In the series of workshops on FAIR services for research data that OpenAIRE is jointly organizing with FAIRsFAIR, EOSC hub and RDA-Europe, the second workshop took place as a part of the larger event ‘Linking Open Science in Austria’. The series of workshops explores: how data infrastructures can work together to meet the challenges of creating, managing, opening and archiving FAIR data.
The aim of the workshops is to:
Look at the landscape of data infrastructures looking to integrate FAIR into their services
Set initial recommendations and to find out what the challenges and priorities are
Jupyter provides a powerful environment for expressing research ideas as notebooks, where code, test and visualizations are easily combined together on an interactive web-frontend. JupyterHub allows to deploy a multi-user service where users can store and run their own notebooks without the need of installing anything on their computers. This is the technology behind the EGI Notebooks service and other similar Jupyter-based services for research.
In this training we will demonstrate how to deploy a JupyterHub instance for your users on top of Kubernetes and explore some of the possible customisations that can improve the service towards your users like integration with authentication services or with external storage systems. After this training, the attendees will be able to deploy their own instance of JupyterHub on their facilities.
Target audience: Resource Center/e-Infrastructure operators willing to provide Jupyter environment for their users.
Pre-requisites: basic knowledge of command-line interface on Linux.
In the hands-on session, the participants will be provided with a VM infected with the 'malware' used in SSC-19.03. They will then be guided through the methods necessary to solve the challenges built into the simulated attack
Elastic Cloud Computing Cluster (EC3) is a tool to create elastic virtual clusters on top of Infrastructure as a Service (IaaS) providers, either public (such as Amazon Web Services, Google Cloud or Microsoft Azure) or on-premises (such as OpenNebula and OpenStack). We offer recipes to deploy TORQUE (optionally with MAUI), SLURM, SGE, HTCondor, Mesos, Nomad and Kubernetes clusters that can be self-managed with CLUES: it starts with a single-node cluster and working nodes will be dynamically deployed and provisioned to fit increasing load (number of jobs at the LRMS). Working nodes will be undeployed when they are idle. This introduces a cost-efficient approach for Cluster-based computing.
The target group of the training is developers and administrators of services that want to integrate to ELIXIR AAI for user authentication and authorisation. The training has hands-on sessions for the participants to integrate their own service (or, a test service provided by the trainers) to ELIXIR AAI.
Keywords: AAI, OpenID Connect, Authentication
Target audience: service administrators in organizations that want to make use of ELIXIR AAI
Difficulty level: Intermediate
Authors: Michal Prochazka, Dominik Frantisek Bucik
The main objective of this webinar is to show how the CompBioMed community can use the EOSC services for managing active research data (i.e. data transfer, storage, and sharing) and for preserving final research data (i.e. data archiving and publishing). In this webinar, we give a brief overview of the EUDAT Services and the data life cycle. We further demonstrate how these services operate and integrate with each other to meet the data management requirements of research communities and comply with the FAIR principles – which require the data to be properly documented, annotated, archived, published and accessible to the wider community.
Target audience: community researchers, data managers and the IT support people.
The first tutorial demonstrates the use of cross-linking data from mass spectrometry to guide protein-protein docking in HADDOCK.
The second tutorial illustrates how metadynamics can be used to sample conformations of a binding pocket; those are subsequently used for docking a ligand using HADDOCK. The conformational sampling approach is following the EDES approach described in the following publication:
This webinar will introduce the Service Management System based on the FitSM standard for IT Service Management developed and deployed by EOSC-hub for EOSC, with a particular focus on the Service Portfolio Management as a key and highly strategic process. The structure of the EOSC Service Portfolios will be also presented.
This webinar will describe the Reference Technical Architecture for EOSC proposed by EOSC-hub during the recent EOSC-hub Technical Workshop.
The proposed architecture is based on the concepts of service composability and interoperability. Service categories and relationships between them will be presented. The process to define interoperability guidelines for different technical areas will be also depicted.
Who should attend:
Service providers, Users, members of other EOSC implementation projects including EOSC cluster projects, members of EOSC working groups, European and national e-infrastructures, European and national research infrastructures
Key Takeaways for attendees
EOSC Technical Reference architecture proposed by EOSC-hub
Classification of services within EOSC
Status of the EOSC-hub work to define interoperability guidelines for EOSC macro-features (Federating core, AAI, Cloud and Container computing, FAIR data management, etc.)
DisVis is a software developed in our lab to visualise and quantify the information content of distance restraints between macromolecular complexes. It is open-source and available for download from our Github repository. To facilitate its use, we have developed a web portal for it.
This tutorial demonstrates the use of the DisVis web server. The server makes use of either local resources on our cluster, using the multi-core version of the software, or GPGPU-accelerated grid resources of the EGI to speed up the calculations. It only requires a web browser to work and benefits from the latest developments in the software based on a stable and tested workflow. Next to providing an automated workflow around DisVis, the web server also summarises the DisVis output highlighting relevant information and providing a first overview of the interaction space between the two molecules with images autogenerated in UCSF Chimera.
The case we will be investigating is the interaction between two proteins of the 26S proteasome of S. pombe, PRE5 (UniProtKB: O14250) and PUP2 (UniProtKB: Q9UT97). For this complex seven experimentally determined cross-links (4 ADH & 3 ZL) are available (Leitner et al., 2014). We added two false positive restraints - it is your task to try to identify these! For this, we use DisVis to try to filter out these false positive restraints while assessing the true interaction space between the two chains. We will then use the interaction analysis feature of DisVis that allows for a more complete analysis of the residues putatively involved in the interaction between the two molecules. To do so, we will extract all accessible residues of the two partners, and give the list of residues to DisVis using its interaction analysis feature. Finally, we will show how the restraints can be provided to HADDOCK in order to model the 3D interaction between the 2 partners.
Characterizing the structure of macromolecular complexes is crucial for understanding their function. For many complexes, however, solving their structure using a single structural biology technique is very challenging.
The MEDCOAST congress in Marmaris (Turkey) is the fourteenth event of the biennial series that was started in 1993 for contributing to coastal and marine sciences, engineering, management and conservation particularly in the Mediterranean and the Black Sea. Since the first event in 1993 (Antalya
IT Service Management is a discipline that helps provide services with a focus on customer needs and in a professional manner. It is widely used in the commercial and public sectors to manage IT services of all types, but current solutions are very heavyweight with high barriers to entry.
T Service Management is a discipline that helps provide services with a focus on customer needs and in a professional manner. It is widely used in the commercial and public sectors to manage IT services of all types, but current solutions are very heavyweight with high barriers to entry.
EOSC-hub receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 777536.