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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, wp2-ExPaNDS

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, wp2-ExPaNDS 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, 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
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, wp3-ExPaNDS

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, wp3-ExPaNDS 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, wp3-ExPaNDS

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, wp3-ExPaNDS 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, wp3-ExPaNDS

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, wp3-ExPaNDS
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
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, wp3-ExPaNDS

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, wp3-ExPaNDS 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, 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
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, 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
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, wp2-ExPaNDS

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, wp2-ExPaNDS
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
Outreach videos about experiments done at ALBA

Here you will find a series of videos about the different applications of synchrotron light. Videos are in Spanish and Catalan, although subtitles are available in English, Catalan and Spanish. Its aim is to transmit in a simple and understandable way a selection of the applications that can...

Keywords: synchrotron, synchrotron light, applications

Resource type: video

Outreach videos about experiments done at ALBA https://pan-training.eu/materials/outreach-videos-about-experiments-done-at-alba Here you will find a series of videos about the different applications of synchrotron light. Videos are in Spanish and Catalan, although subtitles are available in English, Catalan and Spanish. Its aim is to transmit in a simple and understandable way a selection of the applications that can have the synchrotron light in different scientific fields: health, food, environment, cultural heritage, etc. These videos are part of the project FCT-15-9828 "Bringing science to society – Outreach science program of the ALBA Synchrotron", funded by the Spanish Foundation for Science and Technology (FECYT) - Ministry of Economy and Competitiveness and the Foundation Obra Social "la Caixa". synchrotron, synchrotron light, applications general public
Tour of MAX IV accelerators with professor Sverker Werin

Join us in the tour of MAX IV Laboratory's accelerators hosted by Sverker Werin, professor in accelerator physics at Lund University and MAX IV. The electron guns 00:24 Along the linear accelerator 2:59 The bunch compressor 4:42 The 1.5 GeV ring extraction point 5:47 The modulators and...

Keywords: synchrotron, accelerator physics

Resource type: video

Tour of MAX IV accelerators with professor Sverker Werin https://pan-training.eu/materials/tour-of-max-iv-accelerators-with-professor-sverker-werin Join us in the tour of MAX IV Laboratory's accelerators hosted by Sverker Werin, professor in accelerator physics at Lund University and MAX IV. The electron guns 00:24 Along the linear accelerator 2:59 The bunch compressor 4:42 The 1.5 GeV ring extraction point 5:47 The modulators and klystrons 7:03 In the 3.0 GeV storage ring 8:13 The undulators in the 3.0 GeV rings 10:50 The start of the photon beam 11:57 Topping up energy in the storage ring 12:42 In the MAX IV accelerator exhibition 13:39 synchrotron, accelerator physics PaN Community beamline users
Remote operations at BioMAX

BioMAX is a state-of-the-art macromolecular crystallography beamline at MAX IV, the first beamline to open its doors in 2017. Since 2019, BioMAX allows users to perform experiments from remote locations. Users login remotely into BioMAX computers and have full control over the experiments. In...

Keywords: remote operations, automation, diffraction experiments

Resource type: video

Remote operations at BioMAX https://pan-training.eu/materials/remote-operations-at-biomax BioMAX is a state-of-the-art macromolecular crystallography beamline at MAX IV, the first beamline to open its doors in 2017. Since 2019, BioMAX allows users to perform experiments from remote locations. Users login remotely into BioMAX computers and have full control over the experiments. In this video, Ana Gonzalez, BioMAX beamline manager, walks us through a cycle of automated, remote-controlled diffraction experiments. Read more about remote experiments at BioMAX: https://www.maxiv.lu.se/news/biomax-remote-experiments/ remote operations, automation, diffraction experiments beamline users
IR spectromicroscopy and imaging with six decades of dynamic range

Speaker: Dr Ferenc Borondics, SMIS Beamline Manager, SOLEIL, France Infrared spectroscopy has been in scientists’ toolbox for more than a century to obtain information about vibrational properties and low energy electrodynamics of materials. The beginning of the 80s brought the first...

Keywords: infrared spectromicroscopy, imaging

Resource type: video

IR spectromicroscopy and imaging with six decades of dynamic range https://pan-training.eu/materials/ir-spectromicroscopy-and-imaging-with-six-decades-of-dynamic-range Speaker: Dr Ferenc Borondics, SMIS Beamline Manager, SOLEIL, France Infrared spectroscopy has been in scientists’ toolbox for more than a century to obtain information about vibrational properties and low energy electrodynamics of materials. The beginning of the 80s brought the first commercial infrared microscopes to look into fine details. Far-field infrared spectromicroscopy had been pushed to its limits in the 90s at synchrotron facilities by exploiting the unrivaled quality of synchrotron radiation, i.e., low angular divergence and extremely high bandwidth. Synchrotron infrared spectromicroscopy beamlines provide diffraction-limited spatial resolution covering the whole IR range and enable experiments impossible otherwise. Later, the implementation of two-dimensional IR detectors allowed hyperspectral imaging of large samples with high spatial resolution. The turn of the century brought the advent of near-field IR techniques breaking through the diffraction limit. Combining high-brightness IR sources with atomic force microscopes to detect photothermal expansion or near-field scattering allows measurements hundreds of times below the diffraction limit reaching as high as ten-nanometer spatial resolution. Optically sampled photothermal spectromicroscopy has recently become available to bridge the resolution gap between the nanometer and micrometer range. We combine these techniques at the SMIS beamline to enable six orders of magnitude spatial dynamic range in infrared spectromicroscopy and support scientific discovery by exploiting the synchrotron source through commercial and custom instrumentation. In this talk, I will highlight discoveries made by SMIS staff and users enabled by the beamline’s capability and comment on the benefits of emerging, alternative sources. infrared spectromicroscopy, imaging PaN Community beamline users scientists
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
Learning pack: The synchrotron and its lights

The machine and beamlines, optical devices, magnetism vacuum and information about the analytic techniques applied on a synchrotron and through examples of studies carried out at the synchrotron SOLEIL.

Scientific topics: extended x-ray absorption fine structure, absorption spectroscopy

Keywords: synchrotron, optics, monochromators, magnetic fields, ultra-high vacuum, applications, xanes & exafs

Resource type: Document

Learning pack: The synchrotron and its lights https://pan-training.eu/materials/learning-pack-the-synchrotron-and-its-lights The machine and beamlines, optical devices, magnetism vacuum and information about the analytic techniques applied on a synchrotron and through examples of studies carried out at the synchrotron SOLEIL. extended x-ray absorption fine structure absorption spectroscopy synchrotron, optics, monochromators, magnetic fields, ultra-high vacuum, applications, xanes & exafs general public masters students
Learning pack: Synchrotron light

What are the devices and physical phenomena used to emit synchrotron light? An educational introduction to the synchrotron sources. Poster "Exploring matter by the light of SOLEIL"

Keywords: synchrotron light

Resource type: Poster

Learning pack: Synchrotron light https://pan-training.eu/materials/learning-pack-synchrotron-light What are the devices and physical phenomena used to emit synchrotron light? An educational introduction to the synchrotron sources. Poster "Exploring matter by the light of SOLEIL" synchrotron light general public
Learning pack: Optics

What optic devices are used to direct light, concentrate it and select a wavelength? Do they all involve the same technology? An educational introduction to optical instruments. Poster "Optical instruments suited to the light of the SOLEIL"

Keywords: synchrotron, optical instruments

Resource type: Poster

Learning pack: Optics https://pan-training.eu/materials/learning-pack-optics What optic devices are used to direct light, concentrate it and select a wavelength? Do they all involve the same technology? An educational introduction to optical instruments. Poster "Optical instruments suited to the light of the SOLEIL" synchrotron, optical instruments general public