|Utrecht University, Bijvoet Center for Biomolecular Research, the Netherlands|
|Consorzio Interuniversitario Risonanze Magnetiche Di Metalloproteine Paramagnetiche, Florence University, Italy|
|Consejo Superior de Investigaciones Cientificas (and Spanish NGI)|
|Science and Technology Facility Council, UK|
|Provincia Lombardo Veneta Ordine Ospedaliero di SanGiovanni di Dio – Fatebenefratelli, Italy|
|Istituto Nazionale Di Fisica Nucleare, Italy|
|SURFsara (Dutch NGI)|
|CESNET (Czech NGI)|
|Open Science Grid (US)|
The MoBrain competence center is open for additional members. Please email the CC coordinator to join.
MoBrain Consortium in more details
The MoBrain consortium provides expertise in software development, user support and training and innovative technical solutions, gathering the long-standing expertise that the various partners have been building over the years. It covers both the microscopic (structural biology) scale – building on the successful eNMR and WeNMR FP7 e-Infrastructure projects (P01, P02, P07) and their vibrant and still growing user community, adding new expertise in structural biology with cryo-electron microscopy (P03) and x-ray scattering (P04) to serve the ESFRI INSTRUCT community. At the macroscopic level (brain and neurodegenerative research) MoBrain builds on the expertise accumulated in the DECIDE, outGRID, neuGRID and neuGRID4YOU FP7 e-Infrastructure projects (P05) and their associated medical community with the scientific expertise covered by the “The National Centre for Alzheimer’s and Mental Diseases”, Provincia Lombardo Veneta Ordine Ospedaliero di San Giovanni di Dio - Fatebenefratelli (P05) with connections to the Human Brain Project. The technical expertise is covered by the technology-oriented partners (P06, P07) with additional support from several NGIs. The MoBrain competence center has already a worldwide character, since the two Virtual Research Communities already have a large worldwide user base and strong connections in Asia-Pacific (e.g. with Academia Sinica via WeNMR), as well as in the US and Canada (OSG and several research centers and platforms for the brain diseases such as: LONI, C-BRAIN, GAAIN, etc..). A short description of each partner and its expertise is provided in the following.
P01 - The Bijvoet Center for Biomolecular Research (BCBR) is a joint research institute of Utrecht University and the Chemical Sciences Research Council (NWO-CW) whose research focuses on mechanisms of molecular recognition and interactions. It hosts several European experimental infrastructures (in mass spectrometry – FP7 I3 Prime-XS project – and in NMR – FP7 I3 BioNMR project and H2020 project iNext) and is an INSTRUCT center. Within BCBR, the NMR group has a long-standing participation in EU-funded programs, including the e-Infrastructure eNMR and WeNMR projects (the latter was coordinated by Utrecht). The site is operating a grid infrastructure embedded in the Dutch NGI resources. The group has developed several user-friendly web portals for the structural biology community, including the widely used HADDOCK portal. The WeNMR project coordinator, Prof. Bonvin, is member of the EGI User Community Board and of the External Advisory Committee of EGI-InSpire. He will coordinate the CC and lead the DIRAC4EGI (Task 4) and WeNMR/NeuGrid4You integration (Task 6) projects.
P02 - The consortium CIRMMP manages and partially owns one of the best-equipped NMR laboratories in the world: the Magnetic Resonance Center (CERM). CIRMMP is a key lab of the ESFRI infrastructure for Integrated Structural Biology (INSTRUCT, www.structuralbiology.org). CERM has a long tradition of expertise in the characterization of the structure and dynamics of proteins in solution through NMR and is one of the world-leading institutions in structural biology of metalloproteins and in the study of metals in biological systems, both in vitro and in living cells. In addition, this partner has a strong expertise in the application of bioinformatics to the analysis of genome sequences and of metalloproteins. Within this frame, CERM researchers have developed various tools and web servers for the analysis of these systems. In addition, CERM has developed various grid-enabled portals for the analysis and processing of NMR data. These include the AMPS-NMR portal for protein structure refinement and the MaxOcc portal for the study of dynamics in multi-domain proteins. CIRMMP is bringing in a GPU testbed which will be used in Task 5.
P03 - The Spanish National Research Council (CSIC) is the largest public multidisciplinary research organisation in Spain. It collaborates with national and international universities, public RTD organisations, SMEs, companies and other institutions of a scientific/technological nature. The National Centre of Biotechnology (CNB-CSIC) is one of the largest centers of the CSIC organization with research focus in the areas of biomedicine, agriculture and environment. It offers a large set of Research Services and Research Support Services, including Electron Microscopy, hosting the Instruct Image Processing Center (I2PC). The I2PC/CNB is a leading center in the development of software for cryo-EM data processing, with suites like XMIPP that have been downloaded by close to 2000 registered users. Its expertise is particularly relevant for Task 2. CSIC is also the organization that coordinates the Spanish NGI, via the Institute of Physics of Cantabria (IFCA). The engagement of CSIC with distributed computing and EGI is therefore complete. CSIC will be able to provide resources linked to EGI via the Federated Cloud, and expertise when it comes to deploy services on top of EGI resources.
P04 - The Science and Technology Facility Council (STFC) is one of the UK's seven publicly funded Research Councils responsible for supporting, coordinating and promoting research, innovation and skills development. STFC is also the lead partner in the UK NGI. The Scientific Computing Department (SCD) provides large-scale HPC facilities, computing data services and infrastructure, with a long history in European grid computing, being one of the partners in DataGrid, in EGEE I/II/III and EGI InSPIRE. SCD also has a history of developing and supporting software for structural biology. It hosts the CCP4 core team, who support and extend the leading software suite for macromolecular crystallography, components of which, together with other relevant software (NMR, cryo-EM,…) will be made available in customized VMs (Task 3).
P05 - The IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico – Research and Care Institute) San Giovanni di Dio Fatebenefratelli (IRCCS FBF) is the National Centre for Research and Care of Alzheimer’s disease. A leading centre in the field of Alzheimer’s with particular regard to neuroimaging research, it has strong connections with leading academic centres worldwide. About 4,500 persons with Alzheimer’s disease or associated disorders and 1,700 with mental disorders are treated yearly. Neuroscientists at IRCCS FBF have first-hand knowledge of the issues involved with archiving/retrieval of neuroimages and of computationally intensive image analysis algorithms with a long lasting experience in conducting multicentre imaging studies and EC-funded projects. IRCCS FBF led the FP7 neuGRID (ww.neuGRID.eu) e-Infrastructure project and is currently leading the FP7 NEUGRID4YOU (https://www.neugrid4you.eu) e-Infrastructure project, building the neuGRID infrastructure to deliver a Virtual Laboratory offering neuroscientists access to a wide range of datasets and algorithm pipelines, computational resources, services, and a specific support centre.
P06 - Gnubila France (https://gnubila.fr/) is a consulting firm delivering ICT solutions and professional services axed on Grid and Cloud computing with a special emphasis on e-Health and Health Information Systems. Gnubila Technology, on a larger scale, provides cross-sectorial solutions including but not restricted to Information System, Customer Relationship Management and Data Integration for Public Administration, Financial Institutions and Small and Medium Enterprises. Gnubila is implanted in Archamps in France. Gnubila is involved in several national, European and international collaborations including the FP7 projects Ginseng (light grid for e-health and epidemiology), outGRID (www.outgrid.eu) (international cooperation towards neuGRID’s interoperability with US and Canada initiatives) and the current FP7 NEUGRID4YOU (https://www.neugrid4you.eu) project where it is leading the technical supervision and contributing to the design and feasibility toward creating the core of a Worldwide e-Infrastructure for Computational Neurosciences.
P07 – The Istituto Nazionale Di Fisica Nucleare (INFN) is a Public Research Institution that has been developing all along in house open ICT innovative solutions for its own advanced needs of distributed computing and software applications. It has a remarkable excellence expertise on Grid and Cloud technologies and related middleware (INFN was a key partner in the European Middleware Initiative) having fostered and participated, with leadership roles, to many of the large Projects financed by EC that promoted the realization of the EGI. INFN, as a coordinator of the Italian Grid Infrastructure (IGI), is a leader in the development of distributed computing, having established one of the largest European Grid infrastructure, including more than 56 Data Centres. It has supported since 2007 the EGI enmr.eu VO hosting several central services (LFC, VOMS, VO-Nagios) and the related WeNMR VRC.
P08 – SURFsara is the Dutch national Centre for Data and Computing infrastructure, providing a complete package of services including High Performance Computing, networking, data services, visualization, e-Science Support and Cloud Services. SURFsara works together with the academic community (including researchers, educational institutions and academic medical centers) and with industry and SMEs. It is the Dutch NGI, collaborating in technology development projects at EGI and other European e-infrastructure projects such as WE-NMR. SURFsara is, as part of the Dutch TechCentre for Life Sciences (DTL), the ELIXIR-NL node. The Dutch national e-infrastructure service provider has a large user community from life science and health research and is involved in developing a scalable infrastructure for user communities based on use cases and requirements, such as those involved in medical imaging and genomics big data. National projects involve the NFU (federation of academic medical centres) program research data infrastructure, CTMM-TraIT (www.ctmm-trait.nl) infrastructure for medical research, and BBMRI. In this Competence Centre SURFsara will provide cloud resources to test and deploy computational services relevant for the various tasks, as well as connect to the big data biomedical research community.
P10 – CESNET, Association of Legal Entities, is a public non-profit organization established by all the public universities and the Academy of Science of the Czech Republic. Serving as a recognized Czech NREN and NGI, CESNET is a member of several international organizations, including DANTE, TERENA, CEENet and EGI.eu (European Grid Infrastructure). CESNET is also involved in many national and international projects, including GEANT EU Datagrid, EGEE, EMI and EGI-Inspire. CESNET, in cooperation with other data centres (CERIT-SC at Masaryk University in particular) also operates the Czech national grid and cloud environment and it is the key partner in the EGI Federated Cloud. Due to 20 years of relationships with the e-Infrastructure users it has extensive knowledge of the application software from the infrastructure point of view (installation aspects, data throughput, networking and computing requirements, etc.) in structural biology in particular. CESNET is active in GPGPU computing research, and supports several GPU-enabled applications (AMBER, GROMACS, …) on its production infrastructure.
P11 – Open Science Grid - US based EGI peering grid infrastructure. The OSG provides common services and support for resource providers and scientific institutions using a distributed fabric of high throughput computational services. The OSG is jointly funded by the Department of Energy and the National Science Foundation. OSG partners work closely with EGI to provide international researchers access to resources provided by both infrastructures.