Fresh issue


WeNMR, A worldwide e-Infrastructure for NMR and 

structural biology


Period covered: from Nov  1, 2010 to Oct 31, 2011


Project coordinator name, title:  Prof. Alexandre M.J.J. Bonvin


Organization: Utrecht University, The Netherlands


Summary of project objectives


The main objective of WeNMR is to establish an e-Infrastructure-based global virtual research community for structural biology in the life sciences. To this end six objectives are defined:
• To operate, maintain and further develop a user-friendly science gateway for the NMR and SAXS communities,
• To establish a virtual research platform to serve as a digital knowledge repository, data exchange medium, and forum for (interaction with) the user community,
• To provide support to software developers, users and other e-Infrastructure projects in an e-Science knowledge and training centre,
• To foster the adoption and use of e-Infrastructure on a global scale by supporting a wide range of flanking disciplines within the life sciences,
• To operate and consolidate the eNMR Grid infrastructure in line with NGIs and the EGI, and to extend it to interoperate with other worldwide Grid initiatives,
• To develop a model to ensure sustainability of the project.
Description of the work performed since the beginning of the project .


Management and Sustainability


The management of WeNMR has been smoothly over this first period, with all Deliverables and most Milestones being completed on time. Of note, all Deliverables and Milestones scheduled  within this first period have been achieved. Few modifications to operational procedures have been made, with the most prominent one being the implementation of an agreement on the  distribution  of money designated for general outreach activities and the establishment of an MoU with EGI, making WeNMR the 1st Virtual Research Community (VRC) recognized by the EGI. With regard to sustainability, an industrial user panel has been set up and an industrial survey is currently being held, allowing the monitoring of the needs of potential industrial users of the project. Notably, during this first year  21 scientific publications  were generated that acknowledge either the WeNMR project or its direct predecessor, eNMR. Of these, 7 were from completely external users and 14 from consortium members.


Dissemination and Outreach


WeNMR has been extensively promoted worldwide for a broad community through oral and written means of communication. A special flyer advertising WeNMR has been produced and disseminated widely. WeNMR representatives have raised publicity for the project at many key events that focused at the e-Science and structural biology communities, including:
• 8th e-Infrastructure Concertation Meeting (November 2010, Geneva, Switzerland)
• EU-IndiaGrid2 Material Science, Climate Change and Interoperability Workshop (December 2010, Delhi, India)
• CHAIN Launch Event (December 2010, Rome, Italy)
• ISGC (March 2011, Taipei, Taiwan)
• Open Science Grid (March 2011, Boston, USA)
• EGI User forum (April 2011, Vilnius, Lithuania)
• EMBO global exchange lecture course (April 2011, Beijing, China)
• Gordon Conference on Computational Aspects of Biomolecular NMR (May 2011, Lucca, Italy)
• EGI User Virtualization Workshop (May 2011, Amsterdam, the Netherlands)
• IWSG-Life (June 2011, London, UK)
• HealthGrid conference (June 2011, Bristol, UK)
• EGI Technical Forum 2011 (September 2011, Lyon, France)
• CCPN/EU conference (September 2011, Oerias, Portugal)
• e-BioGrid Workshop (November 2011, Amsterdam, the Netherlands)
Outreach towards the WeNMR community has been realized at courses and workshops, some of which were organized together with the Bio-NMR consortium. These workshops have focused on the use of the various web portals that are offered through the WeNMR VRC. The WeNMR VRC also has been extended with tools to generate future rich online surveys to better explore users needs. There are currently surveys available that  collect general user impression of WeNMR, the user opinion about grid security policies, queries about the possibilities for porting software to the grid and a dedicated survey aimed at Industry.
Partner SpronkNMR has deployed outreach activities with WeNMR sustainability in mind.
These included the addition of WeNMR services to a common NMR marketplace hosted by the partner and exploration of a commercial workshop model for WeNMR services.


Operation and Maintenance of the Grid


All WeNMR sites have maintained their middleware constantly up-to-date by timely installing the various releases of INFNGRID gLite. Also, updated versions of the accounting and monitoring software have been installed, allowing for a better management of the WeNMR grid. Various articles and tutorials have been written describing the new gLite features, scripts and tools to facilitate their use by the community.
The number of sites hosted in the WeNMR infrastructure supporting the enmr VO has grown significantly, as has the number of available CPUs for the execution of submitted jobs. With respect to the services offered, no less  than six new portals have been added tot the WeNMR VRC and released for public use (AnisoFIT, MaxOcc, AMBER, GROMACS, SHIFTX2, Antechamber). Portals for automated protein structure determination and an ATSAS SAXS service are about to be released by the time of writing.
With the certification of the BCBR site by the Dutch grid in September, all e-Infrastructure providers within the project are now certified by their respective National or Regional grid authorities. Furthermore, the BCBR and CIRMMP sites have invested in the cluster rooms and extension of computational infrastructure to secure  the sustainability of the infrastructure in the future.


Worldwide grid extension


Worldwide grid extension has included the deployment and testing of a selection of the WeNMR software at sites in  Brazil, Argentina en Venezuela and the addition of a new WeNMR grid site in Taiwan. Together they have successfully added 2040 CPU-cores to the WeNMR grid. Jobs have been running smoothly in Taiwan as well as  at the University of Johannesburg grid sites. Initial steps towards extensions to the OSG grid and SBGrid infrastructure have been made and integration of the SAGrid infrastructure was continued.  The collaboration with the SBGrid VO  in the US  resulted in middleware infrastructure compatible with this VO to be setup at the INFN-Padova site and infrastructure tests being carried out. Over the next period, we aim at expanding the WeNMR grid further towards Latin American and the Asian grid infrastructures. An interoperability roadmap between WeNMR/EGI and SBGrid/OSG has been agreed and first test of WeNMR job submission towards OSG grid have started.


Virtual Research Community portal (VRC)


The initial development of the WeNMR VRC has now been completed. The VRC platform is fully operational, with all major sections in place. A support and expertise center has been put in place and thirty different Help Center areas are available for support by project partners or associated software developers that process the requests. In addition, a large number of standard methods and tutorials have been made available, contributed by the partners of the consortium. After a clear increase of the number of daily visitors during the first half of period 1, which was clearly linked to the outreach activities, the VRC now receives a stable number of approximately 50 unique different visitors per day, from a total visitor population that covers over a 100 different countries. Over the next period, the plan is to migrate the VRC to the latest version of the Drupal content management system, and to further extend the content of the VRC to cover all necessary areas, especially in the form of standard protocols and online movie lectures.


Research Platform


Steady progress was made in the development of protocols for the joined usage of SAXS and NMR data. The HADDOCK software for macromolecular docking has been extended with a Radius of Gyration restraint that can be derived from SAXS data. The method has been optimized with respect to the force constant associated to the restraint energy term and shown to improve docking results using benchmark data. In addition, Partner CIRMMP has provided a portal for the combined use of paramagnetic NMR and SAXS data for the study of conformational flexibility in multi-domain proteins. Partner 7 has made considerable advances in porting parts of the ATSAS software suite for the analysis of SAXS data to the grid. A web based portal of DAMMIF software for rapid shape determination is nearly ready for public release with more portals to follow. The aim for the future is to link these portals to the data storage facility that is used by the graphical user interface of the SAXS beam line remote operation facility. With respect to NMR data, partner RUN has started working on a new iteration of the RECOORD project called NMR_REDO for recalculation of NMR structures in the PDB for which experimental data is available. Furthermore, partner RUN has developed and tested a virtual machine running the CING NMR structure validation software called VirtualCing. This virtual machine is Cloud ready and has been tested as such at SARA (Dutch  High Performance Computing and e-Science Support Center, and supernode in International Science Grid). The results are publically available at the NRG-CING web site. The viability of an end-user platform using a Scientific Linux distribution equipped with the Miramare Interoperable Lite UI (MILU) version of the gLite User Interface operated as virtual machine has been demonstrated by Partner UU by running the HADDOCK tutorials at several workshops. The Partner EMBL-HH also ported their ATSAS application suite to run on the Scientific Linux and is thus ready to run on the grid and the virtual machine. The development of the end user Workflow Management System has suffered slightly due to  serious  health issues of the main developer, but some imminent issues have been resolved through the implementation of dedicated workflow management code. Overall, its development is on schedule, with a first alpha release planned in January 2012.
Description of main results so far 
• WeNMR VRC gateway established (http://www.wenmr.eu) and fully operational.
• WeNMR 1st Virtual Research Community (VRC) recognized by the EGI. MoU signed in Vilnius by Steve Newhouse, EGI director, and Alexandre Bonvin, WeNMR project coordinator, during the 2011 EGI User Forum
• MoU’s signed with EMI, eSciencetalk, EUMEDGRID, EGI-Inspire, ERINA+ and CHAIN
• Eight courses and workshops organized for (potential) WeNMR users, of which three in collaboration with the Bio-NMR project
• WeNMR presented at numerous conferences within and outside Europe
• Six new web portals added to the WeNMR VRC site
• WeNMR grid extended with four new grid sites from Latin America
• First WeNMR jobs successfully run on the US OSG grid (in collaboration with SBGrid)
• WeNMR largest VO in the life sciences area

Expected final results and potential impact and use


The socio economic impact of the project will be assessed in collaboration with the ERINA+ project. Furthermore, WeNMR is participating in a survey from the Fraunhofer Institute for Systems and Innovation Research (ISI) and the Centre for European Economic Research (ZEW). This survey aims at the "Development of impact measures for E-Infrastructures" and is carried out on behalf of the E-Infrastructure Programme of the European Commission, Information Society and Media Directorate General, Unit F3.


Project website information


The WeNMR Virtual Research Community website (http://www.wenmr.eu) forms the central point of access for the users, developers and contributors that are targeted by the WeNMR project, to help them harness the potential of the WeNMR services and thus improve their research. Information, training, technical support and direct access to the grid services are provided through the VRC portals with access on different levels to serve different communities. Active participation of users from various backgrounds is strongly encouraged and available through the Forums, Blogs and Wiki areas of the website.