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SciPhy: A Cloud-Based Workflow for Phylogenetic Analysis of Drug Targets in Protozoan Genomes [chapter]

Kary A. C. S. Ocaña, Daniel de Oliveira, Eduardo Ogasawara, Alberto M. R. Dávila, Alexandre A. B. Lima, Marta Mattoso
2011 Lecture Notes in Computer Science  
Our contribution is the development, implementation and test of SciPhy in public cloud computing environments.  ...  We designed a phylogenetic scientific workflow, named SciPhy, to construct phylogenetic trees from a set of drug target enzymes found in protozoan genomes.  ...  We proposed a scientific workflow for phylogenetic analysis that was executed in parallel using a public cloud.  ... 
doi:10.1007/978-3-642-22825-4_9 fatcat:3xt5qe22tjex3czybjm5hdj73u

Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support

Mohamed Abouelhoda, Shadi Issa, Moustafa Ghanem
2012 BMC Bioinformatics  
The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure.  ...  Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis.  ...  We thank Mohamed Elkalioby from Nile University for his support in establishing the cloud computing infrastructure.  ... 
doi:10.1186/1471-2105-13-77 pmid:22559942 pmcid:PMC3583125 fatcat:arnykmuzbnehnnk73kmfroe36a

Genomics as a service: A joint computing and networking perspective

G. Reali, M. Femminella, E. Nunzi, D. Valocchi
2018 Computer Networks  
In more detail, we analyze the main genomic processing applications, and classify not only the main computing alternatives to run genomics workflows in either a local machine or a distributed cloud environment  ...  It emerges that virtualization, both in computing and networking, is the key for a successful large-scale exploitation of genomic data, by pushing ahead the adoption of the GaaS paradigm.  ...  The more recent survey [5] deals with the execution of genomic services in specifically designed high performance computing (HPC) applications, and deploy them on HPC clouds.  ... 
doi:10.1016/j.comnet.2018.08.005 fatcat:w562rwbavnax7pbtairhtnadje

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

Won Cheol Yim, John C. Cushman
2017 PeerJ  
In recent years, distributed computing environments have become more widely accessible and used due to the increasing availability of high-performance computing (HPC) systems.  ...  Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach.  ...  ACKNOWLEDGEMENTS The authors would like to thank the Information Technology Department at the University of Nevada, Reno for the use of computing time on the High-Performance Computing Cluster (http://  ... 
doi:10.7717/peerj.3486 pmid:28652936 pmcid:PMC5483034 fatcat:qoj5uwhzazf5li6t3e62kxhxey

BioExcel-2 Deliverable 2.4 – Development of a framework for the combination of HPC and HPDA operations

Adam Hospital, Genis Bayarri, Josep Lluis Gelpi, Pau Andrio, Daniele Lezzi, Rosa M Badia, Jorge Ejarque, Javier Alvarez, Salvi Sola, Sandro Barissi, Federica Battistini, Diego Gallego (+2 others)
2020 Zenodo  
This deliverable presents the different approaches of the BioExcel CoE regarding the design and development of a framework for the combination of High Performance Computing (HPC) and High Performance Data  ...  Based on distributed arrays (ds-arrays), dislib divides the input data in blocks that are processed in parallel, eventually performing a reduction to yield the results (map/reduce), reducing the execution  ...  A number of independent calculations could be launched in parallel on HPC supercomputers using the PyCOMPSs workflow manager (work in progress).  ... 
doi:10.5281/zenodo.4916029 fatcat:yqr2fvusv5ftlkyy6nbkyelzoa

BioExcel-2 Deliverable D5.2 - Annotated and Justified Service Catalogue

Yvonne Westermaier, Robert Soliva
2019 Zenodo  
Molecular modelling solutions combine the workflows and training assets as solutions or packages that can be adapted to the needs of the client.  ...  The business-exploitable assets described in this deliverable will be updated at least every six months and they will be prioritized in later deliverables (D5.4 Preliminary Business Plan available at PM18  ...  Exascale computing refers to computing systems capable of at least 10 18 calculations per second. In the case of BioExcel, it may involve Parallel Computational Workflows in Python (PyCOMPSs).  ... 
doi:10.5281/zenodo.5511775 fatcat:6x4ltt6lajcczet7z2jdzqutkq

D3.3 and D4.4: Consolidated Science Demonstrator progress and evaluation reports [article]

Hermann Lederer, Steven Newhouse
2018 Zenodo  
Their input is used to drive and prioritize the integration of the EOSC services in a common homogeneous platform.  ...  To achieve this goal, a selection process for Science Demonstrators through Open Calls has been developed, followed by the execution of two Open Calls.  ...  supercomputing and parallel computing.  ... 
doi:10.5281/zenodo.3387596 fatcat:7svhwma7xrhyfch4qiqeaquruu

BioExcel-2 deliverable D3.6 – Pre-Exascale showcase calculation and Use Case Final Report

Arno Proeme, Alessandra Villa, Alexandre Bonvin, Vytautas Gapsys, Rodrigo Vargas Honorato, Adam Hospital, Esther Sala, Dmitry Morozov, Gerrit Groenhof, Mirko Paulikat, Paolo Carloni
2022 Zenodo  
We demonstrate that the Use Cases serve as exemplars of how important challenges in biomolecular modelling and simulation can be tackled effectively using HPC resources and various combinations of the  ...  Final reports for each Use Case include a summary of work done, scientific results obtained, software and HPC resources used, and how the work has impacted the community.  ...  While the compute intensive parts of the HADDOCK workflow are an example of parallel execution with perfect or near-perfect parallel efficiency, the pre-and post-processing steps are sequential.  ... 
doi:10.5281/zenodo.6451260 fatcat:g2qgl4pxdfg2fochnva5jr6y6u

NGScloud2: optimized bioinformatic analysis using Amazon Web Services

Fernando Mora-Márquez, José Luis Vázquez-Poletti, Unai López de Heredia
2021 PeerJ  
NGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services.  ...  The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next generation sequencing data, have made  ...  Chano for beta-testing of NGScloud2 operability. ADDITIONAL INFORMATION AND DECLARATIONS  ... 
doi:10.7717/peerj.11237 pmid:33959420 pmcid:PMC8054753 fatcat:pb7gzj47rran5hpihifrz4lzga

Book Of Abstracts - 12Th Res Users'Conference

Red Española De Supercomputación
2018 Zenodo  
Book of abstracts of the 12th Users' Conference of the Spanish Supercomputing Network, which was held in Valencia on September 20th 2018.  ...  This book includes the abstracts of the talks and posters presented at the conference.  ...  Acknowledgments The RES gratefully acknowledges Universitat de València for their collaboration in organising this conference, and RDA Europe for their support and sponsorship.  ... 
doi:10.5281/zenodo.1325102 fatcat:3cctfoatjvei7lffoyhr3zhltu

Extreme Big Data (EBD): Next Generation Big Data Infrastructure Technologies Towards Yottabyte/Year

2014 Supercomputing Frontiers and Innovations  
With such comprehensive overhaul of the entire system stack, coupled with advances in both computing and storage, we expect that we could amplify the EBD processing power of existing Cloud datacenters  ...  workflows of both batch and real-time processing, being able to schedule tasks balancing the processing requirements versus minimizing data movement.  ...  The Pwrake workflow system executes a workflow written in Rakefile in parallel assigning processes on a compute node where the input data is stored.  ... 
doi:10.14529/jsfi140206 fatcat:fxzoyb3hgzaallrbrs4jkks2im

GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells

Gerald F Späth, Giovanni Bussotti
2021 Nucleic Acids Research  
Our results illustrate how GIP can be used for the identification of aneuploidy, gene copy number variations, changes in nucleic acid sequences, and chromosomal rearrangements.  ...  To overcome this limitation and better understand the role of genetic changes in enhancing pathogenicity we established GIP, a novel, powerful bioinformatic pipeline for comparative genome analysis.  ...  We also would like to acknowledge Dr Aida Bouratbine for generously providing the Leishmania infantum WGS dataset.  ... 
doi:10.1093/nar/gkab1237 pmid:34928370 pmcid:PMC8989552 fatcat:wibbvnxxkbb23f7yopmnqoncpi

Computer Architecture-Aware Optimisation of DNA Analysis Systems [article]

Hasindu Gamaarachchi
2021 arXiv   pre-print
The optimised software tools are used in complete end-to-end analysis workflows and their efficacy is demonstrated by running on prototypical embedded systems.  ...  Consequently, the full utility of an ultra-portable sequencer for sequencing in-the-field or at the point-of-care is limited by the lack of portable lightweight analytic techniques.  ...  from the parallel computing lab of Intel, yielding 2.4X improvement in performance.  ... 
arXiv:2101.05012v1 fatcat:wcujdqliwzgrxd2zc2wcudbqpu

Towards enabling I/O awareness in task-based programming models

Hatem Elshazly, Jorge Ejarque, Francesc Lordan, Rosa M. Badia
2021 Future generations computer systems  
On the one hand, more parallelism can be created by supporting special tasks for executing I/O workloads, called I/O tasks, that can overlap with the execution of compute tasks.  ...  Although task-based programming models made it possible to achieve higher levels of parallelism by enabling the execution of tasks in large-scale distributed platforms, this parallelism only benefited  ...  We implemented the I/O awareness capabilities in the PyCOMPSs tasking framework and evaluated it with different I/O workloads.  ... 
doi:10.1016/j.future.2021.03.009 fatcat:waigstbhbfajxh35xya6aiiikm

D7.2.1: Technical Support for DECI Projects

Lilit Axner
2012 Zenodo  
This deliverable reports on technical support for DECI (Distributed European Computing Initiative) projects in the first year of the PRACE-2IP project.  ...  enabling help for their projects going beyond the usual assistance in getting access and porting the code to the execution platform.  ...  The aim of this work is the study of the fluid dynamic behavior of underexpanded hydrogen jets by using a High Performance Computing (HPC) methodology.  ... 
doi:10.5281/zenodo.6572366 fatcat:sregqlvigjhm7i2x6kxazowxpe
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