We are pleased to announce that 8 projects have been awarded funding within our Digital Life Sciences Open Call.

Project work will kick off in spring/summer 2021, and we look forward to reporting back on the achievement of small and large project milestones.

Funded Projects

Integrating EU-RI datasets for preclinical and discovery research bioimaging

 

Project team: Sara Zullino, University of Torino

Jean-Marie Burel, Marco Comerci, Philipp Gormanns, Dario Longo, Mario Magliulo, Rafaele Matteoni, Jason Swedlow, Andrea Zaliani

Brief project summary:

European Research Infrastructures (RIs) generate an increasing amount of data across different life science domains, such as animal model strains (INFRAFRONTIER), chemical entities (EU-OpenScreen), and biomedical imaging (Euro-BioImaging). These three RIs are joining forces to try to combine their resources by building novel, open-source tools for integrating the information associated with data belonging to their infrastructures. This will ultimately provide users with free, open access to collections of datasets distributed over multiple sources when making searches by specific keywords.

RIs involved:

Euro-BioImaging

INFRAFRONTIER

EU-OPENSCREEN

A workflow for marine Genomic Observatories data analysis

 

Project team: Christina Pavloudi, Hellenic Centre for Marine Research

Haris Zafeiropoulos, Stelios Ninidakis, Antonis Potirakis, Evangelos Pafilis, Cymon J. Cox, Gianluca De Moro, Robert Finn, Ekaterina Sakharova, Martin Beracochea, Ibon Cancio, Maria Luisa Chiusano, Erwan Corre, Katrina Exter, Nicolas Pade

Brief project summary:

Very large marine metagenomic datasets are produced from the EMBRCʼs Genomic Observatories (GOs) in order to decipher the dynamics of marine ecosystems. This project supported by EOSC-Life will develop a workflow for analyses of such Marine Biology data that will allow researchers to deal better with this increasing amount of data. This initiative will make the data produced by the GOs more easily interpretable by providing the taxonomic inventories of each sample in a timely manner and in a non-technical format.

RIs involved:

EMBRC

ELIXIR

PDB-REDO-cloud: A flexible and scalable engine for computational structural biology

 

Project team: Anastassis Perrakis, Netherlands Cancer Institute

Maarten Hekkelman, Robbie Joosten, Hans Wienk

Brief project summary:

PDB-REDO provides a computational platform to optimize experimentally obtained biomolecular structures that allow a better understanding of the basic chemistry of life. The aim of this project is to deploy the PDB-REDO engine on the cloud to provide a flexible, sustainable and scalable platform for structural biologists. The PDB-REDO-cloud will provide ready-to-go experiments for non-expert users, allow expert users to design their high-throughput computational experiments with access to all PDB-REDO features and finally allow Instruct-ERIC facilities to implement PDB-REDO-cloud into custom workflows.

RIs involved: 

Instruct-ERIC

Expression Atlas’ RNA-Seq and Microarray analysis pipelines migration to workflow environments for cloud deployment and reproducibility

 

Project team: Irene Papatheodorou, EMBL-EBI

Pablo Moreno, Andrey Solovyev, Pedro Madrigal, Jonathan Manning

Brief project summary:

A vast amount of gene expression data is produced and processed daily in diverse areas of Life Sciences. This pilot project aims to modernize the current Expression Atlas gene expression data analysis pipelines, ensuring they are both portable and cloud deployable. Such an initiative will allow Expression Atlas pipelines to move from a strong dependence on the EBI cluster and shared file system to a modern, community maintained, explicit workflow environment that can run outside of the EBI infrastructure. More importantly, the migration of these analysis pipelines should facilitate the re-use and re-analysis of RNA-seq and Microarray data by third parties.

RIs involved: 

ELIXIR

Increasing the FAIRness of Phytolith Data

 

Project team: Emma Karoune, Historic England

Carla Lancelotti, Juan José García-Granero, Marco Madella, Javier Ruiz-Pérez

Brief project summary: 

The project aims to improve the FAIRness of phytolith data by investigating existing datasets and data sharing practices within the discipline. Phytoliths are silica bodies that are deposited in plant cells during the life-cycle of the plant. They are used in different fields of sciences such as archaeology and palaeoecology to address questions of past plant exploitation and environmental and biodiversity changes.
Once the FAIR assessment of existing datasets has been completed, the project aims to introduce recommendations to the phytolith community and model data sharing best practice through developing training material and running training events. Future plans include the creation of an online open repository for phytolith data.
For more information, please see our website: https://open-phytoliths.github.io/FAIR-phytoliths/

RIs involved: 

ELIXIR

EMPHASIS

Reference Data Resource

 

Project team: Ignacio Eguinoa & Frederik Coppens, Flemish Institute for Life Sciences

Björn Grüning

Brief project summary: 

The objective of this project is to develop a centralized, community-supported repository that manages genomic reference data using the reference genome resource manager Refgenie. With this initiative, the accessibility and re-use of datasets will be improved, assets associated with a genome build will be linked under a namespace identifying the genome build and each reference dataset will contain associated metadata with provenance
Information.

Link to the platform: http://refgenie.databio.org/en/latest
Link to the pilot server: http://plantref.databio.org

RIs involved: 

ELIXIR

EMPHASIS

Open Source Secure Data Infrastructure and Processes for Life Sciences (OSSDIP4LIFE)

 

Project team: Andreas Rauber, TU Wien

Martin Weise, Martin Krajiczek, Dietmar Winkler, Tomasz Miksa, Niki Popper

Brief project summary: 

Secure sharing of sensitive data from the data owner to research experts is extremely challenging due to privacy reasons, but also due to the massive risk involved in sharing commercially sensitive data. To address this issue, TU Wien developed a fully open-source based high-security data visiting platform called OSSDIP and is with this EOSC-Life-funded project trying to adapt it to the needs of selected data owners in the life sciences, extending its functionality to support more flexible data analytics. This platform will allow data owners to provide:

  • highly selective access (data visiting)
  • to specific (fine-granular or aggregated) subsets of data
  • for identified individuals
  • for limited periods of time
  • to answer precisely defined questions accepted by the data owner

RIs involved: 

ECRIN

Towards FAIR data for X ray-based structure-guided drug design

 

Project team: Jose A. Marquez, Instruct, EMBL Grenoble (France)

Sameer Velankar

Brief project summary: 

New applications in the field of X-ray-based crystallography such as X-ray based fragment screening have led to a remarkable increase in data production and a bigger dependency from the user community on advanced facilities like those within Instruct-ERIC. However, these facilities are lacking tools to properly support their users with FAIR data handling. To address this issue, this project will work on the development of news tools for automated harvesting, validation, and deposition of such Macromolecular Crystallography data and metadata which should considerably promote re-use and interoperability of this data.

RIs involved: 

Instruct-ERIC

EU-OPENSCREEN

First Digital Life Sciences Open Call - Information for Grantees

Aim & Background of the 1st Open Call

Purpose of the call

Recent advances in research technology have led to a vast increase in data volumes produced by life science research. These datasets, many arising from large-scale screening projects, are beyond what can be handled, shared and analysed using classical tools and often contain treasure troves of data beyond what was analysed in the initial project. Making available data, tools and workflows in the cloud is therefore necessary in order to use the data produced to the fullest extent, both within and beyond the original intended scope of  individual projects. The purpose of this Open Call is to support the development of a wide variety of projects that will contribute to the long-term aims of developing an open digital space for data and tools in the life sciences, fostering interdisciplinary collaborations and advancing data-heavy research areas. The overarching goal of the project is to begin to populate EOSC with tools, data and workflows of use and impact to our life science communities.

Background

The European project EOSC-Life creates an open, digital and collaborative space for life science research. This space will comprise data, tools and computational resources together with supporting policies and services. At the heart of the project are the 13 Life Science Research Infrastructures that provide services  across domains, spanning  areas ranging from structural biology to imaging and through to clinical trials.

To the best of our knowledge, this is the first time that Research Infrastructures have provided a route for scientific users to contribute datasets, tools and workflows into the cloud, supported by training and providing access to technical consultations with Research Infrastructure data experts and tools developers. EOSC-Life will open up a treasure-trove of Research Infrastructure data resources for reuse by the broader scientific community.

What is available?

Successful applicants can expect both funding for the project team equivalent to roughly 1 full-time salary for one year (in the range of 70,000-85,000 EUR per project, subject to evaluation), as well as training and expert advice from within the EOSC-Life consortium, to enable the delivery of complex cloud-connected life science research projects. Within the Open Call process we offer the necessary ‘match-making’ to connect applicants with EOSC-Life experts, who will provide consultation regarding technical feasibility and best practice.

What kind of projects are we looking for?

Proposals should align with the goals of EOSC (European Open Science Cloud) – ie. enabling data sharing for the purpose of furthering scientific research. The project’s overarching aim is to make life science research data publicly available in a FAIR (Findable, Accessible, Interoperable, Reusable) way in the EOSC. 

Proposals should fit with one or more of the following themes:

  • Data curation, handling and integration for publishing into the cloud
  • Tool interoperability, workflows and containerisation
  • Cloud deployment and resources

More specifically, projects could fit into one or more of the following categories:

  • Development of workflows and toolboxes for data preprocessing, sharing and searching
  • Collection, processing, standardisation, FAIRification, and storage of existing data of different varieties, for example in microbiology, pathology, chemoinformatics, drugs and clinical data, via EOSC
  • Algorithmic approaches to generating data sets within the life sciences
  • Integration of existing data sets and repositories across life science fields or within individual research communities
  • Migration of existing workflows into the cloud, adapting these to FAIR data standards and integrating multiple workflows
  • Metadata generation and use, including automation projects

For project examples see our Demonstrator 2 (Cryo EM workflows), Demonstrator 5 (Preclinical image workflows) and Demonstrator 6 (Image repository and scalable mining).

Application Process

How to apply

To apply, you will first need to contact the relevant experts to discuss your project. The final deadline for consultation is 8 December 2020. This step of the process gives you a chance to receive expert advice on your project and to ensure that it is aligned with the goals of the EOSC-Life project. Scientists from both academia and industry are eligible to apply, as long as they are affiliated with an institution that is eligible to receive EU funding. From the application page, you will be able to contact experts specialised in 1) Data curation, handling and integration for publishing into the cloud; 2) Tool interoperability, workflows and containerisation and/or 3) Cloud deployment and resources.

Once you have concluded consultation with our experts, your proposal can then be submitted via the ARIA platform  by 5 pm CET on 22 December 2020.

Proposals will first be assessed on technical feasibility and maturity by experts within the EOSC-Life consortium. They will then be subject to a scientific excellence and impact assessment performed by external experts. We aim to let applicants know the outcome of their application within two months of the submission deadline.

EOSC-Life is committed to assisting with research efforts targeting SARS-CoV-2 and COVID-19.  Within the Digital Life Sciences Open Call scientific projects on SARS-CoV-2 and COVID-19 will be prioritized compared to other projects, if their relevance is striking and if there is an urgent need to start. We offer a fast-tracked review of your proposal if this applies to your project. Contact opencall@eosc-life.eu after you have submitted your proposal to request COVID-19 fast-tracked review.

For full details on the application process, please see our applicant guidelines.

Supporting Documents and Links
Acknowledging EOSC-Life in your publications

Support received by the EOSC-Life project must be clearly stated in the acknowledgement section of a publication with the following sentence: “This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824087”.

Please include our logo on any posters and slides: