Partners

In West-Life the following 10 research organisations join forces to establish innovation pipelines

EMBL

EMBL-EBI is a premier bioinformatics institute that manages data covering a wide spectrum of molecular biology. The Protein Data Bank in Europe (PDBe) is one of the five core database team at the EMBL-EBI. Electron Microscopy Data Bank (EMDB), the public archive for the electron microscopy data was funded at PDBe and is now managed by the international consortium EMDataBank, of which PDBe is a founding member. PDBe works closely with the structural biology and bioinformatics community to develop the necessary data infrastructure for archiving of the macromolecular structure information. Within West-Life PDBe will support the existing services to provide programmatic access to macromolecular structure data and integrate it in the VRE portal. It will also implement data management and access tools for modelled complexes and develop a service to allow assessment of these modelled complexes. EMBL-EBI will provide the required computational resources.

EMBL-HH in Hamburg operates three 3rd generation beamlines at the PETRA III storage ring, with the highest peak-brilliance and lowest beam divergence currently available at a synchrotron source, featuring top-hat beam profile and a broad energy range for experiments. EMBL-HH provides extensive services to the structural biology use community in sample preparation and characterisation, synchrotron data collection and computational services.

People: Sameer Velankar, Victor Lamzin

Utrech University (UU)

The Bijvoet Centre for Biomolecular Research of Utrecht University (UU) is a joint research institute of Utrecht University and the Chemical Sciences Research Council (NOW-CW) whose research focuses on mechanisms of molecular recognition and interactions. It hosts severa European experimental infrastructures (in mass spectrometry – FP7 I3 Prime-XS project – and in NMR – FP7 I3 BioNMR project) and is an Instruct centre. The group has developed several user-friendly web portals for the structural biology community, including the widely used HADDOCK portal. Within West-Life, UU will keep supporting the existing WeNMR service and work toward their integration into the new VRE portal and contribute to the integration of new services. It will also provide a tight connection to Tegi-Engage and in particular the related MoBrain Competence Centre to serve translational research form molecular to brain. UU will also offer its computational resources to the project (>1600 CPU cores, including a grid site part of the Dutch NGI).

People: Alexandre Bonvin

Science & Technology Facilities Council

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 sills development. It hosts the CCP4 core team, who support and extend the leading software suite for macromolecular crystallography, and the newly-formed CCP-EM which aims to provide analogous support for EM. Within West-Life, STFC will contribute cloud computing resources, to be used by the job scheduling services that other partners are developing; implement metadata and data access services which other partners will use to implent the planned user interface; and work with IBM to apply Big Data approaches to structural data.

People: Martyn Winn, Chris Morris, Tomas Kulhanek, Denise Small

Netherlands Cancer Institute

The Netherlands Cancer Institute (Stichting Het Nedrlands Kanker Institute - NKI) is an independent research institute focusing on all aspects of cancer research. The research at the Netherlands Cancer Institute covers all aspects of cancer research , from basic research, via translational research to clinical trials, including a strong basic and translational research activity in the areas of (micro)biology, biochemistry, genetics and immunology. In the West-Life, the group of A. Perrakis from the Department of Biochemistry will continue to provide and significantly extent the ProteinCCD server and continue the more recent PDB_REDO service.

People: Anastassis Perrakis, Robbie Joosten

The National Institute for Nuclear Physics

The Instituto Nazionale Di Fisica Nucleare (INFN) is a Public Research Institution that has been developing all along in house open ICT innovation solutions for its own advanced needs of distributed computing and software applications. 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. Within West-Life, INFN will be responsible for Task 4.1 of WP4, aiming at consolidating, operating and evolving the previous WeNMR computational platform into the new West-Life computational platform and services provisioned from the existing grid and cloud based e-infrastructures and projects. INFN will be providing in kind computing power and storage from their grid and cloud resource centres federated with EGI. INFN will also contribute to the other tasks of WP4 concerning the consolidation of the job management mechanism, the programmatic access to structural biology datasets and the unified security and accounting model, and to WP5 by providing technical support for: the integration of the existing and newly developed scientific portals with the underlying computational platform; the creation of customised end-user VMs and/or containers encapsulating the applications; and by providing knowledge base and user support for the gird an cloud related issues.

People: Marco Verlato

Masaryk University

Masaryk University’s is the second largest Czech University. Project partner is the Centre CERIT-SC) CERIT scientific Cloud), part of the Institute of Computer Science. CERIT-SC is an officially recognized part of the national e-infrastructure, complementing CESNET (NREN) and IT4Innovation (HPC) facilities. CERIT-SC and its predecessor, Supercomputing Centre Brno, has been collaborating with the computational chemistry and structural biology groups at Masaryk University since its founding in 1994, by provisioning the resources and supporting their use. Masaryk University will leverage its experience with infrastructure provisioning as the leading partner of WP4, it will contribute to related activities in WP5, and it will use its expertise in software development, optimization, and parallelization to contribute to developments in WP7.

People: Ales Krenek, Kamil Malinka

Consejo Superior de Investigaciones Cientificas

The Spanish National Research Council (CSIC) is the largest public multidisciplinary research organization in Spain. In turn, 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. CNB-CSIC is particularly strong in cryo Electron Microscopy (cryoEM), with seven independent research groups working in this area, which are serviced by a cryoEM facility with several EM microscopes, including a Thalos Artica equipped with a Falcon III. CNB-CSIC also hosts the Instruct Image Processing Center (I2PC), which is the Center of the European Research Infrastructure, Instruct, specialized in the analysis of cryo Electron Microscopy. CSIC is also the organization that coordinates the Spanish NGI, via the Institute of Physics of Cantabria (IFCA).

People: Jose Maria Carazo, Roberto Marabini Ruiz, Jesus Cuenca

Consorzio Interuniversitario di Risonanze Magnetiche di Metalloproteine

The Consortium CIRMMP manages and partially owns one of the best-equipped NMR laboratories in the world: the Magnetic Resonance Centre (CERM). CIRMMP is a key lab of the ESFRI infrastructure for Integrated Structural Biology ( Instruct). 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. Within West-Life, CIRMMP will be responsible for WP3, with the specific aim to foster the interactions of the project with a number of other large-scale actions that include European/global infrastructures and collaborative projects, scientific data initiatives and science policy development. CIRMMP will also be active in disseminating the achievements and services of West-Life. Regarding services, CIRMMP will be providing dedicated computing power to the West-Life computational infrastructure (WP4) and will be responsible for providing a variety of services via web portals, mainly, but not exclusively, addressing NMR data (WP5). Finally, CIRMMP will be significantly involved in the development of new services and workflows, especially integrating in vitro and in-cell NMR data with data from other structural techniques.

People: Lucia Banci, Antonio Rosato

Instruct

Oxford University (Instruct) is a European Research Infrastructure for Structural Biology. Instruct provides access to its infrastructure since 2011, and through its 16 Instruct Centres in 11 countries offers a very comprehensive palette of technologies and supporting services for structure determination. Instruct also manages an internship programme and a pilot R&D award scheme. Instruct provides information on its infrastructure services and accepts proposals via its website portal, which also hosts a number of associated network groups. In this project, Instruct will provide training and networking activities building on its existing structure and operational models.

People: Susan Daenke, Narayanan Krishnan

Luna Technologies

Luna is a Paris based SME. It develops web applications to enable labs and industrial companies to easily launch simulation jobs on flexible cloud computing resources, in order to lower the barriers to entry to complex scientific simulations. Luna works with labs in nuclear research (IRSN and CEA, France), aerospace (CERFACS and Observatoire de Paris, France), and is currently in discussions with the pharmaceutical company Sanofi to deploy its unified numerical simulation web platform. Within West-Life, Luna will contribute extensions to its flagship product, a unified web application to launch simulations with various codes. The web application is free for academics, and so will be the developed extensions.

People: François Ruty, Mathieu Rivière

West-Life people

Collaborators

EGI

EUDAT