L. Carey, A. E. Darling, and W. Chun-feng, The Design, Implementation, and Evaluation of mpiBLAST, 2003.

G. Aloisio, M. Cafaro, S. Fiore, and M. Mirto, ProGenGrid : A Workflow Service Infrastructure for Composing and Executing Bioinformatics Grid Services. Computer-Based Medical Systems, Proceedings. 18th IEEE Symposium on, pp.555-560, 2005.

S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

A. Amar, R. Bolze, A. Bouteiller, P. Kaur-chouhan, A. Chis et al., Diet: New Developments and Recent Results, CoreGRID Workshop on Grid Middleware (in conjunction with EuroPar2006), number 4375 in LNCS, pp.150-170, 2006.
DOI : 10.1007/978-3-540-72337-0_15

URL : https://hal.archives-ouvertes.fr/hal-01429988

A. Amar, R. Bolze, Y. Caniou, E. Caron, B. Depardon et al., Tunable scheduling in a GridRPC framework, Concurrency and Computation: Practice and Experience, vol.19, issue.9, pp.1051-1069, 2007.
DOI : 10.1002/cpe.1283

URL : https://hal.archives-ouvertes.fr/hal-01428209

J. Angele and M. Weiten, Semantic Technologies in the SIMDAT Grid Project, Semantic Grid : The Convergence of Technologies , number 05271 in Dagstuhl Seminar Proceedings. Internationales Begegnungsund Forschungszentrum fuer Informatik (IBFI), Schloss Dagstuhl, 2005.

A. Anjomshoaa, F. Brisard, M. Drescher, D. Fellows, A. Ly et al., Job Submission Description Language (JSDL) Specification, 2005.

G. Antoniu, L. Bougé, and M. Jan, JuxMem : An adaptive supportive platform for data sharing on the grid, Scalable Computing : Practice and Experience, vol.6, issue.3, pp.45-55, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00000984

D. C. Arnold, S. S. Vahdiyar, and J. J. Dongarra, ON THE CONVERGENCE OF COMPUTATIONAL AND DATA GRIDS, Parallel Processing Letters, vol.11, issue.02n03, pp.187-202, 2001.
DOI : 10.1142/S012962640100052X

A. Bairoch and R. Apweiler, The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000, Nucleic Acids Research, vol.28, issue.1, p.45, 2000.
DOI : 10.1093/nar/28.1.45

P. Bala, J. Pytlinski, M. Nazaruk, V. Alessandrini, D. Girou et al., BioGRID - An European grid for molecular biology, Proceedings 11th IEEE International Symposium on High Performance Distributed Computing, p.412, 2002.
DOI : 10.1109/HPDC.2002.1029942

G. Barish and K. Obraczke, World Wide Web caching: trends and techniques, IEEE Communications Magazine, vol.38, issue.5, pp.178-184, 2000.
DOI : 10.1109/35.841844

A. Bassi, M. Beck, T. Moore, J. S. Plank, M. Swany et al., The Internet Backplane Protocol: a study in resource sharing, Future Generation Computer Systems, vol.19, issue.4, pp.551-561, 2003.
DOI : 10.1016/S0167-739X(03)00033-5

M. Bayer, A. Campbell, and D. Virdee, A GT3 based BLAST grid service for biomedical research, Proceedings of the UK e-Science All Hands Meeting, pp.1019-1023, 2004.

M. Beck, T. Moore, and J. S. Plank, An End-To-End Approach to Globally Scalable Network Storage, SIGCOMM '02 : Proceedings of the 2002 conference on Applications, technologies , architectures, and protocols for computer communications, pp.339-346, 2002.

D. A. Benson, I. Karsch-mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler, GenBank, Nucleic Acids Research, vol.35, issue.Database, p.21, 2007.
DOI : 10.1093/nar/gkl986

H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat et al., The protein data bank. logo, pp.899-907

R. D. Bjornson, A. H. Sherman, S. B. Weston, N. Willard, and J. Wing, TurboBLAST : A Parallel Implementation of BLAST Based on the Turbohub Process Integration Architecture, Parallel and Distributed Processing Symposium., Proceedings International, IPDPS, pp.183-190, 2002.

R. Bolze, F. Cappello, E. Caron, M. Daydé, F. Desprez et al., Grid'5000: A Large Scale And Highly Reconfigurable Experimental Grid Testbed, International Journal of High Performance Computing Applications, vol.20, issue.4, pp.481-494, 2006.
DOI : 10.1177/1094342006070078

URL : https://hal.archives-ouvertes.fr/hal-00684943

R. C. Braun, K. T. Pedretti, T. L. Casavant, T. E. Scheetz, C. L. Birkett et al., Parallelization of local BLAST service on workstation clusters, Future Generation Computer Systems, vol.17, issue.6, pp.745-754, 2001.
DOI : 10.1016/S0167-739X(00)00057-1

K. H. Buetow, Cyberinfrastructure : Empowering a " Third Way, Biomedical Research . Science, vol.44, p.417, 2003.

M. Cannataro, C. Comito, F. Lo-schiavo, and P. Veltri, Proteus, A Grid Based Problem Solving for Bioinformatics : Architecture and Experiments, IEEE Intelligent Informatics Bulletin, vol.3, issue.1, pp.7-18, 2004.

N. Capit, G. Da-costa, Y. Georgiou, G. Huard, C. Martin et al., A batch scheduler with high level components, CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005., 2005.
DOI : 10.1109/CCGRID.2005.1558641

URL : https://hal.archives-ouvertes.fr/hal-00005106

E. Caron, A. Chis, F. Desprez, and A. Su, Design of plug-in schedulers for a GridRPC environment, Future Generation Computer Systems, vol.24, issue.1, pp.46-57, 2008.
DOI : 10.1016/j.future.2007.02.005

URL : https://hal.archives-ouvertes.fr/hal-01428216

E. Caron, P. K. Chouhan, and H. Dail, GoDIET : A Deployment Tool for Distributed Middleware on Grid'5000, EXPGRID workshop. Experimental Grid Testbeds for the Assessment of Large-Scale Distributed Apllications and Tools. In conjunction with HPDC-15, pp.1-8
URL : https://hal.archives-ouvertes.fr/hal-01430520

E. Caron and F. Desprez, Diet: A Scalable Toolbox to Build Network Enabled Servers on the Grid, International Journal of High Performance Computing Applications, vol.20, issue.3, pp.335-352, 2006.
DOI : 10.1177/1094342006067472

URL : https://hal.archives-ouvertes.fr/hal-01429861

R. L. De-carvalho and S. Lifschitz, Database Allocation Strategies for Parallel BLAST Evaluation on Clusters. Dsitributed and Parallel Databases, pp.99-127, 2003.

H. Casanova, Simgrid: a toolkit for the simulation of application scheduling, Proceedings First IEEE/ACM International Symposium on Cluster Computing and the Grid, pp.430-437, 2001.
DOI : 10.1109/CCGRID.2001.923223

A. Chakrabarti, R. A. Dheepak, and S. Sengupta, Integration of Scheduling and Replication in Data Grids, 2004.
DOI : 10.1007/978-3-540-30474-6_41

A. Chervenak, E. Deelman, I. Foster, W. Hoschek, A. Iamnitchi et al., Giggle: A Framework for Constructing Scalable Replica Location Services, ACM/IEEE SC 2002 Conference (SC'02), pp.1-17, 2002.
DOI : 10.1109/SC.2002.10024

B. , D. Fabbro, D. Laiymani, J. M. Nicod, and L. Philippe, Data management in grid applications providers, Proc. of the 1st Intl. Conference on Distributed Frameworks for Multimedia Applications (DFMA'05), pp.315-322

B. Del and F. , ContributionàContribution`Contributionà la gestion des données dans les grilles de calcuì a la demande : de la conceptionàconception`conceptionà la normalisation, Thèse de doctorat, 2005.

F. Desprez and A. Vernois, Simultaneous Scheduling of Replication and Computation for Data-Intensive Applications on the Grid, Journal of Grid Computing, vol.31, issue.1, pp.19-31, 2006.
DOI : 10.1007/s10723-005-9016-2

URL : https://hal.archives-ouvertes.fr/inria-00070546

R. Carvajal-schiaffino, D. G. Cameron, A. P. Millar, C. Nicholson, K. Stockinger et al., Evaluating Scheduling and Replica Optimisation Strategies in OptorSim, 4th International Workshop on Grid Computing (Grid2003, 2003.

F. Desprez, E. Caron, and G. L. Mahec, Dagda : An advanced data manager for the diet middleware, 2008.

F. Desprez, E. Caron, and G. L. Mahec, Parallelization and distribution strategies of large bioinformatics requests over the grid, ICA3PP'08 : Proceedings ot the International Conference on Algorithms and Architectures for Parallel Processing, pp.257-261, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01428318

. Embrace, Embrace website

J. Frey, T. Tannenbaum, M. Livny, I. Foster, and S. Tuecke, Condor-G: a computation management agent for multi-institutional grids, Proceedings 10th IEEE International Symposium on High Performance Distributed Computing, pp.237-246, 2002.
DOI : 10.1109/HPDC.2001.945176

F. Gagliardi, B. Jones, F. Grey, M. E. Bégin, and M. Heikkurinen, Building an infrastructure for scientific Grid computing: status and goals of the EGEE project, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.363, issue.1833, pp.3631729-1742, 1833.
DOI : 10.1098/rsta.2005.1603

Y. Georgiou, J. Leduc, B. Videau, J. Peyrard, and O. Richard, A tool for environment deployment in clusters and light grids, Proceedings 20th IEEE International Parallel & Distributed Processing Symposium, 2006.
DOI : 10.1109/IPDPS.2006.1639691

URL : https://hal.archives-ouvertes.fr/hal-00688748

M. Gouy, C. Gautier, M. Attimonelli, C. Lanave, and G. Paola, ACNUC ??? a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage, Bioinformatics, vol.1, issue.3, pp.167-172, 1985.
DOI : 10.1093/bioinformatics/1.3.167

URL : https://hal.archives-ouvertes.fr/hal-00697905

L. Guy, P. Kunszt, E. Laure, H. Stockinger, and K. Stockinger, Replica Management in Data Grids, In Global Grid Forum, vol.5, 2002.

D. G. Higgins and P. M. Sharp, CLUSTAL: a package for performing multiple sequence alignment on a microcomputer, Gene, vol.73, issue.1, pp.237-244, 1988.
DOI : 10.1016/0378-1119(88)90330-7

P. Honeyman, S. Wa-adamson, and . Mckee, GridNFS : Global Storage for Global Collaborations. Local to Global Data Interoperability-Challenges and Technologies, pp.111-115, 2005.

W. Hoschek, J. Jaen-martinez, A. Samar, H. Stockinger, and K. Stockinger, Data Management in an International Data Grid Project, LECTURE NOTES IN COMPUTER SCIENCE, pp.77-90, 2000.
DOI : 10.1007/3-540-44444-0_8

. European-bioinformatics-institute, European bioinformatics institute website

N. Jacq, C. Blanchet, C. Combet, E. Cornillot, L. Duret et al., Grid as a bioinformatic tool, Parallel Computing, vol.30, issue.9-10, pp.9-101093, 2004.
DOI : 10.1016/j.parco.2004.07.013

URL : https://hal.archives-ouvertes.fr/hal-00427599

M. Jan, JuxMem : un service de partage transparent de données pour grilles de calculs fondé sur une approche pair-` a-pair, Thèse de doctorat, 2006.

H. Kim, H. Kim, and D. Han, Performance Evaluation of BLAST on SMP Machines, LECTURE NOTES IN COMPUTER SCIENCE, vol.4331, p.668, 2006.
DOI : 10.1007/11942634_69

T. Kosar and M. Livny, Stork: making data placement a first class citizen in the grid, 24th International Conference on Distributed Computing Systems, 2004. Proceedings., 2004.
DOI : 10.1109/ICDCS.2004.1281599

A. Krishnan, GridBLAST: a Globus-based high-throughput implementation of BLAST in a Grid computing framework, Concurrency and Computation: Practice and Experience, vol.11, issue.13, pp.1607-1623, 2005.
DOI : 10.1002/cpe.906

J. Kubiatowicz, D. Bindel, Y. Chen, S. Czerwinski, P. Eaton et al., OceanStore, ACM SIGARCH Computer Architecture News, vol.28, issue.5, pp.190-201, 2000.
DOI : 10.1145/378995.379239

D. Lavenier, H. Leroy, M. Wing, M. , R. Andonov et al., GénoGRID : An Experimental Grid for Genomic Applications, 2003.

W. Liu, B. Schmidt, G. Voss, A. Schroder, and W. Muller-wittig, Bio-Sequence Database Scanning on a GPU, 20th IEEE International Parallel & Distributed Processing Symposium (IPDPS 2006)(HICOMB Workshop), 2006.

L. Milanesi and I. Merelli, High Performance GRID Based Implementation for Genomics and Protein Analysis, Studies in health technology and informatics, vol.120, pp.374-380, 2006.

G. M. Morris, D. S. Goodsell, R. S. Halliday, R. Huey, W. E. Hart et al., Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function, Journal of Computational Chemistry, vol.4, issue.14, pp.191639-1662, 1998.
DOI : 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B

H. Ogata, S. Goto, K. Sato, W. Fujibuchi, H. Bono et al., KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.27, issue.1, pp.29-34
DOI : 10.1093/nar/27.1.29

A. Optorsim, Advanced optorsim website. https ://lipforge.enslyon .fr/projects/advancedoptor

W. Pearson, [5] Rapid and sensitive sequence comparison with FASTP and FASTA, Methods in enzymology, vol.183, pp.63-98, 1990.
DOI : 10.1016/0076-6879(90)83007-V

K. T. Pedretti, T. L. Casavant, R. C. Braun, T. E. Scheetz, C. L. Birkett et al., Three Complementary Approaches to Parallelization of Local BLAST Service on Workstation Clusters, PaCT '999 : Proceedings of the 5th International Conference on Parallel Computing Technologies, pp.271-282, 1999.
DOI : 10.1007/3-540-48387-X_29

G. Peng, CDN : Content Distribution Network. Arxiv preprint cs, NI, 2004.

J. Plank, M. Beck, W. Elwasif, T. Moore, M. Swany et al., The Internet Backplane Protocol : Storage in the network, Proceedings of the Network Storage Symposium, 1999.

S. Podlipnig and L. , A survey of Web cache replacement strategies, ACM Computing Surveys, vol.35, issue.4, pp.374-398, 2003.
DOI : 10.1145/954339.954341

K. Ranganathan and I. Foster, Simulation Studies of Computation and Data Scheduling Algorithms for Data Grids, Journal of Grid Computing, vol.1, issue.1, pp.53-62, 2003.
DOI : 10.1023/A:1024035627870

M. Rarey, B. Kramer, T. Lengauer, and G. Klebe, A Fast Flexible Docking Method using an Incremental Construction Algorithm, Journal of Molecular Biology, vol.261, issue.3, pp.470-489, 1996.
DOI : 10.1006/jmbi.1996.0477

R. Le-réseau, Réseau national de télécommunications pour la technologie l'enseignement et la recherche

J. Saltz, S. Oster, S. Hastings, S. Langella, T. Kurc et al., caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid, Bioinformatics, vol.22, issue.15, p.22, 1910.
DOI : 10.1093/bioinformatics/btl272

J. Salzemann, N. Jacq, and V. Breton, Replication and Update of Molecular Biology Databases, IEEE Transactions on Nanobioscience, vol.6, issue.2, 2007.
DOI : 10.1109/TNB.2007.897468

URL : https://hal.archives-ouvertes.fr/in2p3-00214247

J. Salzemann, N. Jacq, G. , L. Mahec, and V. Breton, Replication and Update of Molecular Biology Databases in a Grid Environment, Proceedings of the NET-TAB2006, pp.33-37, 2006.
URL : https://hal.archives-ouvertes.fr/in2p3-00114312

R. Sandberg, Sun Network Filesystem Protocol Specification, Sun Microsystems, Inc, 1985.

R. Sandberg, The Sun Network File System : Design, Implementation and Experience, Proceedings of the Summer 1986 USENIX Technical Conference and Exhibition, 1986.

F. Sanger, S. Nicklen, and A. Coulson, DNA sequencing with chain-terminating inhibitors, Proceedings of the National Academy of Sciences, pp.5463-5467, 1977.
DOI : 10.1073/pnas.74.12.5463

N. Santos and B. Koblitz, Metadata services on the Grid, Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, vol.559, issue.1, pp.53-56, 2006.
DOI : 10.1016/j.nima.2005.11.104

B. Segal, Grid computing: the European Data Grid Project, 2000 IEEE Nuclear Science Symposium. Conference Record (Cat. No.00CH37149), pp.15-20, 2000.
DOI : 10.1109/NSSMIC.2000.948988

S. Amazon, Simple Storage Service) Amazon web services website

C. Stark, B. Breitkreutz, T. Reguly, L. Boucher, A. Breitkreutz et al., BioGRID: a general repository for interaction datasets, Nucleic Acids Research, vol.34, issue.90001, pp.535-539, 2006.
DOI : 10.1093/nar/gkj109

O. Tatebe, Y. Morita, S. Matsuoka, N. Soda, and S. Sekiguchi, Grid Datafarm Architecture for Petascale Data Intensive Computing, 2nd IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGRID'02), pp.102-110, 2002.
DOI : 10.1109/CCGRID.2002.1017117

F. Desprez, V. Breton, E. Caron, and G. L. Mahec, Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare, chapter High Performance BLAST over the Grid, 2008.

S. Venugopal, R. Buyya, and K. Ramamohanarao, A taxonomy of Data Grids for distributed data sharing, management, and processing, ACM Computing Surveys, vol.38, issue.1, p.3, 2006.
DOI : 10.1145/1132952.1132955

A. Vernois, Ordonnancement et réplication de données bioinformatiques dans un contexte de grille de calcul, Thèse de doctorat, 2006.

C. Wang, B. A. Alqaralleh, B. B. Zhou, M. Till, and A. Y. Zomaya, A BLAST Service Built on Data Indexed Overlay Network, Science, pp.16-23, 2005.

J. Wang, A survey of web caching schemes for the Internet, ACM SIGCOMM Computer Communication Review, vol.29, issue.5, pp.36-46, 1999.
DOI : 10.1145/505696.505701

X. Wu and C. W. Tseng, Parallel Computing for Bioinformatics and Computational Biology, chapter Searching Sequence Databases Using High-Performance BLASTs, pp.211-232, 2006.

K. Yagoub, D. Florescu, V. Issarny, and P. Valduriez, Caching Strategies for Data- Intensive Web Sites, Proceedings of the 26th International Conference on Very Large Data Bases, pp.188-199, 2000.
URL : https://hal.archives-ouvertes.fr/inria-00072783

C. Yang, Y. Luo, and C. Lai, Designing computing platform for BioGrid, International Journal of Computer Applications in Technology, vol.22, issue.1, pp.3-13, 2005.
DOI : 10.1504/IJCAT.2005.006798

H. Nakada, S. Matsuoka, K. Seymour, J. Dongarra, C. Lee et al., A GridRPC model and API for End-Users Applications, Global Grid Forum, p.52, 2005.

J. Plank, M. Beck, W. Elwasif, T. Moore, M. Swany et al., The Internet Backplane Protocol : Storage in the network, Storage in the network, NetStore '99 : Network Storage Symposium . Internet2, 1999.

C. Baru, R. Moore, A. Rajasekar, and M. Wan, The SDSC storage resource broker, CASCON First Decade High Impact Papers on, CASCON '10, 1998.
DOI : 10.1145/1925805.1925816

D. C. Arnold, D. Bachmann, and J. Dongarra, Request Sequencing: Optimizing Communication for the Grid, Lecture Notes in Computer Science, p.1213, 1900.
DOI : 10.1007/3-540-44520-X_172

B. , D. Fabbro, D. Laiymani, J. Nicod, and L. Philippe, A Data Persistency Approach for the DIET Metacomputing Environment, Int. Conf. on Internet Computing, 2004.

Y. Aida, Y. Nakajima, M. Sato, T. Sakurai, D. Takahashi et al., Performance Improvement by Data Management Layer in a Grid RPC System, the First International Conference on Grid and Pervasive Computing (GPC2006), pp.324-335, 2006.
DOI : 10.1007/11745693_33

G. Antoniu, L. Bougé, and M. Jan, JuxMem : An Adaptive Supportive Platform for Data Sharing on the Grid, Scalable Computing : Practice and Experience, pp.45-55, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00000984