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COEL: A Web-based Chemistry Simulation Framework [article]

Peter Banda, Drew Blount, Christof Teuscher
2014 arXiv   pre-print
A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and  ...  The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems.  ...  We acknowledge Avi Debnath for his work on DNAstrand visualization, and GridGain for an academic license to use the GridGain HPC technology.  ... 
arXiv:1407.4027v1 fatcat:hsf65clgv5ekbpvq66uoqeclai

Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review

Natalio Krasnogor, Azhar Shah, Daniel Barthel, Piotr Lukasiak, Jacek Blazewicz
2008 Current Bioinformatics  
In this paper we present a trace of these technological changes in Web and Grid technology, including details of emerging infrastructures, standards, languages and tools, as they apply to bioinformatics  ...  ecological observations (e.g. as to ascertain climate change's impact on the biota) is growing at unprecedented speed.  ...  The modeled applications are automatically translated into grid execution scripts corresponding to GRSL (Globus Resource Specification Langue) and are then submitted for execution on grid through GRAM  ... 
doi:10.2174/157489308783329850 fatcat:thpj6eywwvg5tfdqvbw5nch3ty

Stress Fractures of the Tibia after Jogging

Steller EP Unlu C
2014 Journal of Trauma and Treatment  
Finally, the diversity and commonality of these initiatives suggest a comprehensive, unified language.  ...  Based largely on markup meta-languages, such as the Standard General Markup Language (SGML) and the eXtensible Markup Language (XML), these efforts cover a wide range of industries, applications and functions  ...  Structured Methods has developed Human Resource Management Markup Language (HRMML), an XML-based markup language for job postings, job descriptions, and resumes.  ... 
doi:10.4172/2167-1222.s2-006 fatcat:73kmefkhtreindbb5grlmjlj4i

From Proposal to Production: Lessons Learned Developing the Computational Chemistry Grid Cyberinfrastructure

Rion Dooley, Kent Milfeld, Chona Guiang, Sudhakar Pamidighantam, Gabrielle Allen
2006 Journal of Grid Computing  
The Computational Chemistry Grid (CCG) is a 3-year, National Middleware Initiative (NMI) program to develop cyberinfrastructure for the chemistry community.  ...  The final section of the paper looks forward to challenges foreseen in the remaining two years.  ...  Acknowledgements Special thanks Ian Kelley and Jon MacLaren for thoughtful review, as well as Michael Sheetz and the UKy development team for their contribution to the GridChem GUI.  ... 
doi:10.1007/s10723-006-9043-7 fatcat:kd3tvcb2zncg5ccaryoddtvdeq

Reducing Complexity in Management of eScience Computations

Per-Olov Östberg, Andreas Hellander, Brian Drawert, Erik Elmroth, Sverker Holmgren, Linda Petzold
2012 2012 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (ccgrid 2012)  
To illustrate use of the toolkit, we present it in the context of a case study where we extend the capabilities of an existing kinetic Monte Carlo software framework to utilize distributed computational  ...  for computational science -software systems that abstract and virtualize the processes of managing scientific computations on heterogeneous distributed resource systems.  ...  The authors acknowledge MikaelÖhman, Sebastian Gröhn, and Anders Häggström for work related to the project, and the anonymous reviewers for valuable feedback and interesting discussions.  ... 
doi:10.1109/ccgrid.2012.72 dblp:conf/ccgrid/OstbergHDEHP12 fatcat:ofeeyjizkzhevfodvx4ofx6z7i

PROTO-PLASM: parallel language for adaptive and scalable modelling of biosystems

C. Bajaj, A. DiCarlo, A. Paoluzzi
2008 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
PROTO-PLASM may define the model equations, but it is currently focused on the symbolic description of model geometry and on the parallel support of simulations.  ...  One contribution of 12 to a Theme Issue 'The virtual physiological human: building a framework for computational biomedicine I'.  ...  We acknowledge our debt to the visionary work of J. Backus and the FL group at IBM Almaden (A. Aiken, J. H. Williams, E. L. Wimmer and others). We would also credit F. Bernardini, V. Ferrucci, S.  ... 
doi:10.1098/rsta.2008.0076 pmid:18559320 pmcid:PMC3342764 fatcat:tqfuzid77jfvfkszfgkkxei5xq

Programming environments for multidisciplinary Grid communities

N. Ramakrishnan, L. T. Watson, D. G. Kafura, C. J. Ribbens, C. A. Shaffer
2002 Concurrency and Computation  
Rapid advances in technological infrastructure as well as the emphasis on application support systems have signaled the maturity of grid computing.  ...  Today's grid computing environments (GCEs) extend the notion of a programming environment beyond the compile-schedule-execute paradigm to include functionality such as networked access, information services  ...  In general, we envision Symphony as an abstraction layer on top of popular grid middleware systems that will ease and unify the access to grid resources and provide a foundation for collaboration among  ... 
doi:10.1002/cpe.679 fatcat:az2jbb4gqjgxjkucf4jj3cym3u

Open source molecular modeling

Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes
2016 Journal of Molecular Graphics and Modelling  
The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications.  ...  Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable.  ...  helpful feedback on a draft of this manuscript.  ... 
doi:10.1016/j.jmgm.2016.07.008 pmid:27631126 pmcid:PMC5037051 fatcat:jxdvghsiszadjevub22qbjywwm

Language and Runtime Support for Automatic Configuration and Deployment of Scientific Computing Software over Cloud Fabrics

Chris Bunch, Brian Drawert, Navraj Chohan, Chandra Krintz, Linda Petzold, Khawaja Shams
2012 Journal of Grid Computing  
In this paper, we present the design and implementation of Neptune, a simple, domainspecific language based on the Ruby programming language.  ...  Neptune imposes no overhead on application execution, yet significantly simplifies the application deployment process, enables portability across cloud systems, and promotes lock-in avoidance by specific  ...  This often translates into performing special requests based on the parameters present (or absent) in a Neptune job request.  ... 
doi:10.1007/s10723-012-9213-8 fatcat:e7fhynoginf6jngeopr3hxus2a

Domain-Specific Language [chapter]

2014 Encyclopedia of Social Network Analysis and Mining  
In this paper, we present the design and implementation of Neptune, a simple, domainspecific language based on the Ruby programming language.  ...  Neptune imposes no overhead on application execution, yet significantly simplifies the application deployment process, enables portability across cloud systems, and promotes lock-in avoidance by specific  ...  This often translates into performing special requests based on the parameters present (or absent) in a Neptune job request.  ... 
doi:10.1007/978-1-4614-6170-8_110021 fatcat:2szafdkvwfhhpbxi5mguyjchpy

Virtual Human project

Richard C. Ward, Kara L. Kruse, Glenn O. Allgood, Lee M. Hively, K. N. Fischer, Nancy B. Munro, Clay E. Easterly, Glenn O. Allgood, Nickolas L. Faust
2001 Visualization of Temporal and Spatial Data for Civilian and Defense Applications  
This paper describes the development of a comprehensive human modeling environment, the Virtual Human, which will be used initially to model the human respiratory system for purposes of predicting pulmonary  ...  Jobs are then submitted to the agent-based NetSolve server, which looks for available resources on a computational grid of high-performance parallel computers.  ...  biological, chemical, or physical.  ... 
doi:10.1117/12.438121 fatcat:qcxuugaokbhbnkbjojxzhybssm

GEMS: User Control for Cooperative Scientific Repositories [chapter]

Justin M. Wozniak, Paul Brenner, Santanu Chatterjee, Douglas Thain, Aaron Striegel, Jesús Izaguirre
2011 Computer Communications and Networks  
Explicit data placement techniques offer more utility but may bury users with the complexity of system specifics and scripts.  ...  Opportunistic techniques have been widely used to create computational infrastructures and have demonstrated an ability to deliver computing resources to large applications.  ...  Grid construction allows users outside the local system to run jobs or allocate storage on the resource.  ... 
doi:10.1007/978-0-85729-676-4_3 fatcat:h4ugh3gu3vh6jgor524qtnigpy

Bioexcel Deliverable 2.1 – State Of The Art And Gap Analysis

Adam Hospital, Anna Montras, Stian Soiland-Reyes, Alexandre Bonvin, Adrien Melquiond, Josep Lluís Gelpí, Daniele Lezzi, Steven Newhouse, Jose A. Dianes, Mark Abraham, Rossen Apostolov, Emiliano Ippoliti (+2 others)
2016 Zenodo  
For the usability part, we found that improvements could be made to the main codes (GROMACS, HADDOCK and CPMD) to ease their usage, such as web portals providing assistance on how to run, install or use  ...  To help identify potential issues in developing the corresponding pipelines, the use cases have been individually described and analyzed, focusing on the set of functionalities (from the tool catalogue  ...  UU Web portal Web (support xml-rpc access) Internal workflow -python + job management systems (local batch system + script for grid submission for the grid- enabled portal (used both gLite  ... 
doi:10.5281/zenodo.263963 fatcat:o2v7ogjmnbauhn7txp2buz3pem

A GPU Accelerated High Performance Cloud Computing Infrastructure for Grid Computing Based Virtual Environmental Laboratory [chapter]

Francisco Giunta, Raffaele Montella, Giuliano Laccetti, Florin Isaila, Francisco Javier Garca Blas
2011 Advances in Grid Computing  
Section 3 is dedicated to the GPU virtualization technique, to the description of key design choices and of some benchmark results, which demonstrate the light impact of our software stack on overall performance  ...  Otherwise, when grid-computing resources are partially (or totally) dynamically allocated on the cloud, one can have "grids on clouds" [24] .  ...  The resource specification is performed by a description XML file, following the Job Submission Description Language schema [23] .  ... 
doi:10.5772/14594 fatcat:y3dfwoozojeppghlzq3so22roy

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  
Few environments have been developed or deployed to widely share biomolecular simulation data or to enable collaborative networks to facilitate data exploration and reuse.  ...  The identified core data elements were organized into a logical model to guide the design of new databases and application programming interfaces.  ...  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
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