EOSC Activities and Projects

What is EOSC?

The European Open Science Cloud (EOSC) is an environment, governed by the EOSC Association, meant to federate existing research data infrastructures in Europe and realise a web of FAIR data and related services for science, making research data interoperable and machine actionable following the FAIR guiding principles.

Involvement of Instruct-ERIC in EOSC-related activities and projects

Instruct-ERIC is a partner in the EOSC Association and several EOSC-related projects such as EOSC-Life, providing valuable insight and assistance in developing the EOSC environment. As structural biology is an integral component of the life science network, Instruct’s contribution to the EOSC can provide meaningful benefits to the cloud usage of the European science community.

EOSC-Life

EOSC-Life brings together 13 Life Science Research Infrastructures (RIs) to create an open, digital and collaborative space for data resources and data processing workflows in the European Open Science Cloud (EOSC).

Key resources and services developed by EOSC-Life:

WorkflowHub: A Federated Registry of scientific workflows

WorkflowHub is a federated workflow registry developed by EOSC-Life that aims to aggregate established tools, workflows and registries and thus facilitate the discovery and re-use of tools and workflows over a fragmented ecosystem.
 
Workflowhub aims to: 

• support a common API to simplify access for tool developers.
• Increase Interoperability and re-use of workflows by using Standardised workflow identifiers and metadata descriptions
• Facilitate and promote workflow snapshot preservation, publishing, citation, monitoring and credit claiming

Register your workflow or find additional details about the Workflowhub: https://workflowhub.eu

EOSC-Life roadmap

Identifying Interoperable Computational tools and workflows for European Life scientists

EOSC-Life aims to make computational tools and workflows used in the European Life sciences Research Infrastructures interoperable in a common cloud environment.
 
EOSC-Life proposes to unify tools and workflows registries used by our community of scientists into a common discoverability environment by focusing on a limited number of components and tools that will become standards for all
 
This EOSC-Life roadmap represents the current vision of what the common cloud environment could look like

Life Science Login

An authentication service from EOSC-Life

LS Login allows users to access multiple Life Science services through a common Life Science login.

Learn more about LS LOGIN and register: lifescience-ri.eu/ls-login.html

Towards FAIR and open science in the field of structural biology

Pilot projects from Instruct members supported by EOSC-Life:

Fragalysis: a web-based platform for fragment-based drug discovery

The Fragalysis platform was developed in Diamond Light Source, with the support of EOSC-life to enable rapid access to data from fragment screens in a collaborative environment. Fragalysis is a ligand centric platform that provides information regarding ligands and their targets. New screening data can be shared on the platform and the release of structures from new fragment screens to the worldwide community can be done almost in real time as demonstrated during the Covid19 pandemics. The sharing of data thanks to the sophisticated data visualisation tools and the design of molecules is also facilitated in Fragalysis.

Increasing the FAIRness of data and image processing workflows in Cryo Electron Microscopy

Professor Sorzano and Colleagues from Instruct Centre Spain with the support of EOSC-Life developed a new method to handle Cryo-EM data in order to increase the FAIR principles in Cryo-EM microscopy from the moment of data acquisition. This data acquisition and dissemination process aims to allow full traceability and improves reproducibility of results in the Cryo-EM field by making available raw and intermediate data, as well as a JSON file fully describing the executed workflow (including the different steps of the workflow, the parameters used and the results).

IceBear: a research data management tool for structural biology

IceBear is developed at the Instruct Centre Finland at the University of Oulu. It facilitates the management of your data from the crystallisation of your macromolecules of interest to the PDB deposition.

IceBear currently covers
1) crystallization trials,
2) crystal fishing and shipping,
3) linking crystals, datasets, and PDB depositions for full chain of custody.

It gives you a highly task-focused interface and a flexible access rights system. And it's FREE to download and install in your lab.

To find more details about Icebear, try the demo version and install Icebear for free: http://www.icebear.fi/

PDB-REDO Cloud

Instruct members from NKI, Instruct Centre NL, received funding from EOSC-life for two independent projects in order to improve the PDB-REDO platform that aims at optimising crystallographic structure models.

The goal of these two projects is:

1) increase the FAIRness and the reproducibility of the protein structures models optained through PDB-REDO

2) deploy the PDB-REDO engine on the cloud to provide a flexible, sustainable and scalable platform for structural biologists to optimize experimentally obtained biomolecular structures.

Other Instruct projects supported by EOSC-related initiatives

ScipionCloud

Scipion is a workflow management system developed by I2PC in Madrid that integrates many important software packages available to process CryoEM data. EOSC Synergy provided funding to support the developemnt of the ScipionCloud service to allow Instruct users to deploy a dynamic cluster in the cloud to keep processing the data acquired at the facility (see figure). User acquires images at a microscope facility where some automatic preprocessing is done using Scipion. Raw data and projects are stored locally. Later, a user can access the Elastic Cloud Computing Cluster (EC3) portal (or a customized portal embedding EC3 client) using ARIA credentials on the EGI check-in service and deploy an elastic cluster.                                                                                                                          

HADDOCK

The HADDOCK web server: User-Friendly platform for “docking” prediction of Biomolecular Complexes

Instruct Centre NL with the support from EOSC-Hub developed the HADDOCK, an information-driven platform that offers “docking” prediction of the structure of a complex based on the structures of its constituents. This modelling approach can for example be used for drug design as it allows for fast screening for potential drugs.

To find out more about HADDOCK and register: wenmr.science.uu.nl/haddock2.4/

AlphaFill

Providing additional context to existing AlphaFold models.

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing ligands, cofactors and (metal) ions to AlphaFoldmodels or user provided models (both computational and experimental). By adding the molecular context to these protein structures, the models can be more easily appreciated in terms of function and structural integrity. Consequently, the AlphaFill models can be helpful in designing downstream wet-lab experiments and/or computational studies.

All EOSC Projects