An EOSC-Life internal call for academia-industry collaborations sharing data, tools and workflows in the

European Open Science Cloud

 

The second Digital Life Science Call for academia-industry collaborations was aimed at existing EOSC-Life partners who wanted to implement a collaborative project together with SME or industry partners. Out of 10 submitted eligible proposals, 2 projects were selected that – if successful – will demonstrate how companies can leverage cloud-based bioinformatics pipelines for sustainability and how further development of analysis software by commercial companies can add value to open research data bases. 

All submitted applications were first reviewed by the technical experts within the EOSC-Life consortium with regards to their technical impact, feasibility and project maturity, before continuing to scientific evaluation. A selection panel of both internal and external experts chose the winning projects from a shortlist of 8 proposals based on transparent selection criteria.

The following projects were selected for funding:

Funded Projects

 
Accessible and scalable detection and identification of foodborne pathogens

Team lead: Bérénice Batut, University of Freiburg

Industry partner: Biolytix AG

Project team: Ralf Seyfarth, Anna Henger, Engy Nasr

 

Brief project summary:

Metagenomic sequencing has been proposed as a time- and resource effective method for detecting, identifying and characterizing (e.g., resistance or virulence) foodborne pathogens in complex samples in a single sequencing run without prior isolation of the pathogen. The project aims to modernize and open up the current detection pipelines using long-read ONT sequencing technologies, developed by Biolytix AG. Based on Galaxy, modern paradigms of open data science will be applied to ensure the pipelines are FAIR, accessible, scalable but also portable, cloud deployable, maintainable and shareable.

QSM4SENIOR: Ultra-high Field MRI Quantitative Susceptibility Mapping reconstruction of the healthy Brain-aging cohort

Team lead: Alexandre Vignaud, CNRS

Industry partner: Ventio

Project team: Miguel Guevara, Jean-Francois Mangin, Yann Cointepas, Ludovic de Rochefort, Michael Bottländer

 

Brief project summary:

This project will re-use ultra high-field MRI imaging data that has been acquired during a longitudinal study in healthy, aging subjects (the SENIOR study) which has not yet been fully exploited. In particular, the investigation of iron load as a quantitative imaging biomarker for aging and brain disease requires complex image reconstruction techniques. QSM4SENIOR will employ quantitative susceptibility mapping (QSM) using the MEDI software combined to the cloud computing implementation developed by the industry partner Ventio SAS, and FAIRify the imaging data, generating the first quantitative imaging database of highly-resolved 7T MRI data, enhancing the value of the SENIOR database by the addition of a novel imaging biomarker, and targeting interoperability to EOSC-Life cloud research infrastructures.

For more details about the research, read the press release here. 

Industry Internal Call - Information for Grantees

Call Text
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.

Within EOSC-Life, “Work Package 3: Demonstrators and Open Calls for User Projects” will drive the Life Science Research Infrastructures’ (RIs’) connection to EOSC through scientific user projects, selected in an independent review, to begin to populate EOSC with tools, data and workflows of use and impact to our life science communities.

The purpose of this internal call is to identify and support projects that demonstrate how companies can participate in and benefit from open science. It is therefore aimed at those EOSC-Life consortium members with existing collaborations with the private sector that wish to jointly implement a project contributing to the long-term aims of developing an open digital space for data and tools in the life sciences. For full details of eligible projects, see Applicant Guidelines.

What is available?

Applicants can request funding  up to 70,000 EUR per project for personnel costs incurred at the beneficiary or third party to carry out the project. Budget will be allocated accordingly from WP3 funds within the consortium to those beneficiaries implementing the selected project(s). Part of the budget can be used for travel and consumables costs for all applicants (including industrial partners) involved in the project. Cloud credits might be offered in addition through WP7.

Co-funding of projects with own resources or in-kind contributions are possible. In case of co-funding or in-kind contributions, information should be provided in the budget section of the proposal to allow reviewers to assess the feasibility of the proposal. A maximum of 1-2 projects will be funded in this internal call.

Projects can have a maximum duration of 12 months and need to be able to start shortly after notice of award. Projects must end by the end of December 2022.

For details on the required reporting of successfully funded projects, please consult the reporting guidelines.

What kind of projects are we looking for?

Applicants

We are looking for research projects from EOSC-Life partners (beneficiaries and third parties explicitly named in the Grant Agreement) that will be implemented in collaboration with at least one industrial or small-or medium enterprise (SME) partner.

Projects should demonstrate reciprocal benefits for the company and the scientific community, such as potential for long-term collaboration or relevance for both academic and commercial research.

For this internal call, funding for personnel costs can only be allocated to the EOSC-life beneficiary(ies) participating in the project. Industry partners can receive funding for travel and consumables. Cloud credits might be offered in addition through WP7. Applicants will receive the support when needed of EOSC-life technical experts (data, workflow and cloud experts) to help them carry on with their project and ensure that the project aligns with EOSC-life goals. (Part of) the available funding is expected to support their contribution to the project.

We particularly encourage those EOSC-Life partners with existing collaborations with industrial or SME partners or those able to quickly establish such collaborations to apply. Industrial collaborators are expected to contribute actively to the implementation of the project and guide the project with respect to industry needs and project impact on industry. Co-funding of projects with own resources or in-kind contributions from industry are welcome, but not a prerequisite.

Project scope

Applications must fall under one or more of the 13 Life Science domains represented by the EOSC-Life consortium and address one or more of the following themes:

  • Data curation, handling and integration for publishing into the cloud (WP1)
  • Tool interoperability, workflows and containerization (WP2)
  • Cloud deployment and resources (WP7)

The project must present a life-science use-case, and contribute to and/or take advantage of cloud-based data and analysis. The objective of this call is to make data and/or workflows available to the EOSC and the scientific community. Data and workflows should be available at the point of application and should not be generated from scratch.

Proposals in one or more of the following categories would be in scope:

  • Sharing of workflows and toolboxes for data pre-processing, sharing and searching
  • Cloud-compatible solutions for 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

Not in scope are projects aiming to generate new data sets, development of entire new workflows or software solutions, projects only involving data curation, projects without scientific use cases or those developing cloud tools without open access.

In cases where applicants are lacking access to suitable datasets for tool or workflow development and testing, they are encouraged to make use of publicly available datasets from data repositories, e.g., Image Data Repository (IDR), GenBank, Eukaryotic Pathogen Database Resources (EuPathDB).

For examples of the kind of projects we have supported, please take a look at the pilot projects already completed within EOSC-Life: https://www.eosc-life.eu/services/demonstrators/ 

Application process
How to apply

Please note that only EOSC-Life partners (beneficiaries and third parties explicitly named in the Grant Agreement) together with a collaboration partner from industry or an SME are eligible to apply. View our list of eligible beneficiaries and linked third parties. 

For full details on the application process and eligibility, please see our Applicant Guidelines.

Before submission of the proposal, you will need to make contact with one of our EOSC-Life experts from WP1, 2 and/or 7 to discuss your project. This step of the process is mandatory. If the applicant her-/himself is a member of a work package addressed in the proposal (1/2/7), a different technical expert will be assigned during this maturation phase. The maturation phase shall provide additional expert advice and ensure that it is aligned with the goals of the EOSC-Life project. The completion of this short questionnaire will help us assign the right expert to your proposal.

You must have made first contact with the relevant experts to set up an appointment to discuss your proposal before the consultation deadline 5 pm CEST on 28 July 2021. 

Consultations can be carried out throughout the time that the call remains open. However, we strongly urge you to schedule and conclude your expert consultation early to ensure that all questions regarding your proposal can be properly addressed. Our technical experts reserve the right to offer only limited consultation in the final two weeks prior to submission if the number of consultation requests exceeds capacity. Once you have concluded the consultation with our experts, your proposal can then be submitted via the ARIA platform until 5 pm CEST on 29 September 2021.

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.

For full details on the application process and eligibility, please see our Applicant Guidelines.

PLEASE NOTE: THE APPLICATION PERIOD IS NOW CLOSED.

Supporting Documents and Links

(Note: These links will bring you to ARIA on the Instruct-ERIC website, where you also will submit your application.)

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:

Looking for the Internal Call for Sensitive Data? Find it here.