vDiffraction: A serious game about diffraction and crystals
#### This game is a fun way to discover the world of crystals and their symmetries through diffraction.
Crystals are all around us: in our environment (rocks and minerals, etc), in our bodies (sugar, bones, gallstones, etc.) and in technology (metals and alloys, silicon and quartz used for...
Scientific topics: crystallography
Keywords: game, diffraction, crystal diffraction, software
Resource type: game
vDiffraction: A serious game about diffraction and crystals
https://www.ill.eu/users/support-labs-infrastructure/software-scientific-tools/vdiffraction
https://pan-training.eu/materials/vdiffraction-a-serious-game-about-diffraction-and-crystals
#### This game is a fun way to discover the world of crystals and their symmetries through diffraction.
Crystals are all around us: in our environment (rocks and minerals, etc), in our bodies (sugar, bones, gallstones, etc.) and in technology (metals and alloys, silicon and quartz used for microelectronics, etc.). By successively discovering the diffraction of X-rays, neutrons and electrons, scientists in the twentieth century threw the door to the microscopic world wide open by demonstrating that crystals are made up of atoms and molecules and explaining their structure.
Crystals are characterised by the fact that their constituents are arranged in a highly ordered structure. This internal order and its symmetry is clearly visible in the diffraction patterns produced by any crystal. It is this symmetry which is also gives crystals their often amazing shapes, making them highly prized by rockhounds.
Whether you are a senior scientist, a student, or just curious about science, vDiffraction is a serious game that will let you try your hand at crystal diffraction so that you can begin to understand how scientists identify the symmetry characteristics of a crystal. This is the first, crucial step towards understanding the atomic and molecular structure of a crystalline material, in other words what type of atoms and molecules make up the crystal and how they are organised.
crystallography
game, diffraction, crystal diffraction, software
Machine learning in electronic-structure theory
Machine Learning approaches are increasingly being used across many fields of science, with electronic structure theory being no exception. They offer novel approaches to age-old problems. In recent years they have been used in construction of trial wavefunctions, in computing Hamiltonians, and...
Keywords: machine learning, electronic-structure theory
Resource type: video
Machine learning in electronic-structure theory
https://www.youtube.com/watch?v=Sgp0w74k9kQ
https://pan-training.eu/materials/machine-learning-in-electronic-structure-theory
Machine Learning approaches are increasingly being used across many fields of science, with electronic structure theory being no exception. They offer novel approaches to age-old problems. In recent years they have been used in construction of trial wavefunctions, in computing Hamiltonians, and in direct calculation of properties and forces.
These methods are highly versatile and computationally efficient, yet many questions regarding their interpretability and ability to extrapolate information remains unanswered.
How are they being used in electronic structure theory today, and how do they fit into the bigger picture? Would electronic structure theory have looked anything different if it was conceived in the age of machine learning? This seminar seeks to answer these kinds of questions, and was originally given as a trial lecture at the Hylleraas Centre of Quantum Molecular Sciences at the University of Oslo.
machine learning, electronic-structure theory
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://www.youtube.com/watch?v=eL63fo5O-vk
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://www.youtube.com/watch?v=G-vPWwh5NKs
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
Observation of the transition to metal hydrogen
Video from the joint ESRF-ILL colloquia.
Understanding how and when molecular solid hydrogen may transform into a metal has stimulated many theoretical works since the 30’s.
It is still an opened theoretical question and an experimental challenge. The quest for metal hydrogen has pushed major...
Keywords: metal hydrogen, high pressure, insulator-metal phase transition
Observation of the transition to metal hydrogen
https://www.youtube.com/watch?v=XVt2sOUuNh0
https://pan-training.eu/materials/observation-of-the-transition-to-metal-hydrogen
Video from the joint ESRF-ILL colloquia.
Understanding how and when molecular solid hydrogen may transform into a metal has stimulated many theoretical works since the 30’s.
It is still an opened theoretical question and an experimental challenge. The quest for metal hydrogen has pushed major developments of modern experimental high pressure physics and still various claims of its observation have remained unconfirmed. In 2020, we observed and characterized the transition to metal hydrogen near 425 GPa at 80 K [1]. Very recently, the transition to metal deuterium has also been observed, showing a significant isotopic shift in pressure. In this talk, our experimental strategy will be presented as following three steps namely:
1) Demonstrate the possibility to generate pressures well over 400 GPa ( that is the limit of the conventional Diamond Anvil Cell (DAC)) by loading hydrogen in the recently developed Toroidal-DAC[2];
2) Exhibit a reliable non-intrusive signature of the insulator-metal phase transition, i.e. total IR absorption by using the IR synchrotron radiation at SOLEIL;
3) Record combined infrared, Raman and visible observation measurements to disclose the physics at stake at the insulator-metal transition.
On-going experimental developments to further characterize the intriguing properties of metal hydrogen will be discussed.
[1] Synchrotron infra-red spectroscopic evidence of the probable transition to metal hydrogen. P. Loubeyre, F. Occelli and P. Dumas. Nature 577, 631 (2020).
[2] Toroidal diamond anvil cell for fine measurements under extreme static pressures: data on Al, Ar and Au up to 603 GPa. A. Dewaele, P. Loubeyre, F. Occelli, O. Marie and M. Mezouar. Nature Com. 9, 2913 (2018).
metal hydrogen, high pressure, insulator-metal phase transition
The European XFEL: start of user operation
Video from the joint ESRF-ILL colloquia.
In the past decade we have seen very important developments in the field of accelerator based X-ray user facilities, with the advent of 4th generation synchrotron sources and MHz rate free electron lasers. The first hard X-ray free-electron laser,...
Keywords: XFEL, free-electron laser
Resource type: video
The European XFEL: start of user operation
https://www.youtube.com/watch?v=JcM41wYx_Fw
https://pan-training.eu/materials/the-european-xfel-start-of-user-operation
Video from the joint ESRF-ILL colloquia.
In the past decade we have seen very important developments in the field of accelerator based X-ray user facilities, with the advent of 4th generation synchrotron sources and MHz rate free electron lasers. The first hard X-ray free-electron laser, LCLS (US) became operational in 2009 and over the last decade four additional hard X-ray FELs have begun user operation. Among these, the Eu-XFEL is the first hard XFEL powered by a superconducting linear accelerator, which enables MHz rate pulse generation. A specificity of XFELs is their very short pulse duration (10-100fs) opening new scientific opportunities to probe matter at the atomic scale, with chemical selectivity and bulk sensitivity, and at the relevant timescales.
After many years of construction, user operation at the Eu-XFEL ramped up gradually, and between 2017 and 2019 six instruments were delivered to the user community. In this talk I will first briefly introduce the present performance of the facility in terms of electron and photon beam characteristics. I will then give an overview of recent science highlights and comment on some important challenges ahead.
XFEL, free-electron laser
Lecture Series "Basics of Macromolecular Crystallography"
In the first lecture in the lecture Series "Basics of Macromolecular Crystallography", Andrea Thorn gives an overview of protein crystallization, some of its theoretical foundation and lots of practical advice on how (and how not) to crystallize your protein.
The lecture was held on the 9th of...
Scientific topics: macromolecular crystallography
Keywords: Macromolecular Crystallography, crystallography
Resource type: video
Lecture Series "Basics of Macromolecular Crystallography"
https://www.youtube.com/watch?v=mDbmfyOGLIM
https://pan-training.eu/materials/lecture-series-basics-of-macromolecular-crystallography
In the first lecture in the lecture Series "Basics of Macromolecular Crystallography", Andrea Thorn gives an overview of protein crystallization, some of its theoretical foundation and lots of practical advice on how (and how not) to crystallize your protein.
The lecture was held on the 9th of June 2020 via Zoom and attended by 40 participants from different institutions/countries.
See below for the following parts of the lecture.
macromolecular crystallography
Macromolecular Crystallography, crystallography
FAIR Metadata Workshop
Presentation of the ExPaNDS draft metadata framework for FAIR Photon and Neutron (PaN) data.
Keywords: FAIR, metadata, wp2-ExPaNDS
Resource type: video
FAIR Metadata Workshop
https://vimeo.com/685211186
https://pan-training.eu/materials/fair-metadata-workshop
Presentation of the ExPaNDS draft metadata framework for FAIR Photon and Neutron (PaN) data.
FAIR, metadata, wp2-ExPaNDS
PaN Community
ExPaNDS and PaNOSC project members
Cryo electron microscopy
An introduction to the Diamond Light Source cryo-electron microscope facilities.
Scientific topics: cryo x-ray microscopy
Keywords: cryo-electron tomography, single particle analysis
Resource type: video
Cryo electron microscopy
https://vimeo.com/317009040
https://pan-training.eu/materials/cryo-electron-microscopy
An introduction to the Diamond Light Source cryo-electron microscope facilities.
cryo x-ray microscopy
cryo-electron tomography, single particle analysis
Electronic Structure Interpretation from XANES
Introduction to XANES and Metal K-pre-edge XAS analysis to obtain electronic structure information such as symmetry, ligand-field, bonding.
Scientific topics: x-ray absorption near edge structure, x-ray absorption
Keywords: xanes, XAS
Resource type: video
Electronic Structure Interpretation from XANES
https://www.youtube.com/watch?v=T_5Wu3UjxU0
https://pan-training.eu/materials/electronic-structure-interpretation-from-xanes
Introduction to XANES and Metal K-pre-edge XAS analysis to obtain electronic structure information such as symmetry, ligand-field, bonding.
x-ray absorption near edge structure
x-ray absorption
xanes, XAS
Introduction to the Practical Aspects of XAS and EXAFS data Measurement.
A practical guide on how to get prepared to measure distortion free XAS data.
Scientific topics: x-ray absorption, extended x-ray absorption fine structure
Keywords: ssrl, XAS, exafs
Resource type: video
Introduction to the Practical Aspects of XAS and EXAFS data Measurement.
https://www.youtube.com/watch?v=xpv5-DLzX1g
https://pan-training.eu/materials/introduction-to-the-practical-aspects-of-xas-and-exafs-data-measurement
A practical guide on how to get prepared to measure distortion free XAS data.
x-ray absorption
extended x-ray absorption fine structure
ssrl, XAS, exafs
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://xafs.xrayabsorption.org/tutorials.html
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://gitlab.com/soleil-data-treatment/soleil-beamlines/soleil-beamline-sirius/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://gitlab.com/soleil-data-treatment/soleil-beamlines/soleil-beamline-sirius/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://vimeo.com/340202552
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://www.youtube.com/watch?v=a-jE7BM902Q
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://www.youtube.com/watch?v=-unHRyx0gOE
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://www.youtube.com/watch?v=x_3gEDKy6KQ
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://www.youtube.com/watch?v=BTHpau2ok-8
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://gitlab.com/soleil-data-treatment/soleil-beamlines/soleil-beamline-sirius/tutorials/tutorial_edit_nexus/-/blob/main/howto_edit_nexus.ipynb
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://gitlab.com/soleil-data-treatment/soleil-beamlines/soleil-beamline-sirius/tutorials/tutorial_pymca/-/blob/main/PyMca_User_Manual.pdf
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://gitlab.com/soleil-data-treatment/soleil-beamlines/soleil-beamline-sirius/tutorials/tutorial_genx
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://gitlab.com/soleil-data-treatment/soleil-software-projects/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://gitlab.com/soleil-data-treatment/soleil-software-projects/ifit
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://zenodo.org/record/5905351#.Yk6-5S8RoeY
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://zenodo.org/record/6414117
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://zenodo.org/record/4146819
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://github.com/panosc-eu/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://indico.desy.de/event/30039/
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.
SciCat ingestion approaches
https://scicatproject.github.io/documentation/Ingestor/
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