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1. Grid enabled virtual screening against malaria

Author

Jacq, N., Salzemann, J., Jacq, F., Legré, Y., Medernach, E., Montagnat, J., Maass, A., Reichstadt, M., Schwichtenberg, H., Sridhar, M., Kasam, V., Zimmermann, M., Hofmann, M., and Breton, V.

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

WISDOM is an international initiative to enable a virtual screening pipeline on a grid infrastructure. Its first attempt was to deploy large scale in silico docking on a public grid infrastructure. Protein-ligand docking is about computing the binding energy of a protein target to a library of potential drugs using a scoring algorithm. Previous deployments were either limited to one cluster, to grids of clusters in the tightly protected environment of a pharmaceutical laboratory or to pervasive grids. The first large scale docking experiment ran on the EGEE grid production service from 11 July 2005 to 19 August 2005 against targets relevant to research on malaria and saw over 41 million compounds docked for the equivalent of 80 years of CPU time. Up to 1,700 computers were simultaneously used in 15 countries around the world. Issues related to the deployment and the monitoring of the in silico docking experiment as well as experience with grid operation and services are reported in the paper. The main problem encountered for such a large scale deployment was the grid infrastructure stability. Although the overall success rate was above 80%, a lot of monitoring and supervision was still required at the application level to resubmit the jobs that failed. But the experiment demonstrated how grid infrastructures have a tremendous capacity to mobilize very large CPU resources for well targeted goals during a significant period of time. This success leads to a second computing challenge targeting Avian Flu neuraminidase N1., Comment: 34 pages, 5 figures, 3 tables, to appear in Journal of Grid Computing

Published
2006

2. Large Scale In Silico Screening on Grid Infrastructures

Author

Jacq, N., Breton, V., Chen, H. -Y., Ho, L. -Y., Hofmann, M., Lee, H. -C., Legré, Y., Lin, S. -C., Maass, A., Medernach, E., Merelli, I., Milanesi, L., Rastelli, G., Reichstadt, M., Salzemann, J., Schwichtenberg, H., Sridhar, M., Kasam, V., Wu, Y. -T., and Zimmermann, M.

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing, Quantitative Biology - Quantitative Methods
Abstract

Large-scale grid infrastructures for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale in silico docking within the framework of the WISDOM initiative against Malaria and Avian Flu requiring about 105 years of CPU on the EGEE, Auvergrid and TWGrid infrastructures. These achievements demonstrated the relevance of large-scale grid infrastructures for the virtual screening by molecular docking. This also allowed evaluating the performances of the grid infrastructures and to identify specific issues raised by large-scale deployment., Comment: 14 pages, 2 figures, 2 tables, The Third International Life Science Grid Workshop, LSGrid 2006, Yokohama, Japan, 13-14 october 2006, to appear in the proceedings

Published
2006

3. Towards grid-enabled telemedicine in Africa

Author

Jacq, F., Bacin, F., Meda, N., Donnarieix, D., Salzemann, J., Vayssiere, V., Jacq, N., Renaud, M., Traore, F., Meda, G., Nikiema, R., and Breton, V.

Subjects
Physics - Instrumentation and Detectors
Abstract

Telemedicine services are very relevant tools to train local physicians and to improve diagnosis by exchanging medical data. Telemedicine networks allow these exchanges but the set-up of multipoint dynamic telemedicine requires moving towards GRID technologies. A healthgrid is an environment where data of medical interest can be stored and is easily available between the different actors of healthcare. Two telemedicine applications were developed to link physicians from Burkina Faso and France with the perspective of setting up a grid infrastructure between the participating medical sites. A web site to exchange diagnosis on diabetic retinopathy was developed in PHP and another application using web services was developed to exchange patient information between two databases., Comment: 7 pages, 1 figure, IST-Africa 2006 Conference, Pretoria, South Africa, to be published in the proceedings

Published
2006

5. g-INFO portal: a solution to monitor Influenza A on the Grid for non-grid users

Author

Trung-Tung Doan, Quang-Minh Dao, Trong-Hieu Vu, Hong-Phong Pham, Vincent Breton, Hong-Quang Nguyen, Salzemann, J., Yannick Legre, Thanh-Hoa Le, Johan Montagnat, Institut de la francophonie pour l'informatique (IFI), Agence universitaire de la francophonie, High Performance Computing Center (HPCC), Hanoi University of Science and Technology (HUST), Institute of Information Technology, Vietnamese Academy of Science and Technology, PCSV, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), HealthGrid, HealthGrid association (HealthGrid), HealthGrid-HealthGrid, Institute of Biotechnology, Vietnam Academy of Sciences and Technology, Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Equipe MODALIS, Scalable and Pervasive softwARe and Knowledge Systems (Laboratoire I3S - SPARKS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
genetic structures, education, virus diseases, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC]
Abstract

International audience; In this paper, we introduce a portal for monitoring Influenza A on a grid-based system. Influenza A keeps on being a major threat to public health worldwide; especially if one virus can mutate itself so that it acquires the capacity for human to human transmission of H1N1 as well as the high death rate of H5N1. The existing g-INFO (Grid-based Information Network for Flu Observation) project provides a complete system for monitoring flu virus on the Grid. We present here a portal that operates on top of the g-INFO system as a solution for non-grid users to utilize grid services for analyzing molecular biology data of Influenza A.

Published
2011

6. Grid-based International Network for Flu Observation (g-INFO)

Author

Doan, T. T., Bernard, A., Da Costa, A. L., Bloch, V., H Le, T., Yannick Legre, Maigne, L., Salzemann, J., Nguyen, H. Q., Vincent Breton, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Régulations des réactions immunitaires et inflammatoires, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Nice Sophia Antipolis (... - 2019) (UNS), and Pellet, Jeanine

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

International audience

Published
2010

7. The new WISDOM environment

Author

Salzemann, J., Bloch, V., Reichstadt, M., Delahaye, M., Da Costa, A., Tran, T.T., Lee, S., Kim, J., Kim, N., Hwang, S., BRETON, Vincent, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Published
2009

8. Towards semantic and synthactic interoperabilities in life sciences: the case of EMBRACE

Author

Salzemann, J., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR]
Published
2009

9. Une plate-forme bioinformatique en Auvergne

Author

Salzemann, J., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Published
2008

10. HOPE Hospital Platform for E-health

Author

Salzemann, J., De Vlieger, Paul, Maigne, L., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR]
Published
2008

11. A bioinformatics platform: the evolution of the WISDOM environment

Author

Bloch, V., Salzemann, J., Reichstadt, M., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), and WISDOM

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

Demo; Mature and efficient, the WISDOM environment has evolved continuously to take advantage of the Grid computing and storage resources for large-scale drug discovery applications. The environment has also been used on several occasions for other bioinformatics applications, thanks to its flexibility and its simplicity. This new bioinformatics platform just brings the environment to a new level: combining bioinformatics tools altogether within the same framework.

Published
2008

12. A platform for bioinformatics on the grids

Author

Reichstadt, M., Salzemann, J., Bloch, V., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Published
2008

13. HOPE, an open platform for medical data management on the grid

Author

Diarena, M., Nowak, S., Boire, J. Y., Bloch, V., Donnarieix, D., Fessy, A., Grenier, B., Irrthum, B., Legré, Y., Maigne, L., Salzemann, J., Thiam, C., Spalinger, N., Verhaeghe, N., Vlieger, P., Vincent Breton, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Equipe de Recherche en Signal et Imagerie Medicale (ERIM-ERI 14), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, HealthGrid Association (HealthGrid), HealthGrid Association, CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand, T. Solomonides, J.C. Silverstein, J. Saltz, Y. Legré, M. Kratz, I. Foster, V. Breton, and J.R. Beck

Subjects
[INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR], medical data, Medical Records Systems, Computerized, Medical Informatics Computing, Neurosurgery, Access to Information, Databases as Topic, Computer Systems, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, Humans, France, telemedicine, data management, Grid, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Monte Carlo Method, Algorithms, Computer Security, Software, ComputingMilieux_MISCELLANEOUS
Abstract

The paper describes a platform developed for the secure management and analysis of medical data and images in a grid environment. Designed for telemedicine and built upon the EGEE gLite middleware and particularly the metadata catalogue AMGA as well as the GridSphere web portal, the platform provides to healthcare professionals the capacity to upload and query medical information stored over distributed servers. A job submission environment is also available for data analysis. Security features include authentication and authorization by grid certificates, anonymization of medical data and image encryption. The platform is currently deployed on several sites in Europe and Asia and is being customized for applications in the field of telemedicine and medical physics.

Published
2008

14. WISDOM

Author

Salzemann, J., Bloch, V., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), and WISDOM

Subjects
bioinformatics, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], drug-discovery, large scale deployment
Abstract

Demo, Abstracts Book; The environment evolved throughout the development: It was first made of a set ofscripts that generate the jobs, submit the files and check regularly their statuswhile they are on the Grid. Through this abstract we want to present the newenvironement that is based on the AMGA metadata catalog for more flexibility andon a Java environment that can be used through web services. The environment isvery flexible and can be used for any type of bioinformatics application.In thisnew environment we control the job distribution, maintaing the choice of directlysubmitting the executable (push mode) or implementing a two-way submission wherethe system submits generic wrapper jobs which request their paylod (theexecutable and the input data) only when they start to be executed (pull mode).

Published
2008

15. WISDOM: grid enabled identification of active molecules against targets implicated in Malaria

Author

Da Costa, A. L., Kasam, V., Salzemann, J., Bloch, V., Vincent Breton, Rastelli, G., Degliesposti, G., Kang, H. K., Kim, D., Saidani, N., Marechal, E., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Auvergrid, Wisdom, docking, malaria, plasmepsin, in vitro, EGEE, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], virtual screening, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], molecular dynamics
Abstract

à paraître dans l'Abstract book

Published
2008

16. WISDOM : a large scale drug discovery application on the Grid

Author

Salzemann, J., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), and WISDOM

Subjects
Wisdom, malaria, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], grid
Abstract

Présentation en ppt

Published
2008

17. Improving e-Science with Interoperability of the e-Infrastructures EGEE and DEISA

Author

Riedel, M., Memon, A. S., Memon, M. S., Mallmann, D., Venturi, V., Andreetto, P., Marzolla, M., Ferraro, A., Ghiselli, A., Hedman, F., Shah, Z. A., Salzemann, J., Da Costa, A., Bloch, V., Vincent Breton, Kasam, V., Hofmann-Apitius, M., Snelling, D., Berghe, S., Li, V., Brewer, S., Dunlop, A., Silva, N., M. Riedel, A.S. Memon, M.S. Memon, D. Mallmann, A. Streit, V. Venturi, P. Andreetto, M. Marzolla, A. Ferraro, A. Ghiselli, F. Hedman, Zeeshan A. Shah, J. Salzemann, A. Da Costa, V. Breton, V. Kasam, M. Hofmann-Apitiu, D. Snelling, S. van de Berghe, V. Li, S. Brewer, A. Dunlop, and N. De Silva

Abstract

In the last couple of years, many e-Science infrastructures have begun to offer production services to e- Scientists with an increasing number of applications that require access to different kinds of computational resources. Within Europe two rather different multi-national e-Science infrastructures evolved over time namely Distributed European Infrastructure for Supercomputing Applications (DEISA) and Enabling Grids for E-SciencE (EGEE). DEISA provides access to massively parallel systems such as supercomputers that are well suited for scientific applications that require many interactions between their typically high numbers of CPUs. EGEE on the other hand provides access to a world-wide Grid of university clusters and PC pools that are well suited for farming applications that require less or even no interactions between the distributed CPUs. While DEISA uses the HPC-driven Grid technology UNICORE, EGEE is based on the gLite Grid middleware optimized for farming jobs. Both have less adoption of open standards and therefore both systems are technically non-interoperable, which means that no e-Scientist can easily leverage the DEISA and EGEE infrastructure with one suitable client environment for scientific applications. This paper argues that future interoperability of such large e-Science infrastructures is required to improve e-Science in general and to increase the real scientific impact of world-wide Grids in particular. We discuss the interoperability achieved by the OMII-Europe project that fundamentally improved the interoperability between UNICORE and gLite by using open standards. We also outline one specific scientific scenario of the WISDOM initiative that actually benefits from the recently established interoperability.

Published
2008

18. Overview of the gLite middleware

Author

Salzemann, J., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR], [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC]
Published
2007

19. WISDOM : a large scale docking application on the grid

Author

Bloch, V., Lee, H.-C., Salzemann, J., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

PCSV

Published
2007

20. Wisdom

Author

Bloch, V., Breton, Vincent, Salzemann, J., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

PCSV

Published
2007

21. Replication and update of molecular biology databases in a grid environment

Author

Salzemann, J., Jacq, N., Gaël Le Mahec, Vincent Breton, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
web services, Grid computing, biological databases, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], databases replication and update on grid, grid services
Abstract

PCSV, présenté par V. Breton, à paraître dans les proceedings; Update of molecular biology databases is a growing burden on the biomedical research community. As the grid allows to share and replicate data, we propose a service to automatically update the biology databases from a single changing reference using web services. In this paper we report the components, the architecture and the deployment of the update service on the french RUGBI grid infrastructure. RUGBI is a computing grid infrastructure based on existing middleware and technologies for the community of scientists in bioinformatics.

Published
2006

22. In Silico Docking on Grid Infrastructure to Accelerate Structure-based Design Against Influenza A Neuraminidases

Author

Jacq, N., Vincent Breton, C Lee, H., Salzemann, J., Y Chen, H., Milanesi, L., T Wu, Y., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Genomics Research Center (GENOMICS RESEARCH CENTER), Academia Sinica, Institute for Biomedical Technologies (ITB), Consiglio Nazionale delle Ricerche [Roma] (CNR), and National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC]
Abstract

présenté par N. Jacq, à paraître dans the "Abstract Book"; Finding potential compounds that can inhibit the activities of Influenza A neuraminidase N1 subtype variants. Accelerating the discovery of novel potent inhibitors through minimizing non-productive trial-and-error approaches. Improving the efficiency of high throughput screening thanks to the grid infrastructure.

Published
2006

23. In silico docking on EGEE infrastructure: the case of WISDOM

Author

Jacq, N., Vincent Breton, Sridhar, M., Vinod-Kusam, K., Salzemann, J., Yannick Legre, Reichstadt, M., Jacq, F., Hofmann, M., Zimmermann, M., Maas, A., Medernach, E., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det]
Abstract

PCSV, présenté par N. Jacq, transparents sur site, pas de proceedings

Published
2006

24. Les grilles pour le développement médical

Author

Jacq, N., Reichstadt, M., Jacq, F., Salzemann, J., Zimmermann, M., Maas, A., Sridhar, M., Vinodkusam, K., Schwichtenberg, H., Hofmann, M., Vincent Breton, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Communication & Systèmes [Toulouse] (C-S), and Communication & Systèmes-CS-SI France

Subjects
Grille informatique, paludisme, maladie négligée, [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], in silico docking, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC]
Abstract

PCSV, présenté par V. Breton, à paraître dans les Comptes-Rendu de la Conférence; Le développement récent des sciences et technologies de l'information et de la communication permet aujourd'hui la création de véritables infrastructures pour le calcul et le stockage de données hétérogènes à l'échelle régionale, nationale et internationale. Ces infrastructures, appelées grilles informatiques, permettront bientôt d'utiliser les ressources informatiques mutualisées avec autant de facilité que nous utilisons aujourd'hui l'électricité. L'utilisation des grilles afin d'accélérer la découverte de médicaments est une voie très prometteuse pour l'avenir. Par cette approche in silico, le nombre de molécules ainsi que la vitesse de test peuvent être grandement augmentés induisant un coût moindre de développement de médicaments. Du 11 Juillet au 31 Août 2005, l'expérience WISDOM (Wide In Silico Docking On Malaria) a permis de tester rien moins qu'un million de ligands (médicaments potentiels) pour le traitement du paludisme: 1700 ordinateurs à travers le monde ont ainsi été associés à cette démarche permettant de réaliser en un mois ce qui aurait nécessité 80 ans sur un ordinateur classique. L'analyse des résultats est en cours. Par cette approche, on peut souhaiter également que les maladies orphelines puissent bénéficier d'un intérêt nouveau de la part des industries pharmaceutiques, à travers notamment la baisse du coût de développement d'un médicament, principal obstacle actuellement à leur mobilisation.

Published
2005

25. The EMBRACE web service collection.

Author

Pettifer, S., Ison, J., Kalas, M., Thorne, D., McDermott, P., Jonassen, I., Liaquat, A., Fernandez, J.M., Rodriguez, J.M., Pisano, D.G., Blanchet, C, Uludag, M., Rice, P., Bartaseviciute, E., Rapacki, K., Hekkelman, M.L., Sand, O., Stockinger, H., Clegg, A.B., Bongcam-Rudloff, E., Salzemann, J., Breton, V., Attwood, T.K., Cameron, G., Vriend, G., Pettifer, S., Ison, J., Kalas, M., Thorne, D., McDermott, P., Jonassen, I., Liaquat, A., Fernandez, J.M., Rodriguez, J.M., Pisano, D.G., Blanchet, C, Uludag, M., Rice, P., Bartaseviciute, E., Rapacki, K., Hekkelman, M.L., Sand, O., Stockinger, H., Clegg, A.B., Bongcam-Rudloff, E., Salzemann, J., Breton, V., Attwood, T.K., Cameron, G., and Vriend, G.

Abstract

1 juli 2010, Contains fulltext : 89021.pdf (publisher's version ) (Open Access), The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions.

Published
2010

26. PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

Author

Joosten, R.P., Salzemann, J., Bloch, V., Stockinger, H., Berglund, A, Blanchet, C, Bongcam-Rudloff, E., Combet, C., Da Costa, A.L., Deleage, G., Diarena, M., Fabbretti, R., Fettahi, G., Flegel, V., Gisel, A., Kasam, V., Kervinen, T., Korpelainen, E., Mattila, K., Pagni, M., Reichstadt, M., Breton, V., Tickle, I.J., Vriend, G., Joosten, R.P., Salzemann, J., Bloch, V., Stockinger, H., Berglund, A, Blanchet, C, Bongcam-Rudloff, E., Combet, C., Da Costa, A.L., Deleage, G., Diarena, M., Fabbretti, R., Fettahi, G., Flegel, V., Gisel, A., Kasam, V., Kervinen, T., Korpelainen, E., Mattila, K., Pagni, M., Reichstadt, M., Breton, V., Tickle, I.J., and Vriend, G.

Abstract

Contains fulltext : 81681.pdf (publisher's version ) (Open Access)

Published
2009

27. The EMBRACE web service collection

Author

Pettifer, S., primary, Ison, J., additional, Kalas, M., additional, Thorne, D., additional, McDermott, P., additional, Jonassen, I., additional, Liaquat, A., additional, Fernandez, J. M., additional, Rodriguez, J. M., additional, Partners, I.-, additional, Pisano, D. G., additional, Blanchet, C., additional, Uludag, M., additional, Rice, P., additional, Bartaseviciute, E., additional, Rapacki, K., additional, Hekkelman, M., additional, Sand, O., additional, Stockinger, H., additional, Clegg, A. B., additional, Bongcam-Rudloff, E., additional, Salzemann, J., additional, Breton, V., additional, Attwood, T. K., additional, Cameron, G., additional, and Vriend, G., additional

Published
2010
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28. Grid-enabled Virtual Screening Against Malaria

Author

Jacq, N., primary, Salzemann, J., additional, Jacq, F., additional, Legré, Y., additional, Medernach, E., additional, Montagnat, J., additional, Maaß, A., additional, Reichstadt, M., additional, Schwichtenberg, H., additional, Sridhar, M., additional, Kasam, V., additional, Zimmermann, M., additional, Hofmann, M., additional, and Breton, V., additional

Published
2007
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34. HOPE, an Open Platform for Medical Data Management on the Grid.

Author

Solomonides, Tony, Silverstein, Jonathan C., Saltz, Joel, Legré, Yannick, Kratz, Mary, Foster, Ian, Breton, Vincent, Beck, J. Robert, Diarena, M., Nowak, S., Boire, J.Y., Bloch, V., Donnarieix, D., Fessy, A., Grenier, B., Irrthum, B., Legré, Y., Maigne, L., Salzemann, J., and Thiam, C.

Abstract

The paper describes a platform developed for the secure management and analysis of medical data and images in a grid environment. Designed for telemedicine and built upon the EGEE gLite middleware and particularly the metadata catalogue AMGA as well as the GridSphere web portal, the platform provides to healthcare professionals the capacity to upload and query medical information stored over distributed servers. A job submission environment is also available for data analysis. Security features include authentication and authorization by grid certificates, anonymization of medical data and image encryption. The platform is currently deployed on several sites in Europe and Asia and is being customized for applications in the field of telemedicine and medical physics. [ABSTRACT FROM AUTHOR]

Published
2008

35. Grid-Enabled High-Throughput In Silico Screening Against Influenza A Neuraminidase.

Author

Hurng-Chun Lee, Salzemann, J., Jacq, N., Hsin-Yen Chen, Li-Yung Ho, Merelli, I., Milanesi, L., Breton, V., Lin, S.C., and Ying-Ta Wu

Abstract

Encouraged by the success of the first EGEE biomedical data challenge against malaria (WISDOM) , the second data challenge battling avian flu was kicked off in April 2006 to identify new drugs for the potential variants of the influenza A virus. Mobilizing thousands of CPUs on the Grid, the six-week-long high-throughput screening activity has fulfilled over 100 CPU years of computing power and produced around 600 gigabytes of results on the Grid for further biological analysis and testing. In the paper, we demonstrate the impact of a worldwide Grid infrastructure to efficiently deploy large-scale virtual screening to speed up the drug design process. Lessons learned through the data challenge activity are also discussed [ABSTRACT FROM PUBLISHER]

Published
2006
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36. Integration of EMBRACE-Compliant services on the grid

Author

Da Costa, A., Salzemann, J., Bloch, V., Vincent Breton, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]

37. Grid enabled virtual screening against malaria

Author

Jacq, N., Salzemann, J., Jacq, F., Yannick Legre, Medernach, E., Johan Montagnat, Maass, A., Reichstadt, M., Schwichtenberg, H., Sridhar, M., Kasam, V., Zimmermann, M., Hofmann, M., Vincent Breton, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Communication & Systèmes [Toulouse] (C-S), Communication & Systèmes-CS-SI France, Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Fraunhofer Institute for Algorithms and Scientific Computing (Fraunhofer SCAI), Fraunhofer (Fraunhofer-Gesellschaft), and Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
FOS: Computer and information sciences, Data challenge, malaria, in silico docking, virtual screening, grid computing, Quantitative Biology - Quantitative Methods, drug discovery, Computer Science - Distributed, Parallel, and Cluster Computing, FOS: Biological sciences, grid infrastructure, Distributed, Parallel, and Cluster Computing (cs.DC), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Quantitative Methods (q-bio.QM)
Abstract

WISDOM is an international initiative to enable a virtual screening pipeline on a grid infrastructure. Its first attempt was to deploy large scale in silico docking on a public grid infrastructure. Protein-ligand docking is about computing the binding energy of a protein target to a library of potential drugs using a scoring algorithm. Previous deployments were either limited to one cluster, to grids of clusters in the tightly protected environment of a pharmaceutical laboratory or to pervasive grids. The first large scale docking experiment ran on the EGEE grid production service from 11 July 2005 to 19 August 2005 against targets relevant to research on malaria and saw over 41 million compounds docked for the equivalent of 80 years of CPU time. Up to 1,700 computers were simultaneously used in 15 countries around the world. Issues related to the deployment and the monitoring of the in silico docking experiment as well as experience with grid operation and services are reported in the paper. The main problem encountered for such a large scale deployment was the grid infrastructure stability. Although the overall success rate was above 80%, a lot of monitoring and supervision was still required at the application level to resubmit the jobs that failed. But the experiment demonstrated how grid infrastructures have a tremendous capacity to mobilize very large CPU resources for well targeted goals during a significant period of time. This success leads to a second computing challenge targeting Avian Flu neuraminidase N1., 34 pages, 5 figures, 3 tables, to appear in Journal of Grid Computing

38. InterProScan on Grids

Author

Bloch, V., Salzemann, J., Vincent Breton, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], grid

39. La grille au service du développement médical en Afrique

Author

Jacq, F., Bacin, F., Meda, N., Donnarieix, D., Salzemann, J., Vayssiere, V., Jacq, N., Renaud, M., Traore, F., Meda, G., Nikiema, R., Vincent Breton, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand, Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), and UNICANCER

Subjects
Telemedecine, Diabetic retinopathy, Ophtalmology, Exchange of diagnosis, Grid, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Web services
Abstract

PCSV, présenté par F. Jacq, pas de proceedings; Objectives: Telemedicine networks allow to train local physicians and to improve diagnosis by exchanging medical data. But the set-up of multipoint dynamic telemedicine requires moving towards GRID technologies. The objective is to develop telemedicine services for physicians from Burkina Faso and France with the perspective of setting up a grid infrastructure between the participating medical sites. Methods: A web site to exchange diagnosis on diabetic retinopathy was developed in PHP. Another application using web services was developed to exchange patient information on ophthalmology between two databases. Results: The main difficulty comes from limited resources in developing countries including staff skills, bandwidth and funding. But the collaboration with dispensaries opened a door to enhanced collaboration between physicians of France and Burkina Faso Conclusions: These applications are designed with the aim of their use on grids which opens the perspective of multipoint dynamic telemedicine. We are developing a new generation of telemedicine service using experience acquired in the last two years.

40. Demonstration of in silico docking at a large scale on grid infrastructure

Author

Jacq, N., Salzemann, J., Yannick Legre, Reichstadt, M., Jacq, F., Zimmermann, M., Maas, A., Sridhar, M., Vinod-Kusam, K., Schwichtenberg, H., Hofmann, M., Vincent Breton, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), V. Hernandez, I. Blanquer, T. Solomonides, V. Breton, and Y. Legré

Subjects
malaria, grid infrastructure, [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], in silico docking, large scale deployment, drug discovery
Abstract

présenté par N. Jacq

41. PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

Author

Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ, and Vriend G

Abstract

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

Published
2009
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42. WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructures.

Author

Kasam V, Salzemann J, Botha M, Dacosta A, Degliesposti G, Isea R, Kim D, Maass A, Kenyon C, Rastelli G, Hofmann-Apitius M, and Breton V

Subjects
Glutathione Transferase, Humans, Ligands, Matrix Attachment Regions, Pharmaceutical Preparations, Protein Binding, Tetrahydrofolate Dehydrogenase, Computational Biology methods, Drug Delivery Systems, Drug Design, Malaria drug therapy, Medical Informatics organization & administration, Protozoan Proteins
Abstract

Background: Despite continuous efforts of the international community to reduce the impact of malaria on developing countries, no significant progress has been made in the recent years and the discovery of new drugs is more than ever needed. Out of the many proteins involved in the metabolic activities of the Plasmodium parasite, some are promising targets to carry out rational drug discovery., Motivation: Recent years have witnessed the emergence of grids, which are highly distributed computing infrastructures particularly well fitted for embarrassingly parallel computations like docking. In 2005, a first attempt at using grids for large-scale virtual screening focused on plasmepsins and ended up in the identification of previously unknown scaffolds, which were confirmed in vitro to be active plasmepsin inhibitors. Following this success, a second deployment took place in the fall of 2006 focussing on one well known target, dihydrofolate reductase (DHFR), and on a new promising one, glutathione-S-transferase., Methods: In silico drug design, especially vHTS is a widely and well-accepted technology in lead identification and lead optimization. This approach, therefore builds, upon the progress made in computational chemistry to achieve more accurate in silico docking and in information technology to design and operate large scale grid infrastructures., Results: On the computational side, a sustained infrastructure has been developed: docking at large scale, using different strategies in result analysis, storing of the results on the fly into MySQL databases and application of molecular dynamics refinement are MM-PBSA and MM-GBSA rescoring. The modeling results obtained are very promising. Based on the modeling results, In vitro results are underway for all the targets against which screening is performed., Conclusion: The current paper describes the rational drug discovery activity at large scale, especially molecular docking using FlexX software on computational grids in finding hits against three different targets (PfGST, PfDHFR, PvDHFR (wild type and mutant forms) implicated in malaria. Grid-enabled virtual screening approach is proposed to produce focus compound libraries for other biological targets relevant to fight the infectious diseases of the developing world.

Published
2009
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43. Grid enabled high throughput virtual screening against four different targets implicated in malaria.

Author

Salzemann J, Kasam V, Jacq N, Maass A, Schwichtenberg H, and Breton V

Subjects
Humans, Drug Delivery Systems, Drug Design, Malaria drug therapy, Medical Informatics, User-Computer Interface
Abstract

After having deployed a first data challenge on malaria and a second one on avian flu, respectively in summer 2005 and spring 2006, we are demonstrating here again how efficiently the computational grids can be used to produce massive docking data at a high-throughput. During more than 2 months and a half, we have achieved at least 140 million dockings, representing an average throughput of almost 80,000 dockings per hour. This was made possible by the availability of thousands of CPUs through different infrastructures worldwide. Through the acquired experience, the WISDOM production environment is evolving to enable an easy and fault-tolerant deployment of biological tools; in this case it is the FlexX commercial docking software which is used to dock the whole ZINC database against 4 different targets.

Published
2007

44. Grid-enabled high-throughput in silico screening against influenza A neuraminidase.

Author

Lee HC, Salzemann J, Jacq N, Chen HY, Ho LY, Merelli I, Milanesi L, Breton V, Lin SC, and Wu YT

Subjects
Binding Sites, Protein Binding, Protein Interaction Mapping methods, Drug Design, Drug Evaluation, Preclinical methods, Enzyme Inhibitors chemistry, Influenza A virus enzymology, Internet, Neuraminidase chemistry, Sequence Analysis, Protein methods
Abstract

Encouraged by the success of the first EGEE biomedical data challenge against malaria (WISDOM), the second data challenge battling avian flu was kicked off in April 2006 to identify new drugs for the potential variants of the influenza A virus. Mobilizing thousands of CPUs on the Grid, the six-week-long high-throughput screening activity has fulfilled over 100 CPU years of computing power and produced around 600 gigabytes of results on the Grid for further biological analysis and testing. In the paper, we demonstrate the impact of a worldwide Grid infrastructure to efficiently deploy large-scale virtual screening to speed up the drug design process. Lessons learned through the data challenge activity are also discussed.

Published
2006
Full Text
View/download PDF

45. Demonstration of in silico docking at a large scale on grid infrastructure.

Author

Jacq N, Salzemann J, Legre Y, Reichstadt M, Jacq F, Zimmermann M, Maass A, Sridhar M, Vinod-Kusam K, Schwichtenberg H, Hofmann M, and Breton V

Subjects
Europe, Humans, Pharmaceutical Preparations, Software, Malaria drug therapy, Medical Informatics organization & administration
Abstract

WISDOM stands for World-wide In Silico Docking On Malaria. First step toward enabling the in silico drug discovery pipeline on a grid infrastructure, this CPU consuming application generating large data flows was deployed successfully on EGEE, the largest grid infrastructure in the world, during the summer 2005. 46 million docking scores were computed in 6 weeks. The proposed demonstration presents the submission of in silico docking jobs at a large scale on the grid. The demonstration will use the new middleware stack gLite developed within the EGEE project.

Published
2006

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