Barcelona Supercomputing Center

BSC serves as the Spanish national supercomputing facility. The Center hosts MareNostrum 4, one of the most powerful supercomputers in Europe, and has been selected by EuroHPC to host MareNostrum5, one of the three pre-exascale supercomputers in the high-capacity supercomputer network that will operate in the EU by 2021. BSC is a hosting member of the PRACE distributed supercomputing infrastructure and an active participant in the European Processor Initiative, HiPEAC, the ETP4HPC and other international forums such as BDEC. The centre develops technologies for Exascale within the BSC-led Mont-Blanc project and in joint research centres with Intel and IBM. BSC participates in 11 of the 14 CoE funded and leads 4 of them. The Life Sciences Department participates in large international genome networks (ICGC, IRDiRC, GA4GH), and hosts the coordination team and the computational platform of the Spanish National Bioinformatics Institute (INB/ELIXIR-ES).

Three departments from BSC contribute to PerMedCoE, making it a truly joint effort that strengthens the centre’s interdisciplinarity. The Life Sciences and Operations departments will jointly drive the optimisation of personalised medicine software to Exascale architectures. The Computer Sciences department will provide the PyCOMPSs programming environment, which aims at the parallelization of application in distributed platforms, as well as expertise on application performance analysis and a link to POP and BioExcel projects.

Computer Sciences and Life Sciences will jointly coordinate the use cases and set up a benchmarking platform for optimised codes, as well as contributing to the preparation of efficient workflows for the personalised medicine user communities. Taking advantage of its communication expertise in the HPC community and presence in other CoEs, the BSC will also devote a significant effort to position this project and align it with other running CoEs, especially with BioExcel, and with the European Bioinformatics community via ELIXIR.

CSC – IT Center for Science

CSC – IT Center for Science is a Finnish centre of expertise in information technology owned by the Finnish state and higher education institutions. They provide internationally high-quality ICT expert services for higher education institutions, research institutes, culture, public administration and enterprises.

In the context of PerMedCoE, CSC leads the work on the optimization and usability of PerMed workflows in HPC/HPDA. CSC also contributes to the software optimisation for Exascale architecture and to the implementation and benchmark of HPC/Exascale solutions to support PerMed use cases.

The aim is to integrate personalised medicine into the new European HPC/exascale ecosystem, by offering access to HPC/exascale-adapted and optimised software. CSC will be also running a comprehensive set of PerMed use cases.

University of Luxembourg – Luxembourg Centre for Systems Biomedicine

The University of Luxembourg is an international research university with a distinctly multilingual and interdisciplinary character. It was founded in 2003, counts over 6,700 students and more than 2,000 employees from around the world. The University’s faculties and interdisciplinary centres focus on research in several areas, including cross-disciplinary research in Data Modelling and Simulation as well as Health and System Biomedicine.

The LCSB is one of the interdisciplinary research centres at the University of Luxembourg. It is accelerating biomedical research by strengthening the links between systems biology 
and medical research. Collaboration between biologists, medical and computer scientists, physicists, engineers as well as mathematicians is offering new insights into complex biological systems. These findings are essential for understanding principal mechanisms of disease pathogenesis and for developing new tools in diagnostics and therapy. The centre has established strategic partnerships with leading biomedical laboratories worldwide and fosters collaboration with industrial partners.

The LCSB is in charge of developing and optimising a pre-exascale cell level simulation software and leads the development of guidelines for data protection and privacy preservation in an exascale HPC environment. This project is in line with future vision of the Bioinformatics Core at the LCSB and works in synergy with the national strategy of HPC.

Institut Curie

Institut Curie has a strong experience in high-performance computing in cancer research and cancer treatment, with application to personalized medicine. In particular the group is developing mathematical approaches and simulation frameworks to model the functioning of cellular networks. The group also has expertise in analyzing high-throughput molecular data (in particular gene mutations and expression). The group leverages on its know-how in the construction of molecular interaction maps from the analysis of the scientific literature.

In the context of PerMedCoE, the contribution of the group will consist in extending the modelling capabilities, up-scaling their software implementation for high-performance computing, and designing use cases to validate the approach.

University Hospital Heidelberg (UKHD) – Institute for Computational Biomedicine

The Institute for Computational Biomedicine was funded in 2018 and is headed by Prof Julio Saez-Rodriguez. It has ample experience on the functional analysis of genomics data, and in the dynamic modeling of signaling pathways, integrating diverse omics data, using the tool CellNOpt and its derivatives (CARNIVAL and Phonemes). Saez-Rodriguez has been organizing DREAM Challenges for 10 years, and is the only DREAM director outside of USA.

UKHD will contribute to the modeling of signaling networks with CellNOpt, and in connecting the benchmarking activities to the DREAM community.

Atos Spain

Atos is a global leader in digital transformation with 110,000 employees in 73 countries and annual revenue of € 12 billion. European number one in Cloud, Cybersecurity and High-Performance Computing, the Group provides end-to-end Orchestrated Hybrid Cloud, Big Data, Business Applications and Digital Workplace solutions. 

Since 1987, the Research & Innovation (ARI) group in Spain has been involved in research, development and innovation projects, constituting the research and development center for new technologies and a key reference for the entire Atos group. ARI has become a recognized actor in the field of European research, with references in different directorates general of the European Commission. ARI currently occupies the first place in the ranking of the 50 large private European companies that receive funding from the European Commission and the fourth place among all Spanish organizations.

Within PerMedCoe, Atos contributes to the activities related to software optimisation and the definition of the architecture and the workflows in HPC/HPDA using Croupier, a PaaS orchestrator for hybrid (Cloud-HPC) workflows consisting of tasks/jobs executed within remote Cloud-HPC infrastructures. Moreover, Atos leads the sustainability and business plan, and has an important role on the engagement with the industrial community and dissemination of project results.

KTH Royal Institute of Technology 

KTH Royal Institute of Technology, established in 1827, is one of Europe’s top schools for science and engineering. KTH hosts PDC, the leading Swedish Center for High Performance Computing and is member of the Science for Life Laboratory, a national center for molecular biosciences with focus on health and environmental research. KTH has a very strong experience in HPC, and it is well connected and recognized for its expertise throughout EU and abroad. PDC is the coordinator of BioExcel Center of Excellence, a close ally and collaborator of PerMedCoE. PDC is the Swedish lead participant in PRACE, a full member of the ETP4HPC and partner in numerous international initiatives on scientific high-performance computing. The Science for Life Laboratory has built a very strong research community network through education and collaborative exchange, and encourages partnerships and mediates collaborations between players in the Life Science sector.

KTH brings a strong expertise in establishing successful organizations in the field of scientific computing such as BioExcel CoE . KTH will bring experience and ensure strong links between BioExcel and PerMedCoE, while supporting the latter in achieving its objectives towards running a successful and sustainable Center of Excellence. In addition, KTH provides strong expertise in modelling and molecular dynamics simulations as needed for computer aided drug design activities. 

European Molecular Biology Laboratory – outstation European Bioinformatics Institute (EMBL-EBI)

The European Bioinformatics Institute (EMBL-EBI) is an outstation of the European Molecular Biology Laboratory that has a long-standing mission to collect, organise and make available databases for biomolecular science.  EMBL-EBI makes available a collection of databases along with tools to search, download and analyse their content. These databases include nucleotide sequences (European Nucleotide Archive), protein sequences (UniProt), structures (Protein Databank in Europe), genome annotation (Ensembl), gene expression information (ArrayExpress), molecular interactions (IntAct) and pathways (Reactome). Connected to these are linking and descriptive data resources such as protein motifs (InterPro), ontologies and many others. In many of these efforts  EMBL-EBI is a European node in global data-sharing agreements and hosts the ELIXIR hub.

EMBL-EBI trains scientists at all levels to get the most out of publicly available biological data. The EMBL-EBI Training team is involved in several European funded projects and European HPC Centres of Excellence (CoE).

The EMBL-EBI training team leads the PerMedCoE activities (work package) on Dissemination, Outreach and Training. Over the course of the project EMBL-EBI will lead the development of the PerMedCoE competency profile and the resulting PerMedCoE Training programme, which will include face-to-face and remote hands-on training courses and webinars.

Centro Nacional de Análisis Genómico (CNAG-CRG)

The National Genome Analysis Centre (CNAG-CRG) is a non-profit organization founded in 2009 and funded by the Spanish Ministry of Economy and Competitiveness and the Catalan Government through the Economy and Knowledge Department and the Health Department. CNAG-CRG has a staff of 80, more than half holding PhD degrees and more than half are women. Competitive grants and contractual research with the private sector provide additional funds. Its mission is to carry out large-scale projects in DNA sequence analysis for the improvement of quality of life in collaboration with the European and International Research Community.

The CNAG-CRG is integrated with the Centre for Genomic Regulation (CRG), a multidisciplinary research centre focusing on biomedicine. The CRG is one of 25 Spanish research centres of excellence awarded with a highly-competitive ‘Severo Ochoa’ grant and holds the HRS4R Excellence seal of the European Commission.

CNAG-CRG, through Prof Marc A. Marti-Renom and the International and Scientific Affairs team, will be coordinating the efforts of PerMedCoE with those of LifeTime and other relevant initiatives. Providing a bridge with several PerMedCoE potential user communities, CNAG-CRG will contribute to the analysis of stakeholders’ needs, training, dissemination and exploitation, and the actions to ensure long-term sustainability.

Max Delbrück Center For Molecular Medicine (MDC)

The Max Delbrück Center for Molecular Medicine is an internationally renowned biomedical research center in Berlin. It is named after Max Delbrück, one of the founders of modern genetics and molecular biology. Its labs pursue their research in the areas of Cardiovascular and Metabolic Disease, Cancer Research, Diseases of the Nervous System, and Medical Systems Biology.

University Of Ljubljana

University of Ljubljana is the oldest, largest, and internationally best-ranked university in Slovenia. The partner in the PerMedCoE project is the Faculty of Medicine, which is the leading institution for medical research and education in Slovenia. It is an internationally established academic and scientific institution that collaborates with some of the best medical faculties in the world. The faculty is divided into several departments and institutes.

The ELIXIR-SI Centre will participate in the PerMedCoE on behalf of University of Ljubljana. It will collaborate in the creation of building blocks for core functionalities; Exascale-ready personalised medicine technology observatory and benchmarking; stakeholder and training needs analysis; dissemination and communication; training; and strategic alignment. The main focus will be training in e-learning and hosting user-friendly learning management systems with integrated functionalities, where University of Ljubljana has extensive expertise .

ELEM Biotech

Awarded with the EC Seal Of Excellence, ELEM creates models of the human body from patient scans to replicate how they work. These models evolve into virtual populations mirroring the diversity and pathologies of society.