eScience for molecular-scale simulations and the
            <i>e</i>
            Minerals project

Salje, Ekhard K. H.; Artacho, Emilio; Austen, Kat; Bruin, R. P.; Calleja, M.; Chappell, Helen; Chiang, Gen-Tao; Dove, Martin T.; Frame, I; Goodwin, Andrew L.; Dam, Kerstin Kleese van; Marmier, A.; Parker, Stephen C.; Pruneda, Miguel; Todorov, Ilian T.; Trachenko, Kostya; Tyer, R. P.; Walker, Andrew; White, T. O. H.

doi:10.1098/rsta.2008.0195

Cited by 8 publications

(4 citation statements)

References 28 publications

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“…In order to minimize the load on the iRODS/SRB server, some other projects have decided to develop their own metadata systems to deal with metadata and to only let iRODS/SRB handle data access. For example, e Minerals developed the Rcommands server as a metadata server which allows users to extract and query data on their own [12]. However, Rcommands only provides key-value pairs.…”

Section: Methodsmentioning

confidence: 99%

Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute

Chiang

Clapham

et al. 2011

BMC Bioinformatics

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BackgroundIncreasingly large amounts of DNA sequencing data are being generated within the Wellcome Trust Sanger Institute (WTSI). The traditional file system struggles to handle these increasing amounts of sequence data. A good data management system therefore needs to be implemented and integrated into the current WTSI infrastructure. Such a system enables good management of the IT infrastructure of the sequencing pipeline and allows biologists to track their data.ResultsWe have chosen a data grid system, iRODS (Rule-Oriented Data management systems), to act as the data management system for the WTSI. iRODS provides a rule-based system management approach which makes data replication much easier and provides extra data protection. Unlike the metadata provided by traditional file systems, the metadata system of iRODS is comprehensive and allows users to customize their own application level metadata. Users and IT experts in the WTSI can then query the metadata to find and track data.The aim of this paper is to describe how we designed and used (from both system and user viewpoints) iRODS as a data management system. Details are given about the problems faced and the solutions found when iRODS was implemented. A simple use case describing how users within the WTSI use iRODS is also introduced.ConclusionsiRODS has been implemented and works as the production system for the sequencing pipeline of the WTSI. Both biologists and IT experts can now track and manage data, which could not previously be achieved. This novel approach allows biologists to define their own metadata and query the genomic data using those metadata.

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Section: Methodsmentioning

confidence: 99%

Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute

Chiang

Clapham

et al. 2011

BMC Bioinformatics

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“…This is then ingested into, and processed by, an instance of theChempound database system. By contrast, the eMinerals [34] and Materials Grid [35] projects sought to develop automated scientific workflows forhigh-throughput computation in atomic-scale mineralogy and materials science. Theseworkflows combined distributed grid computing [26, 27] with tools to generate input files, extract and analyse output data, andcreate and store key items of metadata [28].…”

Section: Introductionmentioning

confidence: 99%

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

2013

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BackgroundMultidisciplinary integrated research requires the ability to couple thediverse sets of data obtained from a range of complex experiments andcomputer simulations. Integrating data requires semantically richinformation. In this paper an end-to-end use of semantically rich data incomputational chemistry is demonstrated utilizing the Chemical MarkupLanguage (CML) framework. Semantically rich data is generated by the NWChemcomputational chemistry software with the FoX library and utilized by theAvogadro molecular editor for analysis and visualization.ResultsThe NWChem computational chemistry software has been modified and coupled tothe FoX library to write CML compliant XML data files. The FoX library wasexpanded to represent the lexical input files and molecular orbitals used bythe computational chemistry software. Draft dictionary entries and a formatfor molecular orbitals within CML CompChem were developed. The Avogadroapplication was extended to read in CML data, and display molecular geometryand electronic structure in the GUI allowing for an end-to-end solutionwhere Avogadro can create input structures, generate input files, NWChem canrun the calculation and Avogadro can then read in and analyse the CML outputproduced. The developments outlined in this paper will be made available infuture releases of NWChem, FoX, and Avogadro.ConclusionsThe production of CML compliant XML files for computational chemistrysoftware such as NWChem can be accomplished relatively easily using the FoXlibrary. The CML data can be read in by a newly developed reader in Avogadroand analysed or visualized in various ways. A community-based effort isneeded to further develop the CML CompChem convention and dictionary. Thiswill enable the long-term goal of allowing a researcher to run simple“Google-style” searches of chemistry and physics and have theresults of computational calculations returned in a comprehensible formalongside articles from the published literature.Electronic supplementary materialThe online version of this article (doi:10.1186/1758-2946-5-25) contains supplementary material, which is available to authorized users.

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“…To overcome this obstacle, we have used advanced distributed computational methods (GRID computing) as the solution to perform hundreds of thousands of energy calculations in a reasonable amount of time with minimal loss in accuracy. 25,26 GRID computing has been consolidated as an important new field, distinguished from conventional distributed computing, due to its focus on large-scale resource sharing, innovative applications, and, in some cases, high-performance orientation to solving specific problems. 27 Here we present an efficient methodology for calculating the interaction energies between pairs of molecules (dendrimer− drug) along an exploratory path.…”

Section: Introductionmentioning

confidence: 99%

Study of Interaction Energies between the PAMAM Dendrimer and Nonsteroidal Anti-Inflammatory Drug Using a Distributed Computational Strategy and Experimental Analysis by ESI-MS/MS

et al. 2012

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The structure of a dendrimer exhibits a large number of internal and superficial cavities, which can be exploited, to capture and deliver small organic molecules, enabling their use in drug delivery. Structure-based modeling and quantum mechanical studies can be used to accurately understand the interactions between functionalized dendrimers and molecules of pharmaceutical and industrial interest. In this study, we implemented a Metropolis Monte Carlo algorithm to calculate the interaction energy of dendrimer–drug complexes, which can be used for in silico prediction of dendrimer–drug affinity. Initially, a large-scale sampling of different dendrimer–drug conformations were generated using Euler angles. Then, each conformation was distributed on different nodes of a GRID computational system; where its interaction energy was calculate by semi-empirical quantum mechanical methods. These energy calculations were performed for four different non-steroidal anti-inflammatory drugs, each showing different affinities for PAMAM–G4 dendrimer. The affinities were also characterized experimentally by using Cooks’ kinetic method to calculate PAMAM–drug dissociation constants. The quantitative structure–activity relationship between the interaction energies and dissociation constants showed statistical correlations with r2 > 0.9.

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eScience for molecular-scale simulations and the e Minerals project

Cited by 8 publications

References 28 publications

Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute

Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

Study of Interaction Energies between the PAMAM Dendrimer and Nonsteroidal Anti-Inflammatory Drug Using a Distributed Computational Strategy and Experimental Analysis by ESI-MS/MS

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