Since the launch of the project in March 2019, participants of EOSC-Life have been working hard to get data, tools and workflows from the life sciences ready for deployment in the European Open Science Cloud.
For more information about progress during the first half of the EOSC-Life project, please read our Achievements Brochure (click on the image above to see how you can benefit from EOSC-Life outcomes).
The First Cloud Data Deployment Call aims to achieve the following:
Within WP1, ECRIN has been working on the development of the Clinical Research Metadata Repository (MDR), including COVID-19 data, allowing the discovery of clinical studies and related data objects, as there are for example protocol, information sheet and consent form, data management plan, statistical analysis plan, case report form, results, publications, descriptive metadata, etc. MDR contributes to making clinical research data FAIR by increasing data Findability.
WP1 also determined cross-RI interoperability needs for human consented data in general, as well as interoperability needs for cross metadata catalogue queries.Go to Clinical Research Metadata Repository
Bioactivity data sets covering compound repurposing screening of 5600 known drugs and bioactives against SARS-COV-2 providing rapid Access to data for drug development (Euro-BioImaging / EU-OS / ELIXIR)
See publication “Identification of inhibitors of SARS-CoV-2 in-vitro cellular toxicity in human (Caco-2) cells using a large scale drug repurposing collection” available in IDR at DOI:10.17867/10000148a and DOI:10.17867/10000148b.
In addition, as part of our FAIRification effort, we have produced a notebook allowing users to reproduce some of the findings presented in the SARS-CoV-2 paper from EU-OPENSCREEN. The notebook can be run in a cloud infrastructure at EMBL-EBI. View it here.
(Image taken from http://idr.openmicroscopy.org)
The extension of the COVID-19 Data Portal, within WP13, will:
Go to COVID-19 Data Portal
Within EOSC-Life, 8 Scientific and technological pilot projects, “the demonstrators”, representing a broad scope of different life science domains across life sciences research infrastructures have been selected to provide concrete scientific use-cases and guide and structure the work done in EOSC-Life. This set of demonstrators received funding for a year along with support from the data and tools experts from the EOSC-Life consortium to carry on with their project and populate EOSC with concrete exemplary projects sharing data, tools and workflows in the cloud.
The demonstrator projects were selected with the overarching aim of targeting a clear user community and should benefit the scientific community as a whole through the deployment of a diversity of data type and services coming from the different life science research Infrastructure. Demonstrators were supported in their work by WP1 and WP2 and other EOSC-Life WPs.Go to Science Demonstrators
Chemosensitivity assays are commonly used for preclinical drug discovery and clinical trial optimization. However, data from independent assays are often discordant, largely attributed to uncharacterized variation in the experimental materials and protocols.
That is where MICHA (Minimal information for Chemosensitivity Assays) comes in. MICHA is a pipeline to enable the FAIRification of drug screening experiments, developed by EATRIS partners in the scope of EOSC-Life WP1.
Contrarily to existing efforts that are often lacking support from data integration tools, MICHA:
To consolidate the utility of MICHA, we provide FAIRified protocols from 5 major cancer drug screening studies as well as 6 recently conducted COVID-19 studies. This dataset is available at: https://micha-protocol.org/protocols/index.
With the MICHA web server and database, we envisage a wider adoption of a community-driven effort to improve the open access of drug sensitivity assays.
If you would like to contribute new data sets that could be implemented in MICHA to make it more robust and comprehensive, please get in touch with Zia ur Rehman.
MICHA is published in Briefings in Bioinformatics.Go to MICHA
EOSC-Life has established a liaison with the ISO TC 276-WG5, a working group for data integration in biotechnology.Visit ISO
WP1 developed with WP6 partners the use of FAIRSharing to define an EOSC-Life data resources and standards collection.
Together, we elevated discoverability and ease of adoption via use of FAIRsharing.org platform
The LifeMonitor service, developed in EOSC-Life WP2 to facilitate maintenance activities on computational workflows with a focus on sustainability and reusability is now fully operational. Since the first public release in May 2021, the service has continuously progressed in functionality and has been adopted to monitor the workflows of the Galaxy IWC collection. LifeMonitor now offers a web application that allows users to easily register workflows from WorkflowHub and other sources, and to keep track of the test status of multiple workflows at a glance. Test results from GitHub Actions, Jenkins and Travis CI are made accessible under a common interface to clients authenticated with WorkflowHub or GitHub (and soon with LS Login). Interoperability with WorkflowHub is ensured by the adoption of Workflow Testing RO-Crate as a data exchange format. Work is ongoing to complement the core service with a GitHub app for the semi-automated setup of best-practice workflow repositories and their packaging as Workflow Testing RO-Crates for integration with WorkflowHub and LifeMonitor itself.
RO-Crate has been established as a community standard to practically achieve FAIR packaging of research data with their structured metadata. EOSC-Life is a significant contributor to RO-Crate development to support workflow life cycle from deposition and archiving in WorkflowHub (a European-wide repository of computational workflows in of life sciences) along with the wider spectrum of workflow execution (WfExS, SCHeMa), monitoring (Life Monitor), reporting (OpenEBench), provenance (Common Provenance Model) and workflow submissions for regulatory sciences (BioCompute Objects).
RO-Crate is supported by open source tooling, and is now being adapted outside life sciences, from cultural heritage (PARADISEC) to Machine-actionable Data Management Plans (maDMP), as well as institutional repositories based on Dataverse (Harvard Data Commons). Within EOSC, RO-Crate is also used by Earth Sciences for data cubes (RELIANCE) and for data collaboration (CS3MESH4EOSC). The RO-Crate Community is open for anyone to join, and meet regularly to consider new use cases, improve the specifications and tooling, as well as coordinating implementation across EOSC projects.
Click the links to find out more about achievements in Work Package 2 on tools collaboratory and workflows:
EOSC-Life’s cloud deployment and cloud resources work package has set up a helpdesk system that can be contacted by sending
an email to email@example.com—currently limited to project participants—to provide support for technologies within the project (e.g. Galaxy). The helpdesk system follows a support procedure to offer consistent answers to all users.
While the majority of life science services are openly accessible to anyone across the world, many of them require researchers to sign in using a username and password. Sensitive data and licensed resources of course require strong security for access. In these cases, research services have implemented local access management solutions and issued their own usernames and passwords. As a consequence, researchers quickly became overloaded with having to remember numerous login credentials.
The Life Science Login enables researchers to use their home organisation credentials or community or commercial identities (e.g. ORCID, LinkedIn) to sign in and access data and services they need. It also allows service providers (both in academia and industry) to control and manage access rights of their users and create different access levels for research groups or international projects. For example, two different researchers in the same university may be working on different European or national research projects and may need access to completely different data or compute resources. Life Science Login ensures that they can access the right resources, using their university credentials, while making sure they can’t see each others’ data.
The 1st EOSC-Life Open Call for projects sharing data, tools and workflows in the cloud generated a huge amount of interest across the scientific community. Ultimately, 8 projects were awarded funding and launched in spring 2021.Read about the Digital Life Sciences Open Call and funded projects
Sharing sensitive data is a specific challenge within EOSC-Life. For that reason, a toolbox is developed in WP4, providing references and links to recommendations, procedures, and best practices, as well as to software tools. As a first step, a tagging (categorisation) system has been developed and published, allowing consistent labelling and categorisation of resources most relevant to sensitive data sharing. In the next weeks, this categorisation system will be evaluated in a pilot study by 6 research infrastructures.
Work Package 6 has made progress toward FAIRification of data in the following areas:
Terms4FAIRskills is a terminology for the skills, competencies and knowledge necessary to make data FAIR and to keep it FAIR (https://terms4fairskills.github.io/). The terminology can be used to assist with the creation and assessment of stewardship curricula; to facilitate the annotation, discovery and evaluation of FAIR-enabling materials (e.g. training) and resources; and to enable the formalisation of job descriptions and CVs with recognised, structured competencies.Go to Terms4FAIRskills
On the 14th of April , Euro-BioImaging ERIC and Instruct-ERIC hosted a virtual workshop on the topic of remote access to infrastructures and their users’ training. The workshop received funding from EOSC-Life. It brought together 124 participants from four different continents, clearly indicating the interest and need of this topic under the current public health situation.
The event included plenary sessions with short presentations, break-out sessions with specific topics, and panel discussions, overall encouraging interaction and discussion among participants. It was ranked as very good or excellent by a majority of the participants that answered the feedback survey.
To read what participants had to say, see our news item here.
Photo credit: Henok Karvonen, Multimedia producer, Turku BioImaging, Finland
The Galaxy Admin community hosted a workshop in Jan 2021 which covered introductory and advanced topics you need to know to set up your own production, high-performance and multi-user Galaxy instance. This course received funding from EOSC-Life.
59 participants from across 5 continents took part in the training, including 6 from the EOSC-Life community. Participants learnt about how to install, configure, customize, and extend their own production-ready Galaxy servers. The course was taught completely asynchronously with a mix of written tutorials, videos recorded by the instructor community and videos auto-generated from the slides. Intensive, hands-on sessions were taught by experienced instructors from the Galaxy Community. All the contents of the training will remain online permanently at https://github.com/galaxyproject/admin-training/tree/2021-online. The bulk of the work consisted of the participants working at their own pace through the materials prepared for them. For the duration of the training (and a week after) the participants were granted access to a virtual machine exclusive to them.
To read what participants had to say, see our news item here.More information on the event can be found in the Gallantries github
RIs & scientists planning EOSC-related training for the Life Science community (EOSC staff and end-users) from both within and outside the EOSC-Life consortium.
Aim of the Training Open Calls
Round 1 – June 2020 (pilot)
Round 2 – November 2020
View here the funded projects from the First Open Call.
View here the funded projects from the Second Open Call.Go to Training Open Call