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Keywords: VISA 

Access tomotools from visa.esrf.fr

Short description on how to: - connect to visa.esrf.fr (the ESRF's Virtual Research Environment) - create an instance (if needed) - load 'tomotools' module - run a simple reconstruction with nabu from CLI - display the reconstruction with silx view - unload the module

Scientific topics: tomography

Keywords: tomography, tomotools, nabu, VISA

Resource type: video

Access tomotools from visa.esrf.fr https://pan-training.eu/materials/access-tomotools-from-visa-esrf-fr Short description on how to: - connect to visa.esrf.fr (the ESRF's Virtual Research Environment) - create an instance (if needed) - load 'tomotools' module - run a simple reconstruction with nabu from CLI - display the reconstruction with silx view - unload the module tomography tomography, tomotools, nabu, VISA
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
Containerized Serial Crystallography “CrystFEL” VISA workflow

Experiments generate up to 150 TB per day of data saved at the measurement facility. Such large datasets are impractical for users to take home. Subsequent analysis needs to be performed remotely making it attractive for deployment as a cloud-like use case. Involving EOSC in the analysis and...

Scientific topics: crystallography

Keywords: CrystFEL, Serial crystallography, pulsed X-ray beam, VISA

Resource type: workflow

Containerized Serial Crystallography “CrystFEL” VISA workflow https://pan-training.eu/materials/containerized-serial-crystallography-crystfel-visa-workflow Experiments generate up to 150 TB per day of data saved at the measurement facility. Such large datasets are impractical for users to take home. Subsequent analysis needs to be performed remotely making it attractive for deployment as a cloud-like use case. Involving EOSC in the analysis and re-use of this data is an appropriate use case. Serial crystallography is a beam-line technique for collecting information on the structure of a protein without growing large protein crystals. Instead, a large number of small protein crystals are held in a pulsed X-ray beam. In a second step, the series of produced images are used to reconstruct a precise 3-D image of the protein structure. Serial crystallography is the preferred technique for obtaining diffraction data of proteins at room temperature, where radiation damage from the X-ray beam starts rapidly. The standard software for analysing serial crystallography is “CrystFEL”. The proposed workflow was rendered in a standard fashion, which would allow it to be easily adopted by arbitrary systems or also other containerized applications. The only requirements are an Apptainer installation on the system and a Docker or Singularity/Apptainer image of the application, as well as an adjustment of the configuration file for the wrapper script. crystallography CrystFEL, Serial crystallography, pulsed X-ray beam, VISA research data scientist scientific
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