow a user story! A journey through the PaN data services. https://pan-training.eu/zenodomaterials/expands-workshop-follow-a-user-story-a-journey-through-the-pan-data-services The ExPaNDS Workshop "Follow a user story", which took place on the 24th of January in Hamburg, Germany (hybrid), aimed to provide a "User Journey", taking the audience on the road of the "European Open Science Cloud Photon and Neutron Data Services". The objective was to demonstrate how as a user, one can benefit from the services developed during the project. The story began with a FAIR journey presented by Brian Matthews, an EOSC demo from Marta Gutierrez, followed by a demo of the training platform from Oliver Knodel. The last two stops of the journey were two demos from the VISA portal (Silvan Schoen and Michael Schuh) and the search API/Harvesting services (PaN Portal, etc) presented by Carlo Minotti. The session was chaired by Clara Albert. Find the presentations & prerecorded demos on Zenodo. The recording will be available very soon. expands, EOSC, data services, FAIR, VISA, PaN portal
UmbrellaID Workshop: Keycloak

This one day training is dedicated to the PaN community IT people that want to enable community AAI for their users. At the end of the training it is expected that you understand what UmbrellaID and the EOSC AAI federation is. A hands on session shall demonstrate how to integrate your services...

Keywords: UmbrellaID

Resource type: slides, video

UmbrellaID Workshop: Keycloak https://pan-training.eu/materials/umbrellaid-workshop-keycloak This one day training is dedicated to the PaN community IT people that want to enable community AAI for their users. At the end of the training it is expected that you understand what UmbrellaID and the EOSC AAI federation is. A hands on session shall demonstrate how to integrate your services with UmbrellaID using Keycloak. If you want to actively participate in the hands on session, you need to have your own Keycloak installation, see the following checklist. If you don't have that, you can still participate in the workshop and also take part in the hands on session as an observer. Checklist for the hands on session: - An installation of Keycloak - Internet access from the host where they have installed Keycloak (ideally direct access, but HTTP proxy and reverse HTTP proxy are also valid) - DNS resolution for the host with Keycloak installed should be in place and should be identical from everywhere (I.E. the machine should be referenced with the same domain name from the RI/lab intranet and public internet network) - A valid X509 server certificate The session recordings can be found here: 1. https://umbrellaid.org/zoom/2022-05-03-UmbrellaID-Workshop-Session-1.mp4 2. https://umbrellaid.org/zoom/2022-05-03-UmbrellaID-Workshop-Session-2.mp4 UmbrellaID PaN Community
ETH Lib4RI: Research Data Management – The Basics

Research data management best practices in the ETH Lib4RI, the Library for the Research Institutes within the ETH Domain: Eawag, Empa, PSI & WSL

Keywords: data catalogue, data management, metadata, SciCat

Resource type: slides

ETH Lib4RI: Research Data Management – The Basics https://pan-training.eu/materials/eth-lib4ri-research-data-management-the-basics Research data management best practices in the ETH Lib4RI, the Library for the Research Institutes within the ETH Domain: Eawag, Empa, PSI & WSL data catalogue, data management, metadata, SciCat research scientists postdocs PhD students ExPaNDS and PaNOSC project members PaN users PaN Community researchers
Joint Public Session ExPaNDS/PaNOSC on metadata catalogues (SciCat implementation) and future perspectives

Presentations from public joint WP3 Meeting for ExPaNDS and PaNOSC, which took place in hybrid format from SOLEIL (France) and via Zoom on the 3rd November 2022. A recording of the event can be found on the ExPaNDS website: https://expands.eu/presentations/ Video recording (direct link to...

Keywords: expands, PaNOSC, open data, wp3-ExPaNDS

Resource type: slides

Joint Public Session ExPaNDS/PaNOSC on metadata catalogues (SciCat implementation) and future perspectives https://pan-training.eu/materials/work-package-3-public-meeting Presentations from public joint WP3 Meeting for ExPaNDS and PaNOSC, which took place in hybrid format from SOLEIL (France) and via Zoom on the 3rd November 2022. A recording of the event can be found on the ExPaNDS website: https://expands.eu/presentations/ Video recording (direct link to vimeo) will be available soon. expands, PaNOSC, open data, wp3-ExPaNDS data managers
NOBUGS 2022

The 13th NOBUGS Conference was held at Paul Scherrer Institute, Villigen, Switzerland on September 19-22, 2022. The goal of the NOBUGS (New Opportunities for Better User Group Software) Conference Series is to foster collaboration and exchange between scientists and IT professionals working on...

Keywords: NOBUGS, scientific software

Resource type: video, slides

NOBUGS 2022 https://pan-training.eu/materials/nobugs-2022 The 13th NOBUGS Conference was held at Paul Scherrer Institute, Villigen, Switzerland on September 19-22, 2022. The goal of the NOBUGS (New Opportunities for Better User Group Software) Conference Series is to foster collaboration and exchange between scientists and IT professionals working on software for X-ray, neutron and muon sources from around the world. Program Themes: - Data acquisition systems - Data reduction - User interfaces - Data catalogs/Electronic Notebooks - Data Streaming - Use of (commercial) Cloud Systems - Web Tools - Workflow Engines & Tools - Other Relevant Topics NOBUGS, scientific software
Virtual Infrastructure for Scientific Analysis (VISA) Workshop

We invite you to view our workshop – hosted jointly by ExPaNDS and PaNOSC! VISA provides remote data analysis services giving access to experimental data, analysis software, compute infrastructure and expert-user support (IT and Scientific). The online half-day Workshop is open to all external...

Keywords: VISA, expands, PaNOSC, remote data analysis services

Resource type: slides

Virtual Infrastructure for Scientific Analysis (VISA) Workshop https://pan-training.eu/materials/virtual-infrastructure-for-scientific-analysis-visa-workshop We invite you to view our workshop – hosted jointly by ExPaNDS and PaNOSC! VISA provides remote data analysis services giving access to experimental data, analysis software, compute infrastructure and expert-user support (IT and Scientific). The online half-day Workshop is open to all external stakeholders (especially scientists and IT staff but not limited to). We aim to demonstrate to beamline scientists the possibilities offered by VISA for data analysis and gathering IT staff around the table to discuss about the development and further deployment of the platform. VISA has been developed at a critical time (during the COVID-19 crisis) to answer data analysis needs and allowing remote instrument control. It provides simplified access for scientists to data analysis tools, offers remote support to users from experts and allows them to remotely control their experiments with the assistance of on-site instrument scientists. VISA allows a user to use the Remote Desktop as if they were sitting in front a data treatment workstation at the host institute and embeds JupyterLab directly accessible from the same platform interface. Initially developed at the Institut Laue-Langevin (ILL) in Grenoble, France and further deployed in the context of PaNOSC, VISA enables the PaN research infrastructures (PaN RIs) to work together on further scientific collaborations to solve 21st century challenges. The first session of the workshop showcases the implementation of VISA at the PaN RIs through ExPaNDS and PaNOSC partner’ demos and illustrate its use for scientific users and others. The second session in the afternoon focuses on presentations on VISA development and deployment (on OpenStack and other infrastructures), paving the way for a roundtable discussion on the future of VISA: sustainability and future collaborations. Video recording (direct link to vimeo) will be available soon. VISA, expands, PaNOSC, remote data analysis services
A deep dive into the mathematics of Machine Learning

Crash course on Machine Learning

Keywords: machine learning

Resource type: slides

A deep dive into the mathematics of Machine Learning https://pan-training.eu/materials/a-deep-dive-into-the-mathematics-of-machine-learning Crash course on Machine Learning machine learning research data scientist masters students PhD students
Neutrons for Magnetic Nanostructures on Surfaces: Beyond the Specular Intensity Wars

Polarized Neutron Reflectometry (PNR) is a great method to study magnetism of surface near structures on the nm scale. It is especially useful for functional materials and fundamentals of nano magnetism. The applications of the technique and the related grazing incidence scattering include...

Scientific topics: polarized neutron reflectometry, grazing incidence small angle neutron scattering

Keywords: polarized neutron reflectometry, grazing incidence scattering, magnetic nanoparticles, GISANS

Resource type: video, slides

Neutrons for Magnetic Nanostructures on Surfaces: Beyond the Specular Intensity Wars https://pan-training.eu/materials/neutrons-for-magnetic-nanostructures-on-surfaces-beyond-the-specular-intensity-wars Polarized Neutron Reflectometry (PNR) is a great method to study magnetism of surface near structures on the nm scale. It is especially useful for functional materials and fundamentals of nano magnetism. The applications of the technique and the related grazing incidence scattering include multiferroic heterostructures, correlated electron systems, exchange bias, superconductors, magnetic nanoparticles and spin textures like skyrmions. Many of these systems have in common that the sample sizes are small, leading to intensity limited experiments. [...] polarized neutron reflectometry grazing incidence small angle neutron scattering polarized neutron reflectometry, grazing incidence scattering, magnetic nanoparticles, GISANS
Seeing the chemistry in biology using neutron crystallography

New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible in neutron structures. Using X-rays allows one to see structure, while...

Keywords: macromolecular neutron crystallography, biological macromolecules, neutron

Resource type: video, slides, scientific article

Seeing the chemistry in biology using neutron crystallography https://pan-training.eu/materials/seeing-the-chemistry-in-biology-using-neutron-crystallography New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible in neutron structures. Using X-rays allows one to see structure, while neutrons allow one to reveal the chemistry inherent in these macromolecular structures. A number of surprising and sometimes controversial results have emerged from recent neutron structures; because it is difficult to see or predict hydrogen atoms in X-ray structures, when they are seen by neutrons they can be in unexpected locations with important chemical and biological consequences. Here we describe examples of chemistry seen with neutrons for the first time in biological macromolecules over the past few years. macromolecular neutron crystallography, biological macromolecules, neutron
Neutron crystallography to inform drug design targeting SARS-CoV-2 main protease

Talk from one of the ILL colloqia. See colloquia list at the bottom for other talks. COVID-19, caused by SARS-CoV-2, remains a global health threat after two years of the pandemic even with available vaccines and therapeutic options. The viral main protease (Mpro) is indispensable for the...

Keywords: COVID research, neutron, drug development, neutron crystallography

Resource type: video, slides

Neutron crystallography to inform drug design targeting SARS-CoV-2 main protease https://pan-training.eu/materials/neutron-crystallography-to-inform-drug-design-targeting-sars-cov-2-main-protease Talk from one of the ILL colloqia. See colloquia list at the bottom for other talks. COVID-19, caused by SARS-CoV-2, remains a global health threat after two years of the pandemic even with available vaccines and therapeutic options. The viral main protease (Mpro) is indispensable for the virus replication and thus is an important target for small-molecule antivirals. Computer-assisted and structure-based drug design strategies rely on atomic scale understanding of the target biomacromolecule traditionally derived from X-ray crystallographic data collected at cryogenic temperatures. Conventional protein X-ray crystallography is limited by possible cryo-artifacts and its inability to locate the functional hydrogen atoms crucial for understanding chemistry occurring in enzyme active sites. Neutrons are ideal probes to observe the protonation states of ionizable amino acids at near-physiological temperature, directly determining their electric charges – crucial information for drug design. Our room-temperature X-ray crystal structures of Mpro brought rapid insights into the reactivity of the catalytic cysteine, malleability of the active site, and binding modes with clinical protease inhibitors. The neutron crystal structures of ligand-free and inhibitor-bound Mpro were determined allowing the direct observation of protonation states of all residues in a coronavirus protein for the first time [1,2]. At rest, the catalytic Cys-His dyad exists in the reactive zwitterionic state (Fig. 1), with both Cys145 and His41 charged, instead of the anticipated neutral state. Covalent inhibitor binding results in modulation of the protonation states. This information was used to design nanomolar hybrid reversible covalent inhibitors with robust antiviral properties. High-throughput virtual screening, utilizing ORNL’s supercomputing capabilities, in conjunction with in vitro assays identified a lead noncovalent compound with sub-micromolar affinity. The neutron structure of Mpro in complex with the noncovalent inhibitor was used in a structure-activity relationship (SAR) study guided by virtual reality structure analysis to novel Mpro inhibitors with imporved affinity to the enzyme [3]. Our research is providing real-time data for atomistic design and discovery of Mpro inhibitors to combat the COVID-19 pandemic and prepare for future threats from pathogenic coronaviruses. [1] D.W. Kneller et al. Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography. J. Biol. Chem.295, 17365-17373 (2020). [2] D.W. Kneller et al. Direct observation of protonation state modulation in SARS-CoV-2 main protease upon inhibitor binding with neutron crystallography. J. Med. Chem.64, 4991-5000 (2021). [3] D.W. Kneller et al. Structural, electronic and electrostatic determinants for inhibitor binding to subsites S1 and S2 in SARS-CoV-2 main protease. J. Med. Chem.64, 17366-17383 (2021). The authors acknowledge support by the National Virtual Biotechnology Laboratory, US Department of Energy. COVID research, neutron, drug development, neutron crystallography
Workshop on Metadata Catalogues

Presentations from the Workshop on Metadata Catalogues, which took place virtually via Zoom on the 4th April 2022.

Keywords: data catalogue, SciCat, ICAT, expands, panet, PaNOSC, metadata, data management, data processing, wp3-ExPaNDS

Resource type: slides, video

Workshop on Metadata Catalogues https://pan-training.eu/materials/workshop-on-metadata-catalogues Presentations from the Workshop on Metadata Catalogues, which took place virtually via Zoom on the 4th April 2022. data catalogue, SciCat, ICAT, expands, panet, PaNOSC, metadata, data management, data processing, wp3-ExPaNDS data curator data managers research data engineer ExPaNDS and PaNOSC project members PaN users PaN Community
ExPaNDS mid-term review

Slides of the presentations done during the ExPaNDS midterm review.

Keywords: expands

Resource type: slides

ExPaNDS mid-term review https://pan-training.eu/materials/expands-mid-term-review Slides of the presentations done during the ExPaNDS midterm review. expands ExPaNDS and PaNOSC project members
DAPHNE4NFDI: Science driven data management solutions for the user community

Slides (and other resources) of the presentations done at this workshop, including a presentation of ICAT and SciCat.

Keywords: ICAT, SciCat, PaNOSC, expands, wp3-ExPaNDS

Resource type: slides

DAPHNE4NFDI: Science driven data management solutions for the user community https://pan-training.eu/materials/daphne4nfdi-science-driven-data-management-solutions-for-the-user-community Slides (and other resources) of the presentations done at this workshop, including a presentation of ICAT and SciCat. ICAT, SciCat, PaNOSC, expands, wp3-ExPaNDS PaN Community ExPaNDS and PaNOSC project members PaN users data curator data managers research data engineer engineers
Persistent Identifiers for Facilities Research Workshop

Our workshop on Persistent Identifiers (PIDs) reflected on practices of PIDs used in facilities research, an update on state-of-the art and recent developments about PIDs elsewhere and discussions around the actual and desired levels of PIDs adoption across facilities research lifecycle. You...

Keywords: pid, persistent identifiers, expands, wp2-ExPaNDS

Resource type: video, slides

Persistent Identifiers for Facilities Research Workshop https://pan-training.eu/materials/persistent-identifiers-for-facilities-research-workshop Our workshop on Persistent Identifiers (PIDs) reflected on practices of PIDs used in facilities research, an update on state-of-the art and recent developments about PIDs elsewhere and discussions around the actual and desired levels of PIDs adoption across facilities research lifecycle. You can read our report and view the presentations in the links below. pid, persistent identifiers, expands, wp2-ExPaNDS facility staff
Librarian Symposium

Our Librarian Symposium was aimed at librarians and data managers who work with and support PaN science facilities. In particular, the symposium focused on the interface between publications and data. How can we bring these together better for the benefit of all? Where are the gaps? What do we...

Keywords: expands, open data, persistent identifiers, pid, PUMA project, publishing experiments, F-UJI tool, FAIR, FAIR metrics, wp2-ExPaNDS

Resource type: video, slides

Librarian Symposium https://pan-training.eu/materials/librarian-symposium-am-session Our Librarian Symposium was aimed at librarians and data managers who work with and support PaN science facilities. In particular, the symposium focused on the interface between publications and data. How can we bring these together better for the benefit of all? Where are the gaps? What do we need to bridge them? Watch our video recordings for the AM and PM sessions, you can also find our report and presentations below. expands, open data, persistent identifiers, pid, PUMA project, publishing experiments, F-UJI tool, FAIR, FAIR metrics, wp2-ExPaNDS librarians data managers data curator
Beamline FAIRness Assessment Presentation

The presentation which took place on the 15th November 2021, organised by the ExPaNDS project where Markus Kubin and Gerrit Guenther gave an overview of "Assessing the FAIRness of a prototypical PaN instrument at BESSY II".

Keywords: BESSY II, FAIR, expands, open data, wp2-ExPaNDS

Resource type: video, slides

Beamline FAIRness Assessment Presentation https://pan-training.eu/materials/beamline-fairness-assessment-presentation The presentation which took place on the 15th November 2021, organised by the ExPaNDS project where Markus Kubin and Gerrit Guenther gave an overview of "Assessing the FAIRness of a prototypical PaN instrument at BESSY II". BESSY II, FAIR, expands, open data, wp2-ExPaNDS
McStas and McXtrace schools

This repository contains teaching material related to McStas and McXtrace schools 2019-

Keywords: McStas, McXtrace, simulation, neutron simulation, x-ray simulation

Resource type: git, tutorial, slides, e-learning

McStas and McXtrace schools https://pan-training.eu/materials/mcstas-and-mcxtrace-schools This repository contains teaching material related to McStas and McXtrace schools 2019- McStas, McXtrace, simulation, neutron simulation, x-ray simulation PaN Community beamline users
DOI, FAIR and MX COVID-19 use case

Frank von Delft presents: DOI, FAIR and MX COVID-19 use case at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).

Keywords: COVID research, FAIR, fragalysis, drug development, XChem, PDB, zenodo, wp5-ExPaNDS

Resource type: video, slides

DOI, FAIR and MX COVID-19 use case https://pan-training.eu/materials/doi-fair-and-mx-covid-19-use-case Frank von Delft presents: DOI, FAIR and MX COVID-19 use case at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021). COVID research, FAIR, fragalysis, drug development, XChem, PDB, zenodo, wp5-ExPaNDS
Machine Learning-based Spectra Classification

Yue Sun presents: Machine Learning-based Spectra Classification at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).

Scientific topics: spectroscopy

Keywords: machine learning, XFEL, FAIR, large dataset, NeXus, spectroscopy, wp5-ExPaNDS

Resource type: video, slides

Machine Learning-based Spectra Classification https://pan-training.eu/materials/machine-learning-based-spectra-classification Yue Sun presents: Machine Learning-based Spectra Classification at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021). spectroscopy machine learning, XFEL, FAIR, large dataset, NeXus, spectroscopy, wp5-ExPaNDS PaN Community scientists
TELBE data analysis workflow and the PaN training platform UX

Jan-Christoph Deinert presents: TELBE data analysis workflow and the PaN training platform UX at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).

Keywords: training platform, workflow, TELBE, FAIR, data correction, wp5-ExPaNDS

Resource type: video, slides

TELBE data analysis workflow and the PaN training platform UX https://pan-training.eu/materials/telbe-data-analysis-workflow-and-the-pan-training-platform-ux Jan-Christoph Deinert presents: TELBE data analysis workflow and the PaN training platform UX at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021). training platform, workflow, TELBE, FAIR, data correction, wp5-ExPaNDS
Neutron diffraction from Boro-carbon for efficient structural analysis and defect detection

Mousumi Upadhyay Kahaly presents: Neutron diffraction from Boro-carbon for efficient structural analysis and defect detection at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).

Scientific topics: neutron diffraction, inelastic scattering

Keywords: McStas, simulation, inelastic neutron scattering, ab-initio, neutron scattering, neutron, neutron diffraction, defect detection, structural analysis, wp5-ExPaNDS

Resource type: video, slides

Neutron diffraction from Boro-carbon for efficient structural analysis and defect detection https://pan-training.eu/materials/neutron-diffraction-from-boro-carbon-for-efficient-structural-analysis-and-defect-detection Mousumi Upadhyay Kahaly presents: Neutron diffraction from Boro-carbon for efficient structural analysis and defect detection at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021). neutron diffraction inelastic scattering McStas, simulation, inelastic neutron scattering, ab-initio, neutron scattering, neutron, neutron diffraction, defect detection, structural analysis, wp5-ExPaNDS PaN Community scientists
Tomography Case Study

Kamel Madi presents: Tomography Case Study at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).

Keywords: tomography, pid, doi, FAIR, large dataset, 3Dmagination, wp5-ExPaNDS

Resource type: video, slides

Tomography Case Study https://pan-training.eu/materials/tomography-case-study Kamel Madi presents: Tomography Case Study at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021). tomography, pid, doi, FAIR, large dataset, 3Dmagination, wp5-ExPaNDS
Describe data by scripts for future reuse

Petr Čermák presents: Describe data by scripts for future reuse at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).

Keywords: metadata, open data, FAIR, figshare, binder, data processing, wp5-ExPaNDS

Resource type: video, slides

Describe data by scripts for future reuse https://pan-training.eu/materials/describe-data-by-scripts-for-future-reuse Petr Čermák presents: Describe data by scripts for future reuse at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021). metadata, open data, FAIR, figshare, binder, data processing, wp5-ExPaNDS