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 hosts several European experimental infrastructures (in mass spectrometry – FP7 I3 Prime-XS project – and in NMR – FP7 I3 BioNMR project) and is an INSTRUCT ESFRI center. It is operating a grid infrastructure site embedded in the Dutch NGI resources and supported by SURFSara. UU has been leading the WeNMR e-Infrastructure project (www.wenmr.eu) and has tight connections with the European Grid Initiative and the Open Science Grid in the US. UU has hosted over the years several HPC-Europe and HPC-Europe2 projects. UU will be leading under the new EGI-Engage project the MoBrain competence center to serve translational research from molecule to brain.
Fundacio Institut de Recerca Biomedica (IRB Barcelona)
IRB is leading the Life Science panel of European Exascale Software Initiative (www.eesi-project.eu/) 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 (www.prace-ri.eu/prace-the-scientific-case-for-hpc/). 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 the proposal 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 excellencearound 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 is a member of the ELIXIR RI for distributed data in the life sciences through its membership of the ELIXIR-UK Node (Goble is UK Node Deputy Director and co-leads the ELIXIR Data Interoperability workstream). It is a partner of the ESFRI prep phase ISBE (Infrastructure for Systems Biology – Europe) and leads the work package on data and model management as well as co-drafting the business case. It is a partner of the FAIRDOM project, a special arrangement of 4 national funding councils (BBSRC, NWO, BBMF and SystemsX) to establish a data and model management infrastructure for Systems Biology, to support the ERASysAPP ERANet and the previous SysMO, EraSysBio+ ERANets and the German GrossProjekt Virtual Liver Network. UNIMAN are core partners of the IMI Open PHACTS for open innovation in pharmacology and pre-competitive drug discovery. Goble is an investigator of the Software Sustainability Institute UK, where UNIMAN lead the Data and Software Carpentry training and Fellows (PALs) outreach: they are also responsible for Data and Software Carpentry training in ELIXIR UK are running a pilot to roll out across the ELIXIR Nodes. In the UK Goble is a co-investigator of the newly established Manchester SynBioChem Synthetic Biology Centre, where she is responsible for data/model management.
European Molecular Biology Laboratory (EMBL-EBI)
EMBL-EBI (www.ebi.ac.uk) is the outstations of the European Molecular Biology Laboratory (EMBL; www.embl.org) 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.
Forward Technologies is a Stockholm-based consultancy company. Our primary area of expertise lies in providing funding, business development solutions and market entry support to high technology start-ups, SME and research organizations in Europe. Our clients value our competences in communicating and packaging the value of their ideas and innovations into comprehensive project and business plans. In collaboration with our customers, we have been successful in numerous applications for public funding to providers locally in Sweden (Vinnova), and on European level. In many cases, we have also taken an active part in executing and reporting the funded projects. In addition, we have performed several business development projects for our clients including performing technical due diligence on potential in-licensing candidates, and identifying and contacting potential customers and collaborators.
Forward Technologies is fully owned and co-located with Serendipity Innovations, a privately owned investment company and business incubator for technology development companies based on academic research. At the moment Serendipity innovations portfolio consists of 11 companies within clean tech, medtech, biotech and IT, several of which are relevant actors for the BioExcel center. Forward Technologies was initially an integral part of Serendipity Innovations and was founded in order to serve the portfolio companies needs within public financing and project planning. During the spring of 2014 Forward Technologies was spun out into an independent company and all relevant competencies were transferred to the new company. Over the last years Forward Technologies has worked closely with several of the companies within Serendipity Innovations portfolio both in terms or raising funds but also with project management, technical due diligence and IP strategy. In addition, we aided Serendipity Innovations in creating a pitchbook for the portfolio companies.
Barcelona Supercomputing Center
BSC is the national supercomputing center in Spain and contributes with links to the HPC projects, through the operations and computer science departments, 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 HiPEAC, the ETP4HPC and other international forums such as BDEC. The centre develops technologies for Exascale within the BSC-led Mont-Blanc project, in the DEEP and DEEP-ER projects and the Human Brain Flagship project. BSC has also established joint research centers on Exascale with Intel and IBM. BSC 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.
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.