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

Go to Current EOSC-Life Internal Calls

Find more information on the

Digital Life Sciences Internal Call

for Academia-Industry Collaborations

(Application deadline 29 September 2021)

Find more information on the

Digital Life Sciences Internal Call

Sensitive Data

(Application deadline 29 September 2021)