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XAFS, EXAFS, and XANES tutorials

xafs.xrayabsorption.org (also xafs.org) is a community site for x-ray absorption fine-structure (XAFS) and related spectroscopies. It is part of the web pages sponsored by the International XAFS Society, https://xrayabsorption.org/.

Scientific topics: extended x-ray absorption fine structure, x-ray absorption fine structure, x-ray absorption near edge structure

Keywords: xanes & exafs, xafs, exafs, xanes

Resource type: community site

XAFS, EXAFS, and XANES tutorials https://pan-training.eu/materials/xafs-exafs-and-xanes-tutorials xafs.xrayabsorption.org (also xafs.org) is a community site for x-ray absorption fine-structure (XAFS) and related spectroscopies. It is part of the web pages sponsored by the International XAFS Society, https://xrayabsorption.org/. extended x-ray absorption fine structure x-ray absorption fine structure x-ray absorption near edge structure xanes & exafs, xafs, exafs, xanes
JupyLabBook

A Jupyter Notebook used as an interactive lab book on the beamline SIRIUS (SOLEIL Synchrotron).

Keywords: labbook, jupyter notebook, SIRIUS beamline

Resource type: git, jupyter notebook

JupyLabBook https://pan-training.eu/materials/jupylabbook A Jupyter Notebook used as an interactive lab book on the beamline SIRIUS (SOLEIL Synchrotron). labbook, jupyter notebook, SIRIUS beamline
JupyFluo

JupyFluo is a Jupyter Notebook to analyze X-Ray Fluorescence (XRF) experiments on the beamline SIRIUS at the synchrotron SOLEIL. The notebook should be first set up by an Expert following the instructions in the "Expert" section. User can then follow the guidelines in the "User" section to start...

Scientific topics: x-ray fluorescence

Keywords: X-ray fluorescence, jupyter notebook, SIRIUS beamline

Resource type: git, jupyter notebook

JupyFluo https://pan-training.eu/materials/jupyfluo JupyFluo is a Jupyter Notebook to analyze X-Ray Fluorescence (XRF) experiments on the beamline SIRIUS at the synchrotron SOLEIL. The notebook should be first set up by an Expert following the instructions in the "Expert" section. User can then follow the guidelines in the "User" section to start using the notebook. Please note that the notebook is currently in development. As such, be skeptical about any unexpected results. Any feedback on the notebook or the code is welcome. x-ray fluorescence X-ray fluorescence, jupyter notebook, SIRIUS beamline
Bruce Ravel XAS course 2011

Bruce Ravel XAS course 2011 In November 2011 Bruce Ravel gave a course on the Demeter package at diamond.

Scientific topics: x-ray absorption spectroscopy

Keywords: XAS, demeter, athena

Resource type: video

Bruce Ravel XAS course 2011 https://pan-training.eu/materials/bruce-ravel-xas-course-2011 Bruce Ravel XAS course 2011 In November 2011 Bruce Ravel gave a course on the Demeter package at diamond. x-ray absorption spectroscopy XAS, demeter, athena
The Braggs Legacy

The scientific and human story behind the past, present and future of one of the most important ever developments in science. 100 years after it was first developed, crystallography is still a driving force of scientific discovery and innovation. Revealing the hidden structure and beauty of...

Scientific topics: crystallography

Keywords: bragg's law, crystallography, history

Resource type: video

The Braggs Legacy https://pan-training.eu/materials/the-braggs-legacy The scientific and human story behind the past, present and future of one of the most important ever developments in science. 100 years after it was first developed, crystallography is still a driving force of scientific discovery and innovation. Revealing the hidden structure and beauty of materials, it gives an insight into the invisible. This film from Diamond Light Source celebrates the work and lives of Sir William Henry Bragg and his son, Sir William Lawrence Bragg. Together, they established a new scientific discipline. A son with the theoretical understanding and father with the experimental technique to harness this knowledge. The technique emerged a century ago, but its power to reveal the minutiae of matter is as strong today as it was then. This film journeys through the key experiments and insights from 1912, and the torrent of discoveries that followed. With interviews and commentaries from leading scientists and historians of today, it is an exploration of the scientific and human story behind the past, present and future of one of the most important ever developments in science. crystallography bragg's law, crystallography, history general public
X-ray fluorescence spectroscopy (XRF)

Synchrotron X-ray techniques for industry R&I: X-ray fluorescence spectroscopy at the ESRF by Dr Gema Martinez-Criado

Scientific topics: x-ray fluorescence spectroscopy

Keywords: XRF

Resource type: video

X-ray fluorescence spectroscopy (XRF) https://pan-training.eu/materials/x-ray-fluorescence-spectroscopy-xrf Synchrotron X-ray techniques for industry R&I: X-ray fluorescence spectroscopy at the ESRF by Dr Gema Martinez-Criado x-ray fluorescence spectroscopy XRF PaN Community
Small and wide angle X-ray scattering (SAXS & WAXS)

Synchrotron X-ray techniques for industry R&I: SAXS & WAXS at the ESRF by Dr Michael Sztucki

Scientific topics: small angle x-ray scattering, wide angle x-ray scattering

Keywords: SAXS, WAXS

Resource type: video

Small and wide angle X-ray scattering (SAXS & WAXS) https://pan-training.eu/materials/small-and-wide-angle-x-ray-scattering-saxs-waxs Synchrotron X-ray techniques for industry R&I: SAXS & WAXS at the ESRF by Dr Michael Sztucki small angle x-ray scattering wide angle x-ray scattering SAXS, WAXS PaN Community
Extended X-ray absorption fine structure (EXAFS) spectroscopy

Synchrotron X-ray techniques for industry R&I: Extended X-ray absorption fine structure (EXAFS) spectroscopy at the ESRF by Dr Sakura Pascarelli

Scientific topics: extended x-ray absorption fine structure

Keywords: xanes & exafs

Resource type: video

Extended X-ray absorption fine structure (EXAFS) spectroscopy https://pan-training.eu/materials/extended-x-ray-absorption-fine-structure-exafs-spectroscopy Synchrotron X-ray techniques for industry R&I: Extended X-ray absorption fine structure (EXAFS) spectroscopy at the ESRF by Dr Sakura Pascarelli extended x-ray absorption fine structure xanes & exafs PaN Community
How to read/edit a nexus file using h5py

A tutorial notebook on how to read and edit a nexus file using h5py.

Keywords: NeXus

Resource type: git, jupyter notebook

How to read/edit a nexus file using h5py https://pan-training.eu/materials/how-to-read-edit-a-nexus-file-using-h5py A tutorial notebook on how to read and edit a nexus file using h5py. NeXus
PyMca tutorial

A manual and a tutorial notebook on how to use PyMca to fit XRF data obtained on the beamline SIRIUS. To use the notebook first uncompress files.zip and save.zip

Scientific topics: x-ray fluorescence

Keywords: PyMca, XRF

Resource type: pdf, git

PyMca tutorial https://pan-training.eu/materials/pymca-tutorial A manual and a tutorial notebook on how to use PyMca to fit XRF data obtained on the beamline SIRIUS. To use the notebook first uncompress files.zip and save.zip x-ray fluorescence PyMca, XRF
GenX tutorial

howto_batch The notebook batch_genx.ipynb details the different steps on how to use GenX with command lines. The aim is to batch fits for XRR without the GUI. To do so we edit the .hgx files, which are just hdf5 files. The script batch_genx.py is a condensed script without all the details...

Scientific topics: x-ray reflectivity

Keywords: GenX, jupyter notebook, XRR

Resource type: git, jupyter notebook

GenX tutorial https://pan-training.eu/materials/genx-tutorial howto_batch The notebook batch_genx.ipynb details the different steps on how to use GenX with command lines. The aim is to batch fits for XRR without the GUI. To do so we edit the .hgx files, which are just hdf5 files. The script batch_genx.py is a condensed script without all the details from the notebook. howto_parameters Explains what are the different parameters in the GUI. x-ray reflectivity GenX, jupyter notebook, XRR
cif2hkl

A program that computes structure factors |F^2| for neutrons, x-rays, and electrons. *cif2hkl* - CrysFML based utility for generating .lau/.laz files for e.g. McStas. *Purpose* : Reads a CIF/CFL/SHX/PCR crystallographic description and generates a HKL F^2 reflection list.

Keywords: McStas, McXtrace, CrysFML, structure factor

Resource type: Git

cif2hkl https://pan-training.eu/materials/cif2hkl A program that computes structure factors |F^2| for neutrons, x-rays, and electrons. *cif2hkl* - CrysFML based utility for generating .lau/.laz files for e.g. McStas. *Purpose* : Reads a CIF/CFL/SHX/PCR crystallographic description and generates a HKL F^2 reflection list. McStas, McXtrace, CrysFML, structure factor
iFit: a simple library to analyze data

The iFit library (pronounce [eye-fit]) is a set of methods to load, analyze, plot, fit and optimize scientific data sets and models, and export results. iFit is based on Matlab, but can also be launched without Matlab license (stand-alone version).Matlab The library focuses on doing the math...

Keywords: McStas, DFT, phonons, matlab

Resource type: Git, tool

iFit: a simple library to analyze data https://pan-training.eu/materials/ifit-a-simple-library-to-analyze-data The iFit library (pronounce [eye-fit]) is a set of methods to load, analyze, plot, fit and optimize scientific data sets and models, and export results. iFit is based on Matlab, but can also be launched without Matlab license (stand-alone version).Matlab The library focuses on doing the math right. Any text file can be imported straight away, and a large set of binary files are supported. Any data dimensionality can be handled, including event based data sets (even though not all methods do work for these). Any model can be assembled for fitting data sets. McStas, DFT, phonons, matlab
Advanced infrastructure for PIDs in Photon and Neutron RIs

This deliverable accumulates results of ExPaNDS works on the topic of persistent identifiers (PIDs) in facilities research. It refers to the substantial effort of persistent identifiers adoption in facilities and in a larger research ecosystem, and provides a general guidance, as well as...

Keywords: persistent identifiers

Resource type: project deliverable

Advanced infrastructure for PIDs in Photon and Neutron RIs https://pan-training.eu/materials/advanced-infrastructure-for-pids-in-photon-and-neutron-ris This deliverable accumulates results of ExPaNDS works on the topic of persistent identifiers (PIDs) in facilities research. It refers to the substantial effort of persistent identifiers adoption in facilities and in a larger research ecosystem, and provides a general guidance, as well as prioritised recommendations for research information practitioners who consider going beyond the current levels of persistent identifiers adoption by photon and neutron research infrastructures. persistent identifiers facility staff scientists
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

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 data curator data managers research data engineer ExPaNDS and PaNOSC project members PaN users PaN Community
Report on status, gap analysis and roadmap towards harmonised and federated metadata catalogues for EU national Photon and Neutron RIs

Report on status, gap analysis and roadmap towards harmonised and federated metadata catalogues for EU national Photon and Neutron RIs

Keywords: expands, D3.1

Resource type: Document

Report on status, gap analysis and roadmap towards harmonised and federated metadata catalogues for EU national Photon and Neutron RIs https://pan-training.eu/materials/report-on-status-gap-analysis-and-roadmap-towards-harmonised-and-federated-metadata-catalogues-for-eu-national-photon-and-neutron-ris Report on status, gap analysis and roadmap towards harmonised and federated metadata catalogues for EU national Photon and Neutron RIs expands, D3.1 ExPaNDS and PaNOSC project members
PaNOSC search scoring

It illustrates how the Scoring service is designed, how to deploy it and integrate it with the local data catalogue system and the PaN Search api

Keywords: expands, PaNOSC, scoring

Resource type: github

PaNOSC search scoring https://pan-training.eu/materials/panosc-search-scoring It illustrates how the Scoring service is designed, how to deploy it and integrate it with the local data catalogue system and the PaN Search api expands, PaNOSC, scoring PaN Community ExPaNDS and PaNOSC project members data curator data managers research data engineer
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
SciCat ingestion approaches

Ingesting Data into SciCat. This manual collects various approaches for ingesting data.

Resource type: wiki

SciCat ingestion approaches https://pan-training.eu/materials/scicat-ingestion-approaches Ingesting Data into SciCat. This manual collects various approaches for ingesting data. PaN Community ExPaNDS and PaNOSC project members engineers research data engineer
Common search API definition

This document summarises the development of a common search API achieved in the PaNOSC Work Package 3. It explains the rationale behind the development and many of the decisions made as well as the general process that was followed.

Keywords: PaNOSC, expands, SciCat, ICAT

Resource type: Document

Common search API definition https://pan-training.eu/materials/common-search-api-definition This document summarises the development of a common search API achieved in the PaNOSC Work Package 3. It explains the rationale behind the development and many of the decisions made as well as the general process that was followed. PaNOSC, expands, SciCat, ICAT PaN Community ExPaNDS and PaNOSC project members engineers research data engineer data managers data curator
Demonstrate ICAT and SciCat released with APIs compatible with ExPaNDS federated EOSC services

Demonstration release of ICAT and SciCat with APIs compatible with ExPaNDS federated EOSC services and its connection to milestone Metadata catalogue as EOSC service in the domain of photon and neutron (PaN) science

Keywords: D3.3

Demonstrate ICAT and SciCat released with APIs compatible with ExPaNDS federated EOSC services https://pan-training.eu/materials/demonstrate-icat-and-scicat-released-with-apis-compatible-with-expands-federated-eosc-services Demonstration release of ICAT and SciCat with APIs compatible with ExPaNDS federated EOSC services and its connection to milestone Metadata catalogue as EOSC service in the domain of photon and neutron (PaN) science D3.3
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

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 PaN Community ExPaNDS and PaNOSC project members PaN users data curator data managers research data engineer engineers
PaNET implementation by the pan-ontologies-API RESTful service

The application provides a data catalogue independent implementation retrieval and processing of ontologies from an external source. Currently, only the PaNET ontology is implemented. Below is a schematic data flow depicting the role of the pan-ontologies-api.

Keywords: expands, PaNOSC, data catalogue, ontology

Resource type: git, github, Git Project

PaNET implementation by the pan-ontologies-API RESTful service https://pan-training.eu/materials/pan-ontologies-api The application provides a data catalogue independent implementation retrieval and processing of ontologies from an external source. Currently, only the PaNET ontology is implemented. Below is a schematic data flow depicting the role of the pan-ontologies-api. expands, PaNOSC, data catalogue, ontology PaN Community ExPaNDS and PaNOSC project members
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

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 facility staff
h5web: stand-alone, web-based viewer to explore HDF5 files

H5Web is a collection of React components to visualize and explore data. It consists of two packages: - @h5web/lib: visualization components built with react-three-fiber. - @h5web/app: a stand-alone, web-based viewer to explore HDF5 files.

Keywords: hdf5, Visualization

Resource type: tool

h5web: stand-alone, web-based viewer to explore HDF5 files https://pan-training.eu/materials/h5web-stand-alone-web-based-viewer-to-explore-hdf5-files H5Web is a collection of React components to visualize and explore data. It consists of two packages: - @h5web/lib: visualization components built with react-three-fiber. - @h5web/app: a stand-alone, web-based viewer to explore HDF5 files. hdf5, Visualization
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

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 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

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
ExPaNDS Guidance Note: Key Policy Elements within a Photon and Neutron Research Infrastructure Data Policy Framework (revised - final version)

The text of this ExPaNDS Guidance Note is extracted from ExPaNDS deliverable [D2.3: Final data policy framework for Photon and Neutron RIs](https://doi.org/10.5281/zenodo.5205824). The Guidance Note covers the 21 elements that comprise the final version of the ExPaNDS data policy framework. These...

Keywords: data policy, expands, FAIR

Resource type: Document

ExPaNDS Guidance Note: Key Policy Elements within a Photon and Neutron Research Infrastructure Data Policy Framework (revised - final version) https://pan-training.eu/materials/expands-guidance-note-key-policy-elements-within-a-photon-and-neutron-research-infrastructure-data-policy-framework-revised-final-version The text of this ExPaNDS Guidance Note is extracted from ExPaNDS deliverable [D2.3: Final data policy framework for Photon and Neutron RIs](https://doi.org/10.5281/zenodo.5205824). The Guidance Note covers the 21 elements that comprise the final version of the ExPaNDS data policy framework. These elements fall under nine broad themes: 1. General drivers and principles 2. Roles and responsibilities 3. Scope 4. Enabling FAIR data 5. Necessary restrictions to data sharing 6. Availability of infrastructure and responsibility for costs 7. Data management planning requirements 8. Recognition and reward for data usage 9. Reporting requirements, compliance monitoring, and any possible sanctions The Guidance Note is intended as a short-form, ready-access tool for policy makers working on data policy within Photon and Neutron Research Infrastructures. For additional context around the development of the ExPaNDS data policy framework, see the D2.3 deliverable and its earlier, draft version [D2.1: Draft extended data policy framework for photon and neutron RIs](https://doi.org/10.5281/zenodo.4014811). data policy, expands, FAIR
RDMO - Research Data Management Organiser

A tool to support the planning, implementation, and organisation of research data management.

Keywords: FAIR, DMP

Resource type: tool

RDMO - Research Data Management Organiser https://pan-training.eu/materials/rdmo-research-data-management-organiser A tool to support the planning, implementation, and organisation of research data management. FAIR, DMP data curator research data scientist research data engineer instrument scientist PaN users
PaNdata software catalogue

PaNdata software catalogue is a database of software used mainly for data analysis of neutron and photon experiments.

Scientific topics: photon and neutron technique, crystallography, imaging, macromolecular crystallography, nuclear resonant scattering, powder diffraction, ptychography, radiotherapy, small angle x-ray scattering, small angle inelastic scattering, single crystal diffraction, surface crystallography, tomography

Keywords: software, FAIR, catalogue

Resource type: tool

PaNdata software catalogue https://pan-training.eu/materials/pandata-software-catalogue PaNdata software catalogue is a database of software used mainly for data analysis of neutron and photon experiments. photon and neutron technique crystallography imaging macromolecular crystallography nuclear resonant scattering powder diffraction ptychography radiotherapy small angle x-ray scattering small angle inelastic scattering single crystal diffraction surface crystallography tomography software, FAIR, catalogue scientists neutron community Photon Community research data scientist