{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,3,31]],"date-time":"2022-03-31T22:37:26Z","timestamp":1648766246383},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations \u2013 a characteristic of the emerging field of systems biology.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this paper we present a lightweight generic framework for combining disparate computational resources at multiple sites (ranging from local computers and clusters to established national Grid services). A detailed guide describing how to set up the framework is available from the following URL: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/igrid-ext.cryst.bbk.ac.uk\/portal_guide\/\" ext-link-type=\"uri\">http:\/\/igrid-ext.cryst.bbk.ac.uk\/portal_guide\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>This approach is particularly (but not exclusively) appropriate for large-scale biology projects with multiple collaborators working at different national or international sites. The framework is relatively easy to set up, hides the complexity of Grid middleware from the user, and provides access to resources through a single, uniform interface. It has been developed as part of the European ImmunoGrid project.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-407","type":"journal-article","created":{"date-parts":[[2008,10,14]],"date-time":"2008-10-14T06:13:58Z","timestamp":1223964838000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Towards a lightweight generic computational grid framework for biological research"],"prefix":"10.1186","volume":"9","author":[{"given":"Mark D","family":"Halling-Brown","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David S","family":"Moss","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adrian J","family":"Shepherd","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,10,2]]},"reference":[{"key":"2392_CR1","unstructured":"ImmunoGrid[http:\/\/www.immunogrid.eu]"},{"issue":"24","key":"2392_CR2","doi-asserted-by":"publisher","first-page":"3350","DOI":"10.1093\/bioinformatics\/btm408","volume":"23","author":"F Castiglione","year":"2007","unstructured":"Castiglione F, Pappalardo F, Bernaschi M, Motta S: Optimization of HAART by means of Genetic Algorithms and agent based models of HIV infection. Bioinformatics 2007, 23(24):3350\u20133355.","journal-title":"Bioinformatics"},{"key":"2392_CR3","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1186\/1471-2105-7-352","volume":"7","author":"P-L Lollini","year":"2006","unstructured":"Lollini P-L, Motta S, Pappalardo F: Discovery of cancer vaccination protocols with a genetic algorithm driving an agent based simulator. BMC Bioinformatics 2006, 7: 352.","journal-title":"BMC Bioinformatics"},{"key":"2392_CR4","unstructured":"National Grid Service[http:\/\/www.grid-support.ac.uk\/]"},{"key":"2392_CR5","unstructured":"Distributed European Infrastructure for Supercomputing Applications[http:\/\/www.deisa.org\/]"},{"key":"2392_CR6","unstructured":"TeraGrid[http:\/\/www.teragrid.org\/]"},{"key":"2392_CR7","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1016\/j.cpc.2006.11.011","volume":"176","author":"PV Coveney","year":"2007","unstructured":"Coveney PV, Saksena RS, Zasada SJ, McKeown M, Pickles S: The Application Hosting Environment: Lightweight Middleware for Grid-Based Computational Science. Comp Phys Comm 2007, 176: 406\u2013418.","journal-title":"Comp Phys Comm"},{"key":"2392_CR8","first-page":"50","volume-title":"Proceedings of the Second IEEE International Conference on e-Science and Grid Computing","author":"SJ Zasada","year":"2006","unstructured":"Zasada SJ, Saksena RS, Coveney PV, McKeown M, Pickles S: Facilitating User Access to the Grid: A Lightweight Application Hosting Environment for Grid Enabled Computational Science. Proceedings of the Second IEEE International Conference on e-Science and Grid Computing 2006, 50."},{"key":"2392_CR9","first-page":"91","volume-title":"Proc 2nd IEEE International Conference on e-Science and Grid Computing","author":"TM Sloan","year":"2006","unstructured":"Sloan TM, Menday R, Seed T, Illingworth M, Trew AS: DESHL \u2013 standards based access to a heterogeneous European supercomputing infrastructure. Proc 2nd IEEE International Conference on e-Science and Grid Computing 2006, 91."},{"key":"2392_CR10","unstructured":"The Globus Alliance[http:\/\/www.globus.org]"},{"key":"2392_CR11","unstructured":"EBI[http:\/\/www.ebi.ac.uk]"},{"issue":"5","key":"2392_CR12","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1034\/j.1399-0039.2003.00112.x","volume":"62","author":"S Buus","year":"2003","unstructured":"Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S: Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens 2003, 62(5):378\u2013384.","journal-title":"Tissue Antigens"},{"issue":"7","key":"2392_CR13","doi-asserted-by":"publisher","first-page":"2904","DOI":"10.1063\/1.1773132","volume":"121","author":"J H\u00e9nin","year":"2004","unstructured":"H\u00e9nin J, Chipot C: Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys 2004, 121(7):2904\u20133004.","journal-title":"J Chem Phys"},{"key":"2392_CR14","unstructured":"PI2S2[http:\/\/www.pi2s2.it\/]"},{"key":"2392_CR15","unstructured":"gLite[http:\/\/glite.web.cern.ch\/glite\/]"},{"key":"2392_CR16","volume-title":"Proceedings of Grid Open Days at the University of Palermo","author":"E Mastriani","year":"2007","unstructured":"Mastriani E, Halling-Brown MD, Shepherd AJ, Motta S: ImmunoGrid-PI2S2 Integration Architecture. Proceedings of Grid Open Days at the University of Palermo 2007."},{"key":"2392_CR17","volume-title":"Proceedings of the UK e-Science All Hands Meeting 31st August \u2013 3rd September, Nottingham UK","author":"A Richards","year":"2004","unstructured":"Richards A, Schmidt J, Dew PM, Youhanaie F, Ford M, Geddes N: Production Quality e-Science Grid. Proceedings of the UK e-Science All Hands Meeting 31st August \u2013 3rd September, Nottingham UK 2004."},{"key":"2392_CR18","unstructured":"GridSAM[http:\/\/gridsam.sourceforge.net\/2.0.1\/index.html]"},{"key":"2392_CR19","first-page":"1","volume-title":"Future Generation Computer Systems 613","author":"J Almond","year":"1999","unstructured":"Almond J, Snelling D: UNICORE: Uniform Access to Supercomputing as an Element of Electronic Commerce. Future Generation Computer Systems 613 1999, 1\u201310."},{"key":"2392_CR20","volume-title":"Proceedings of the 2nd TeraGrid Conference","author":"SJ Zasada","year":"2007","unstructured":"Zasada SJ, Cheney BG, Saksena RS, Suter JL, Coveney PV, Essex JW: Production Level Scientific Simulation Management on International Federated Grids. Proceedings of the 2nd TeraGrid Conference 2007."},{"key":"2392_CR21","unstructured":"OMII[http:\/\/www.omii.ac.uk]"},{"key":"2392_CR22","unstructured":"Apache Tomcat[http:\/\/www.tomcat.apache.org]"},{"key":"2392_CR23","unstructured":"Halling-Brown MD: Portal Guide.[http:\/\/igrid-ext.cryst.bbk.ac.uk\/portal_guide\/]"},{"key":"2392_CR24","unstructured":"Internet X.509 Public Key Infrastructure Certificate Management Protocols, IETF RFC 2510[http:\/\/www.faqs.org\/rfcs\/rfc2510.html]"},{"key":"2392_CR25","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1109\/HPDC.2001.945181","volume-title":"Proceedings of the Tenth International Symposium on High Performance Distributed Computing (HPDC-10)","author":"J Novotny","year":"2001","unstructured":"Novotny J, Tuecke S, Welch V: An Online Credential Repository for the Grid: MyProxy. In Proceedings of the Tenth International Symposium on High Performance Distributed Computing (HPDC-10). IEEE Press; 2001:104\u2013111."},{"key":"2392_CR26","unstructured":"Sun Developer Network, Java Web Start Technology[http:\/\/java.sun.com\/products\/javawebstart]"},{"key":"2392_CR27","unstructured":"JNLP[http:\/\/java.sun.com\/products\/javawebstart\/download-spec.html]"},{"key":"2392_CR28","first-page":"21","volume-title":"6th Austrian-Hungarian Workshop on Distributed and Parallel Systems (DAPSYS 2006) in conjunction with the Austrian Grid Symposium 2006, Innsbruck, Austria","author":"A Kert\u00e9sz","year":"2006","unstructured":"Kert\u00e9sz A, Kacsuk P: A Taxonomy of Grid Resource Brokers. 6th Austrian-Hungarian Workshop on Distributed and Parallel Systems (DAPSYS 2006) in conjunction with the Austrian Grid Symposium 2006, Innsbruck, Austria 2006, 21\u201323."},{"key":"2392_CR29","volume-title":"CoreGRID Technical Report Number TR-0116","author":"A Kert\u00e9sz","year":"2007","unstructured":"Kert\u00e9sz A, Kacsuk P, Rodero I, Guim F, Corbalan J: Meta-Brokering requirements and research directions in state-of-the-art Grid Resource Management. CoreGRID Technical Report Number TR-0116 2007."},{"key":"2392_CR30","unstructured":"JPGraph[http:\/\/www.aditus.nu\/jpgraph]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-407.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T03:25:12Z","timestamp":1630466712000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-407"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,10,2]]},"references-count":30,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2392"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-407","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,10,2]]},"assertion":[{"value":"30 June 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 October 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 October 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"407"}}