These are the partners of the BioExcel consortium:
KTH Royal Institute of Technology
KTH is a member of the European Technology Platform for High Performance Computing (ETP4HPC), and through the Swedish National Infrastructure for Computing (SNIC) a member of PRACE, EUDAT, and EGI, with KTH being the coordinator of the Swedish participation in PRACE. KTH coordinates the EPiGRAM project, which investigates Exascale programming models and is a partner of the FP7 Exascale flagship project CRESTA. In these projects, KTH focuses on application scalability as well as performance analysis directly relevant to BioExcel. KTH is also a member of the Human Brain Project. KTH is the lead partner of the Swedish e-Science Research Centre (SeRC), a national large-scale e-Science initiative, and Science for Life Laboratory, the national infrastructure for research in molecular life science. The participating researchers are also involved in BILS, the Swedish bioinformatics infrastructure for life science, as well as the Center for Biomembrane Research (CBR). Erik Lindahl is the principal investigator of the GROMACS project, with additional developers all over the world (e.g. ORNL, RIKEN, Univ. Tokyo, Stanford, Univ. Virginia, and the Max-Planck Society), and the KTH team collaborates with the NSF-S2I2 project for a “Sustainable Software Innovation Institute for Chemistry, Materials, and Biomolecular Simulation”.
Universiteit Utrecht, and in particular the Bijvoet Center for Biomolecular Research, houses advanced infrastructures for the analysis of proteins and other biomolecules using NMR, X-ray crystallography, cryo-electron microscopy and mass spectrometry. It is an INSTRUCT-ERIC center with a long-standing participation in EU-funded programs, including in particular several e-Infrastructure projects over the years among which WeNMR (coordinated by Utrecht), EGI-Engage, INDIGO-Datacloud, BioExcel and the recent EOSC-Hub project. The UU partner is developing the integrative, information-driven docking platform HADDOCK for the modelling of biomolecular complexes offered to the community as a user-friendly web portal, counting to date >12500 registered users worldwide. The UU partner also operates several grid-enabled web portals for structural biology including the HADDOCK, DISVIS, POWERFIT portals (see http://haddock.science.uu.nl), sending >10 millions jobs per years to the European Open Science Cloud resources (via the HTC resources coordinated by EGI). Those portals are integrated in the WeNMR thematic services made available through the EOSC-portal. The HADDOCK software developed by the group is also used by several major pharma companies, providing direct links with industry.
Fundacio Institut de Recerca Biomedica (IRB Barcelona)
IRB is leading the Life Science panel of European Exascale Software Initiative and is partner of ABC (Ascona B-DNA Consortium) that is an international initiative with more than 15 members that study the dynamics of DNA molecule. ABC is currently part of the EUDAT community and is developing tools to be integrated on the top of EUDAT services (B2SAFE, etc). IRB lead the Life Science panel of PRACE Scientific case. IRB also participates in ELIXIR through its Spanish national node, the National Institute of Bioinformatics. The goal of ELIXIR is to orchestrate the collection, quality control and archiving of large amounts of biological data produced by life science experiments. ELIXIR is creating an infrastructure that integrates research data and ensures a seamless service provision that is easily accessible to all. In this way, open access to these rapidly expanding and critical datasets will facilitate discoveries that benefit humankind.
Forschungszentrum Jülich manages one of the most important supercomputing centres in the world and operates supercomputers of the highest performance class in Europe. In cooperation with renowned hardware and software vendors like IBM, Intel and ParTec, it meets the challenges that arise from the development of exaflop systems. As a member of the German Gauss Centre for Supercomputing, it has coordinated the construction of the European research infrastructure “PRACE – Partnership for Advanced Computing in Europe” since 2008. In July 2010, Forschungszentrum Jülich has joined the Centre Europeen de Calcul Atomique et Moleculaire, CECAM, as an active node. The Jülich CECAM Node is active in the fields of Computational Science, Soft Matter Research and Materials Sciences. It has a strong focus on computer simulations, where methods, algorithms and codes are developed and applied on various types of high performance parallel computer architectures. Forschungszentrum Jülich has recently recognized the relevance of computational molecular biology by establishing an Institute of advanced simulation (IAS-5/INM-9), particularly dedicated to HPC-based biomolecular simulation. Forschungszentrum Jülich and its institutes are involved in several areas of research within the Human Brain Project, the European Union FET Flagship Initiative to understand the human brain using simulation. In order to make it a reality, researchers from 23 countries are working together to build a unique infrastructure that will allow them to establish and further develop a brain research and information technology network. Some of the deliverables of BioExcel will be directly employed in the Human Brain Project, which is expected to last for ten years.
The University of Edinburgh
The University of Edinburgh is represented in BioExcel by two world-class institutes: EPCC and the Roslin Institute. Both have extensive international engagements, which they will link into the work of the CoE. EPCC is a leading member of the international HPC community. It is recognised worldwide for its work in HPC research and leads national, European and International collaborations. In particular it leads the CRESTA FP7 Exascale software project, the FORTISSIMO FP7 HPC for Manufacturing SMEs project and is a key member of the PRACE Research Infrastructure and projects. At the same time it is part of the Intel Parallel Computing Center initiative and is also an NVIDIA CUDA Research Center. It is part of Cray’s Exascale Research Initiative in Europe, which is part of its Exascale Technology Centre. The Roslin Institute is a leading member of the worldwide biosciences community focussed on enhancing the lives of animals and humans through worldclass research in animal biology. As such it collaborates with similar centres of excellence around the world. In addition to extensive international academic interactions, over 60 international commercial partners are engaged with the institute.
The University of Manchester
University of Manchester‘s eScience Lab research group led by Professor Carole Goble has since 2001 been focused on research and development around tools designed for data driven and computational research, supporting the coming together of people, data and methods in a particular research area; this is also know as an e-laboratory. The group’s research and projects span a wide array of topics, including eScience, bioinformatics, biodiversity, scholarly communication, reproducible science, workflows, linked data, provenance, community building and knowledge representation. The team have been consistently publishing software as Open Source and have since its beginning advocated and supported Open Science best practices across domains.
The group is involved in multiple European initiatives, with a strong presence within the European-wide life science organization ELIXIR; Goble is Head of Node of ELIXIR-UK, and the group participate in EU projects EXCELERATE (FAIR data, TeSS training portal), CORBEL (data access and integration), EOSCPilot (open service platforms), EOSC-Life (incl. a European wide workflow repository), FAIRplus, IBISBA (synthetic biology) and Synthesis+. The eScience Lab plays an important part of providing Research Software Engineer training as co-lead of Software Sustainability Institute UK and running UK-wide activities for Data and Software Carpentry. Through ISBE activities the group has a key role in FAIRDOM (main developers of FAIRDOMHub) and had an integral part in founding Open PHACTS. International collaborations include Common Workflow Language (where the group has been heavily involved since its early days), Research Objects (led by the group), BioCompute Objects, Mendeley Data and NIH Data Commons, European Open Science Cloud (EOSC) initiatives, Research Data Alliance (RDA), Force11, and the Apache Software Foundation.
European Molecular Biology Laboratory (EMBL-EBI)
EMBL-EBI is the outstations of the European Molecular Biology Laboratory that has a long-standing mission to collect, organise and make available databases for biomolecular science. The 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 the EMBL-EBI is a European node in global data-sharing agreements and hosts the ELIXIR hub and leads the Cloud Task Force within Elixir and is one of the main contributors to the Elixir Technical Services activities.
Max Planck Gesellschaft Zur Foerderung der Wissenschaften
Max Planck Gesellschaft has close relationships with key Max Planck researchers working internationally on and with simulation codes in different science areas, including life sciences for which codes as ESPRESSO++ or FHIaims with large international user communities are highly suitable. MPG-RZG is a partner in PRACE (as a third party to GCS, the German member of PRACE), in EUDAT and EUDAT2. MPG-RZG has a key role in the organisation of the annual international HPC summer school on challenges in computational sciences (www.ihpcss.org) supported by PRACE (EU), XSEDE (NSF, US), ComputeCanada (Canada) and AICS/RIKEN (Japan) and with established relationships to the involved organisations.
Barcelona Supercomputing Center
BSC is the national supercomputing center in Spain and contributes with links to the HPC projects, through the Computer Science department, as well as to the Bioinformatics community through the Life Science department. 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 Workflows and Distributed Computing group involved in the project, develops PyCOMPSs/COMPSs, a task-based programming models for distributed computing platforms that is used in BioExcel to build biomolecular simulation workflows. The group develops technologies and software in other EU funded projects like ExaQUte, Tango, LANDSUPPORT or mf2C. BSC has also established joint research centers on Exascale with Intel and IBM, and its Life Sciences Department on Artificial Intelligence and Personalised Medicine with IBM and Lenovo.
The Life Sciences Department hosts the coordination team and the computational platform of the Spanish National Bioinformatics Institute (INB) that looks after the activities of the INB groups across Spain, as well as impulses and coordinates TransBioNet, a reference network of bioinformatics groups at Health Research Institutions of Spain. BSC also participates in ELIXIR through its Spanish national node (INB/ELIXIR-ES). The goal of ELIXIR is to orchestrate the collection, quality control and archiving of large amounts of biological data produced by life science experiments. ELIXIR is creating an infrastructure that integrates research bioinformatics data and tools and ensures a seamless service provision that would be easily accessible to all to facilitate discoveries that benefit humankind.
Ian Harrow Consulting
Ian Harrow Consulting (IHC) is a UK-based consultancy company which provides expert services in Project Management, Bioinformatics and Text Mining for numerous clients in the Life Science industry. IHC participates in precompetitive collaboration through associate partnership with the Open PHACTS foundation, management of projects for Pistoia Alliance and previous representation of Pfizer at the EMBL-EBI Industry programme. IHC is involved with global consortia such as Global Alliance for Genomics and Health and ELIXIR, the EU infrastructure for Life Science information. IHC brings an extensive network of professional connections from over 30 years experience working in the Pharmaceutical and Life Science industry.
Norman Consulting is an enterprise based in Norway which provides consulting services for the pharmaceutical, biotechnology and related life sciences industries, and specialises in: project management, business development, innovation support, scientific evaluation, funding applications and training. Norman Consulting has strong links with the Pistoia Alliance, a global alliance of life science companies, vendors, publishers and academic institutions which work together to lower barriers to pre-competitive innovation in R&D. Drawing on its professional network as well as its expertise in innovation, drug discovery and structural biology, Norman Consulting will act as one of the main outreach channels to the biotech and pharma industries, focusing on understanding user and community needs and market potential, thus paving the way to ensure business sustainability of the BioExcel CoE.
The University of Jyväskylä
The University of Jyväskylä is an internationally renowned research university and an expert in education that focuses on human and natural sciences. JYU will coordinate the development of the multi-scale QM/MM interface and will use the new interface to carry out the use cases focused on rational design of fluorescent proteins for bionanoscopy.
Nostrum Biodiscovery (NBD) is the first joint spin-off of the Barcelona Supercomputing Center and the Institute of Research in Biomedicine. It started operations in late 2016. The company develops and exploits computational chemistry and simulation methods to drive early drug discovery projects for a range of pharma and biotech clients, both in Europe and the US. It is also engaged in disruptive drug discovery projects with academic institutions such as universities and hospitals. Within Bioexcel, NBD will be involved in the development and testing of workflows and use cases and will participate in sustainability and industry outreach efforts.