E-science infrastructures for molecular modeling and parametrization |
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| Institution: | 1. Servicio de Cardiología, Hospital Reina Sofía, Universidad de Córdoba (IMIBIC), Córdoba, España;2. Institute of Cardiology, Catholic University of the Sacred Heart, Roma, Italia;3. Servicio de Cardiología, Hospital Dr. Negrín, Universidad de Las Palmas, Las Palmas de Gran Canaria, España;1. Dow Division of Health Services Research, Department of Urology, University of Michigan, Ann Arbor, MI, USA;2. Center for Healthcare Outcomes & Policy, University of Michigan, Ann Arbor, MI, USA;3. Department of General Surgery, University of Michigan, Ann Arbor, MI, USA;4. Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI, USA;1. Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kota Bharu, Kelantan, Malaysia;2. School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kota Bharu, Kelantan, Malaysia;3. Hospital Raja Perempuan Zainab II, 15586 Kota Bharu, Kelantan, Malaysia;1. Advanced Medical and Dental Institute, University Sains Malaysia, Bertam13200 Kepala Batas, Malaysia;2. Institute fur Experimentelle Pathologie, Unversitat Munster, D48149 Munster, Germany |
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| Abstract: | E-science infrastructures are becoming the essential tools for computational scientific research. In this paper, we describe two e-science infrastructures: Science and Engineering Applications Grid (SEAGrid) and molecular modeling and parametrization (ParamChem). The SEAGrid is a virtual organization with a diverse set of hardware and software resources and provides services to access such resources in a routine and transparent manner. These essential services include allocations of computational resources, client-side application interfaces, computational job and data management tools, and consulting activities. ParamChem is another e-science project dedicated for molecular force-field parametrization based on both ab-initio and molecular mechanics calculations on high performance computers (HPCs) driven by scientific workflow middleware services. Both the projects share a similar three-tier computational infrastructure that consists of a front-end client, a middleware web services layer, and a remote HPC computational layer. The client is a Java Swing desktop application with components for pre- and post-data processing, communications with middleware server and local data management. The middleware service is based on Axis2 web service and MySQL relational database, which provides functionalities for user authentication and session control, HPC resource information collections, discovery and matching, job information logging and notification. It can also be integrated with scientific workflow to manage computations on HPC resources. The grid credentials for accessing HPCs are delegated through MyProxy infrastructure. Currently SEAGrid has integrated several popular application software suites such as Gaussian for quantum chemistry, NAMD for molecular dynamics and engineering software such as Abacus for mechanical engineering. ParamChem has integrated CGenFF (CHARMM General Force-Field) for molecular force-field parametrization of drug-like molecules. Long-term storage of user data is handled by tertiary data archival mechanisms. SEAGrid science gateway serves more than 500 users while more than 1000 users use ParamChem services such as atom typing and initial force-field parameter guess at present. |
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| Keywords: | Science gateways Cyberinfrastructure E-science GridChem Virtual organizations XSEDE Scientific workflows Science and engineering simulation and design Computational chemistry Molecular modeling |
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