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Leveraging the national cyberinfrastructure for biomedical research

Richard LeDuc, Matthew Vaughn, John M Fonner, Michael Sullivan, James G Williams, Philip D Blood, James Taylor, William Barnett
2014 JAMIA Journal of the American Medical Informatics Association  
In the USA, the national cyberinfrastructure refers to a system of research supercomputer and other IT facilities and the high speed networks that connect them.  ...  Specialized web portals, support centers, and virtual organizations can be constructed on these resources to meet defined computational challenges, specifically for genomics.  ...  Center for Genome Analysis Support, or Indiana University.  ... 
doi:10.1136/amiajnl-2013-002059 pmid:23964072 pmcid:PMC3932465 fatcat:mla5vg3t4vcjnno5igcwnxxmrq

Editorial of special section on multimedia applications and ubiquitous computing

Tai-hoon Kim, Sabah Mohammed
2013 Journal of Supercomputing  
In "Development of a Virtualized Supercomputing Environment for Genomic Analysis," authors presented the design and implementation of a virtualized supercomputing environment that provides functions for  ...  Authors also presented a virtualized system architecture that takes data locality into account for the data intensiveness of NGS analysis.  ... 
doi:10.1007/s11227-013-0945-4 fatcat:6ovelfav4nda3hj432vbblih7y

DNA Data Bank of Japan

Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Toshiaki Katayama, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2016 Nucleic Acids Research  
The DNA Data Bank of Japan (DDBJ) (http://www. ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987).  ...  We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc. org), in collaboration with the  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Chiharu Kawagoe, and all members of DDBJ Center for  ... 
doi:10.1093/nar/gkw1001 pmid:27924010 pmcid:PMC5210514 fatcat:sbslos5mnbgnpfurvzabh2svki

Parallel performance evaluation and profiling of multiple sequence nucleotide alignment on the supercomputer BlueGene/P

Plamenka Borovska, Veska Gancheva, Stoyan Markov, Ivailo Georgiev, Emilyan Asenov
2011 Proceedings of the 6th IEEE International Conference on Intelligent Data Acquisition and Advanced Computing Systems  
The goal of this paper is to estimate the scalability of parallel sequence alignment on the supercomputer BlueGene/P for the case study of investigating the interaction between influenza virus A and the  ...  Bioinformatics is a scientific area requiring powerful computing resources for exploring large sets of biological data. Sequence alignment is an important method in DNA and protein analysis.  ...  Acknowledgement: This work is supported by the National Science Fund, Bulgarian Ministry of Education and Science, Grant DCVP 02/1.  ... 
doi:10.1109/idaacs.2011.6072747 dblp:conf/idaacs/BorovskaGMGA11 fatcat:6kkdzanmibhovf5iazfrkhdzha

DNA data bank of Japan (DDBJ) progress report

Jun Mashima, Yuichi Kodama, Takehide Kosuge, Takatomo Fujisawa, Toshiaki Katayama, Hideki Nagasaki, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2015 Nucleic Acids Research  
This paper briefly reports on the activities of the DDBJ Center over the past year including submissions to databases and improvements in our services for data retrieval, analysis, and integration.  ...  In addition, the DDBJ Center develops semantic web technologies for data integration and sharing in collaboration with the Database Center for Life Science (DB-CLS) in Japan.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Chiharu Kawagoe, and all members of DDBJ Center for their assistance in data collection, annotation, release, and software development  ... 
doi:10.1093/nar/gkv1105 pmid:26578571 pmcid:PMC4702806 fatcat:dsvzn2iivjb7jhqnqhoehswhtu

The Convergence of New Technology With the Delivery of Health Care Services

J. Lyle Bootman
2013 American Journal of Pharmaceutical Education  
All of these players contributed to building a new supercomputer-based high-speed fiber network that cuts the time for genome analysis for cancer patients from 8 or more weeks down to an amazing 47 seconds  ...  The story was about the launch of the country's fastest genomic supercomputing platform.  ... 
doi:10.5688/ajpe7711 pmid:23460753 pmcid:PMC3578322 fatcat:2wcnuzzz6zd75lcwezonvxormu

Catering to Domain (Genomics) specific eResearch needs [article]

Dinindu Senanayake, Nooriyan Poonawala
2019 Figshare  
Also, implementing eResearch training tools such as genomics virtual labs will assist beginners' level bioinformaticians/computationalbiologists to acquire advance skills within an interactive environment  ...  Providing eResearch capability and training catered to a specific domain such as Genomics presents its own set of challenges and opportunities.  ...  Project Image Courtesy of : https://www.sciencephoto.com/media/211270/view/supercomputers-at-celera-dn a-sequencing Image Courtesy of : http://cen.xraycrystals.org/dna.html A.  ... 
doi:10.6084/m9.figshare.8066948 fatcat:5bnh2z54kbdsfojkdcxkhmy2ke

LPMX: A pure rootless composable container system [article]

Xu Yang, Masahiro Kasahara
2021 bioRxiv   pre-print
Container virtualization systems such as Singularity isolate environments, helping developers avoid conflicts between tools.  ...  Delivering tools for genome analysis to users is often difficult given their complex dependencies and conflicts.  ...  Acknowledgements The super-computing resource was provided in part by Human Genome Center (the University of Tokyo), in part by NIG supercomputer at ROIS National Institute of Genetics.  ... 
doi:10.1101/2021.06.04.445363 fatcat:2dlizoef3zg2xl6fy2c7yixkv4

New approach to Genomics Experiments Taking Advantage of Virtual Laboratory System

Luiza Handschuh, Marcin Lawenda, Piotr Stępniak, Marek Figlerowicz, Maciej Stroiński, Jan Węglarz
2009 Computational Methods in Science and Technology  
One of the exemplary domain is genomics -a new branch of science that developed rapidly in the last decade. As the genome research is very complex, it must be supported by professional informatics.  ...  Here, the general aspects of virtual laboratory systems are presented together with perspectives of their implementation in genomics in order to automate and facilitate this area of research.  ...  Acknowledgments The work was supported by the grant from the Polish State Committee for Scientific Research No. PBZ-MniI-2/1/2005 to M.F.  ... 
doi:10.12921/cmst.2009.15.01.31-40 fatcat:7qtx5vo7vvdbzc7qajenfvhffa

How to catch a cloud

Nadia Drake
2015 Nature  
Anyone who wants to reproduce, for example, the microbial-genome analysis described in one paper can access a snapshot of the authors' virtual machine on the Amazon cloud, simply by paying for Amazon computing  ...  explorers: StarCluster is a tool developed at the Massachusetts Institute of Technology in Cambridge that helps to build a virtual research-computing cluster on Amazon's platform.  ... 
doi:10.1038/522115a pmid:26040891 fatcat:xodcssb7pbdaxbka72ectg7lea

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data

H. Nagasaki, T. Mochizuki, Y. Kodama, S. Saruhashi, S. Morizaki, H. Sugawara, H. Ohyanagi, N. Kurata, K. Okubo, T. Takagi, E. Kaminuma, Y. Nakamura
2013 DNA Research  
The proposed pipeline consists of two analysis components: basic analysis for reference genome mapping and de novo assembly and subsequent high-level analysis of structural and functional annotations.  ...  Users may smoothly switch between the two components in the pipeline, facilitating web-based operations on a supercomputer for high-throughput data analysis.  ...  Acknowledgements: We thank Yasuhiro Tanizawa, Natsuko Sakakura, Shigeki Watanabe, and Naoko Sakamoto for the support of pipeline users. We particularly thank Toshihisa Okido for helpful discussions.  ... 
doi:10.1093/dnares/dst017 pmid:23657089 pmcid:PMC3738164 fatcat:ayzq4fhuvvdwpoqw7qjsre25ii

An Interface for Biomedical Big Data Processing on the Tianhe-2 Supercomputer

Xi Yang, Chengkun Wu, Kai Lu, Lin Fang, Yong Zhang, Shengkang Li, Guixin Guo, YunFei Du
2017 Molecules  
We tested the utility and performance of Orion using a big genomic dataset and achieved a satisfactory performance on Tianhe-2 with very few modifications to existing applications that were implemented  ...  In summary, Orion provides a practical and economical interface for big data processing on Tianhe-2.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules22122116 pmid:29194413 fatcat:kipnriahdfa7xicfy7jrznbulu

SupraBiology 2014: Promoting UK-China collaboration on Systems Biology and High Performance Computing

Ettore Murabito, Riccardo Colombo, Chengkun Wu, Malkhey Verma, Samrina Rehman, Jacky Snoep, Shao-Liang Peng, Naiyang Guan, Xiangke Liao, Hans V. Westerhoff
2015 Quantitative Biology  
Systems Biology in Education Computational Biology on the Tianhe-2 Supercomputer The report ends with a discussion section relating the ideas that have been pushed forward to establish collaborations  ...  In particular, the material hereby presented is organized around five main areas of interest: Systems Biology in medicine Computational methods of Systems Biology Computational Biology for Industry Computational  ...  A multi-layered model of epidermis, for example, has been developed to allow in silico clinical trials for surfactant-induced skin damage.  ... 
doi:10.1007/s40484-015-0039-9 fatcat:qu4tcgwuhfbfveg55e2vlzmbvy

Workload Management Portal for High Energy Physics Applications and Compute Intensive Science

V. Aulov, K. De, D. Drizhuk, A. Klimentov, D. Krasnopevtsev, R. Mashinistov, A. Novikov, D. Oleynik, A. Poyda, E. Ryabinkin, I. Tertychnyy, A. Teslyuk
2015 Procedia Computer Science  
The portal can be used not only for High Energy Physics (HEP) applications, but also for other compute-intensive sciences such as bioinformatics with genome and sequence analysis; astrophysics with cosmic  ...  As a part of this work, we have designed, developed and deployed a portal to submit payloads to heterogeneous computing infrastructure.  ...  Department of Energy  ... 
doi:10.1016/j.procs.2015.11.064 fatcat:hgu3xjyddzb4nhrpsvdhof7mhi

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  ...  developers.  ...  Cloud deployments: MuGVRE infrastructure has been designed as a fully virtualized environment.  ... 
doi:10.1101/602474 fatcat:ikxzgfug55dlznv6lxd5fqb3ae
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