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A Web/grid portal implementation of BioSimGrid: a biomolecular simulation database

B. Wu, M. Dovey, M.H. Ng, K. Tai, S. Murdock, P. Jeffreys, S. Cox, J. Essex, M.S.P. Sansom
2004 International Conference on Information Technology: Coding and Computing, 2004. Proceedings. ITCC 2004.  
Our thanks to all of our colleagues in the Oxford and Southampton simulation labs, to Ivaylo Kostadinov in the Oxford e-Science Center, and to the Southampton Regional e-Science Centre for their encouragement  ...  Acknowledgements Many thanks to our BioSimGrid partners (L. Caves, C. Laughton, D. Moss and O. Smart) for their input to this project. BioSimGrid is funded by BBSRC and DTI.  ...  PortalLib -delivering the web front-end A web portal implementation involves a large number of web pages, which are based on HTML code.  ... 
doi:10.1109/itcc.2004.1286589 dblp:conf/itcc/WuDNTMJCES04 fatcat:iiy6ussgozckpphfwzdexr57uq

BioSimGrid: Grid-enabled biomolecular simulation data storage and analysis

Muan Hong Ng, Steven Johnston, Bing Wu, Stuart E. Murdock, Kaihsu Tai, Hans Fangohr, Simon J. Cox, Jonathan W. Essex, Mark S.P. Sansom, Paul Jeffreys
2006 Future generations computer systems  
This paper details the usage and implementation of BioSimGrid using a combination of commercial databases, the Storage Resource Broker and Python scripts, gluing the building blocks together.  ...  It introduces a case study of how BioSimGrid can be used for better storage, retrieval and analysis of biomolecular simulation data.  ...  We thank our collaborators in the BioSimGrid Consortium: Charles Laughton, Adrian Mulholland, Leo Caves, David Moss, Oliver Smart, Marc Baaden and Katherine Cox.  ... 
doi:10.1016/j.future.2005.10.005 fatcat:4mgb7hmafbdhxh3wlefrd4e5rm

Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology

J.C. Thibault, D.R. Roe, K. Eilbeck, T.E. Cheatham III, J.C. Facelli
2015 SAR and QSAR in environmental research (Print)  
Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems.  ...  In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data.  ...  Computational support was provided by the Center for High Performance Computing (CHPC) at the University of Utah.  ... 
doi:10.1080/1062936x.2015.1076515 pmid:26387907 pmcid:PMC4672732 fatcat:q2d6eytnhzbavmxm7e2f2s4bmm

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing

Julien C Thibault, Daniel R Roe, Julio C Facelli, Thomas E Cheatham
2014 Journal of Cheminformatics  
In this paper we present the results of a process aimed at assessing the needs of the community for data representation standards to guide the implementation of future repositories for biomolecular simulations  ...  The benefits of a common logical model for biomolecular simulations was illustrated through various use cases, including data storage, indexing, and presentation.  ...  Thanks to the CHPC staff for hardware and software support that allowed the implementation of the prototypes. http://www.jcheminf.com/content/6/1/4  ... 
doi:10.1186/1758-2946-6-4 pmid:24484917 pmcid:PMC3915074 fatcat:c2vui3cmazezfa5jbgdmsd4edm

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

Julien C. Thibault, Thomas E. Cheatham, Julio C. Facelli
2014 Journal of Chemical Information and Modeling  
In this paper, we introduce iBIOMES Lite, a lightweight tool for biomolecular simulation data indexing and summarization.  ...  As the amount of data generated by biomolecular simulations dramatically increases, new tools need to be developed to help manage this data at the individual investigator or small research group level.  ...  BioSimGrid 1 was deployed in the UK to integrate several computational centers into a grid, where data could be deposited, searched, and analyzed.  ... 
doi:10.1021/ci500173w pmid:24830957 pmcid:PMC4076027 fatcat:c2fabuwwojhy5kxmlvrj64r7l4

Towards Institutional Infrastructures for e-Science: The Scope of the Challenge

Paul A. David, Michael J. Spence
2003 Social Science Research Network  
system simulation.  ...  of databases, which was implemented in the United Kingdom as the Copyright and Rights in Databases Regulations, 1997.  ...  Southampton has a CS department with grid expertise; Reading does the Biodiversity analytic tools; the others provide data. BiosimGRID A GRID Database for biomolecular simulations.  ... 
doi:10.2139/ssrn.1325240 fatcat:a4bogiz2wbf7lggq5ijwonshua