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Buttressing volatile desktop grids with cloud resources within a reconfigurable environment service for workflow orchestration

Stephen C Winter, Christopher J Reynolds, Tamas Kiss, Gabor Z Terstyanszky, Pamela Greenwell, Sharron McEldowney, Sandor Acs, Peter Kacsuk
2014 Journal of Cloud Computing: Advances, Systems and Applications  
RESWO (Reconfigurable Environment Service for Workflow Orchestration) is a virtual platform-as-a-service cloud model that allows leaner customised environments to be assembled and deployed within a cloud  ...  However, the deployments of such environments can be challenging, even where user requirements are comparatively modest.  ...  The computational requirements here were to run Autodock many times for many small molecules screened for many docking sites.  ... 
doi:10.1186/2192-113x-3-1 fatcat:hzd5zuvufffrdblrsf3xiw3o6a

Cloud Computing: A Detailed Relationship to Grid and Cluster Computing

Ikechukwu Nwobodo
2015 International Journal of Future Computer and Communication  
Cloud computing concept is a development trend based on several successful researches in computing areas such as virtualization, grid computing, cluster computing and distributed computing.  ...  Cloud computing continues to maintain a rapid growth while constituting a viable alternative to conventional computing.  ...  Globus DemoGrid was the first to be released as a tool for the development of instructional grid environment capable of being deployed using virtual machines on a physical resource or cloud environments  ... 
doi:10.7763/ijfcc.2015.v4.361 fatcat:vmaq6ewixjektdnrczmksro5cm

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  
This deliverable describes the state of the art and gives a technological gap analysis in the portable environments for computing and data resources of BioExcel.  ...  We review the commonly used technologies for computational infrastructures, a selection of workflow managers for computational biology and three important repositories for biomolecular data.  ...  4: Multi-scale modeling of molecular basis for odor and taste • Description: Multi-scale modeling of molecular basis for odor and taste: study of enzymatic reactions involved in the cascade triggered  ... 
doi:10.5281/zenodo.263963 fatcat:o2v7ogjmnbauhn7txp2buz3pem

Bioexcel Deliverable 2.3 - User Feedback And Future Roadmap

Adam Hospital, Josep Lluís Gelpí, Jose A. Dianes, Pau Andrio, Darren J. White, Emiliano Ippoliti, Adrien Melquiond, Vytautas Gapsys
2017 Zenodo  
User experience will be the main focus for the cloud portal that is expected to offer a growing number of tools and deployable VMs in the coming months.  ...  Future roadmaps for the BioExcel Cloud Portal and for the workflows and computational infrastructures are presented, which showcase the work planned for the rest of the project.  ...  blocks for Virtual Screening.  ... 
doi:10.5281/zenodo.1060946 fatcat:i4exxpnhpbaqnglrltelddzw6a

Cloud-Based High Throughput Virtual Screening in Novel Drug Discovery [chapter]

Abdurrahman Olğaç, Aslı Türe, Simla Olğaç, Steffen Möller
2019 Msphere  
This may be a seed for further inter-disciplinary development of VS to be applied by drug hunters.  ...  Virtual screening (VS) is one of the most often applied CADD methods used in rational drug design, which may be applied in early stages of drug discovery pipeline.  ...  PaaS: Platform as a Service is a technical concept for an aggregation of services to facilitate software running in support of IaaS to scale in multi-user, multi-project environments.  ... 
doi:10.1007/978-3-030-16272-6_9 fatcat:dihdpicowrg4vbsirumu3o4ezi

MuGVRE. A virtual research environment for 3D/4D genomics [article]

Laia Codo, Genis Bayarri, Javier Alvarex-Cid-Fuentes, Javier Conejero, Adam Hospital, Romina Royo, Dmitry Repchevsky, Marco Pasi, Athina Meletiou, Mark D. McDowall, Fatima Reham, Jose A. Alcantara (+17 others)
2019 bioRxiv   pre-print
Multiscale Genomics (MuG) Virtual Research Environment (MuGVRE) is a cloud-based computational infrastructure created to support the deployment of software tools addressing the various levels of analysis  ...  scheduler), for complex workflows requiring distributed or multi-scale executions schemes.  ...  Cloud deployments: MuGVRE infrastructure has been designed as a fully virtualized environment.  ... 
doi:10.1101/602474 fatcat:ikxzgfug55dlznv6lxd5fqb3ae

AutoDock Gateway for Molecular Docking Simulations in Cloud Systems [chapter]

Zoltán Farkas, Péter Kacsuk, Tamás Kiss, Péter Borsody, Ákos Hajnal, Ákos Balaskó, Krisztián Karóczkai
2015 Cloud Computing with e-Science Applications  
Autodock Vina is particularly useful for virtual screening, whereby a large set of ligands can be compared for docking suitability with a single receptor.  ...  of the molecular energy surface. 23 The WISDOM project [16] is an international initiative to enable a virtual screening pipeline on a grid infrastructure.  ... 
doi:10.1201/b18021-11 fatcat:ukz6lkplsvfenakzt7uco2eoce

BioExcel Deliverable D2.4 - Final Release of Workflows and Modular Tools for User Services

Adam Hospital, Anna Montras, Josep Lluís Gelpí, Daniele Lezzi, Rosa Maria Badia, Steven Newhouse, Jose Antonio Dianes, Pau Andrio, Luís Jordà, Stian Soiland-Reyes, Darren J White, Adam Carter (+3 others)
2019 Zenodo  
Finally, the services provided and the present phase for the two deployment environments, development and production, is outlined.  ...  for different types of users.  ...  Pilot Use Case 5: Virtual Screening • Use case summary Virtual screening is a computational technique used in the early phases of a drug discovery in almost every pharmaceutical company nowadays.  ... 
doi:10.5281/zenodo.3236256 fatcat:vdacumustjaafbozovyktxtdnm

High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL

John E. Stone, Peter Messmer, Robert Sisneros, Klaus Schulten
2016 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)  
We discuss the implementation of EGL support in VMD, a widely used molecular visualization application, and we outline benefits of the approach for molecular visualization tasks on petascale computers,  ...  We then provide a brief evaluation of the use of EGL in VMD, with tests using developmental graphics drivers on conventional workstations and on Amazon EC2 G2 GPUaccelerated cloud instance types.  ...  ACKNOWLEDGMENTS The authors acknowledge support from NIH grants 9P41GM104601 and 5R01GM098243-02, the CUDA Center of Excellence at the University of Illinois, and the Blue Waters sustained-petascale computing  ... 
doi:10.1109/ipdpsw.2016.127 pmid:27747137 pmcid:PMC5061511 dblp:conf/ipps/StoneMSS16 fatcat:c7tesj4k45hf5fjkljwlmjkxba

Report On The Progress Of The Deployment Of Consolidated Platform And Its Interactions With Infrastructure

Verlato. Marco
2017 Zenodo  
gradual integration of the existing isolated solutions to a single computing and data processing environment, based on the state of the art grid and cloud open source software tools and frameworks.  ...  The document starts with an updated description of the resources potentially available for the project from the EGI e-infrastructure, on top of which the consolidated West-Life platform is being built.  ...  The portal code was redesigned to submit jobs to a virtual cluster created by the cloud deployment, and the code implementing the molecular dynamics protocol was upgraded to work with Gromacs version 5  ... 
doi:10.5281/zenodo.1123236 fatcat:ibxn3qxv5naudaloq5hb2tbm7y

Chemistry42: An AI-based platform for de novo molecular design [article]

Yan A. Ivanenkov, Alex Zhebrak, Dmitry Bezrukov, Bogdan Zagribelnyy, Vladimir Aladinskiy, Daniil Polykovskiy, Evgeny Putin, Petrina Kamya, Alexander Aliper, Alex Zhavoronkov
2021 arXiv   pre-print
Chemistry42 is a core component of Insilico Medicine Pharma.ai drug discovery suite that also includes target discovery and multi-omics data analysis (PandaOmics) and clinical trial outcomes predictions  ...  Chemistry42 is a software platform for de novo small molecule design that integrates Artificial Intelligence (AI) techniques with computational and medicinal chemistry methods.  ...  Conflicts of Interest Disclosure Y.A.I, A.Z., D.B., B.Z., V.A., D.P., E.P., P.K., A.A., A.  ... 
arXiv:2101.09050v1 fatcat:sxodprcm6fdq3phmll6hz6lwxq

Cloud Computing in Healthcare and Biomedicine

Barbara Calabrese, Mario Cannataro
2015 Scalable Computing : Practice and Experience  
In fact, in the recent years it has been adopted for the deployment of several applications in healthcare and bioinformatics both in academia and in the industry.  ...  to the use of such platforms for the storage and analysis of patients data.  ...  AutoDockCloud [57] is a workflow system that enables distributed screening on a cloud platform using the molecular docking program AutoDock.  ... 
doi:10.12694/scpe.v16i1.1057 fatcat:k5s2o37zcrge5pvbwimhotbsca

Towards reproducible computational drug discovery

Nalini Schaduangrat, Samuel Lampa, Saw Simeon, Matthew Paul Gleeson, Ola Spjuth, Chanin Nantasenamat
2020 Journal of Cheminformatics  
The reproducibility of experiments has been a long standing impediment for further scientific progress.  ...  on model development and deployment, (6) use case scenarios for streamlining the computational drug discovery protocol.  ...  Likit Preeyanon from the Department of Community Medical Technology for fruitful discussions.  ... 
doi:10.1186/s13321-020-0408-x pmid:33430992 fatcat:bvdcvjhi4jhlnifpc25t6cjthq

Ground-based High Spectral Resolution Lidar observation of aerosol vertical distribution in the summertime Southeast United States

Jeffrey S. Reid, Ralph E. Kuehn, Robert E. Holz, Edwin W. Eloranta, Kathleen C. Kaku, Shi Kuang, Michael J. Newchurch, Anne M. Thompson, Charles R. Trepte, Jianglong Zhang, Samuel A. Atwood, Jenny L. Hand (+3 others)
2017 Journal of Geophysical Research - Atmospheres  
Abstract: As part of the Southeast  ...  ., "Ground based high spectral resolution lidar observation of aerosol vertical distribution in the summertime Southeast United States" (2017). NASA Publications. 233.  ...  Funding for the deployment of  ... 
doi:10.1002/2016jd025798 fatcat:krpahfiyx5bizfdv53hqcsoi7e

Phenomenal Biannual Progress Report - D1.4.3

PhenoMeNal Consortium
2017 Zenodo  
This deliverable is a comprehensive report of the PhenoMeNal consortium's activities and performance towards meeting the objectives and goals of the project from September 2016 (M13) - February 2017 (M18  ...  Several of the service centers are currently establishing a multi-site de.NBI cloud as the basis for a futureoriented compute structure in Germany.  ...  Both services will be accessible via a secure Virtual Research Environment (VRE) which can be deployed from the Virtual Research Environment Gateway (VRE) to a compatible cloud provider (Google, Amazon  ... 
doi:10.5281/zenodo.832247 fatcat:vugt5j5corcx3ijig5fxamckdm
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