Presentations

This document provides guidance for understanding and implementing the set of workflows included in this collection. It outlines best practices and recommendations to ensure successful setup and execution of automated and real-time image processing pipelines.

Guidelines for using Scipion in the context of on-the-fly image processing at cryo-EM facilities. This document is divided into three main sections:

• On-the-fly processing: Monitoring data acquisition in real time.

• Processing workflows and templates: Building familiarity with creating and customizing workflows and templates in Scipion.

• Scipion with queue systems: Demonstrating Scipion’s behavior and integration with SLURM-based queueing systems.

High-Performance Computing (HPC) environments are integral to quantum chemistry and computationally intense research, yet their complexity poses challenges for non-HPC experts. Navigating these environments proves challenging for researchers lacking extensive computational knowledge, hindering efficient use of domain specific research software. The prediction of mass spectra for in silico annotation is therefore inaccessible for many wet lab scientists. Our main goal is to facilitate non-experts ...

To make your workflow FAIR (Findable, Accessible, Interoperable, Reusable), register it in WorkflowHub, a workflow registry with rich metadata capture for workflow discovery and sharing, and value-added services, for workflow testing (LifeMonitor), execution and publication.

The EuroScienceGateway, Biodiversity Genomics Europe and BioDT projects will use WorkflowHub to organise, share and publish their workflows.

This was Ask Me Anything and Bring Your Own Workflow (AMA & BYOW) specifically ...

Provenance registration is becoming more and more important, as we increase the size and number of experiments performed using computers. In particular, when provenance is recorded in HPC environments, it must be efficient and scalable. In this paper, we propose a provenance registration method for scientific workflows, efficient enough to run in supercomputers (thus, it could run in other ...

Session during the Innovative HPC workflows for industry (https://eflows4hpc.eu/event/innovative-hpc-workflows-for-industry/) that describes how Workflow Provenance is recorded with COMPSs: the background on the tools used, how the recording has been designed, and how to use it and inspect metadata.

This document provides a detailed explanation of all the workflows, including their functionalities, problems they address, advantages, disadvantages, implementation requirements, and open points for future versions.

In the age of high-throughput data, computational workflows have made data processing tasks flexible, manageable, and automated. To administer different computational activities in a workflow, different workflow management systems (WMS) are used that necessitate a sophisticated level of standardisation. Standardisation and reproducibility can be achieved by using standard formats for specifying workflows, such as Common Workflow Language (CWL), and provenance gathering with the standard W3C PROV ...

Presented at Swedish eResearch Centre meeting, 13 may 2022