A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Filters
Leveraging the national cyberinfrastructure for biomedical research
2014
JAMIA Journal of the American Medical Informatics Association
Preserved Fulltext
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
2013
Journal of Supercomputing
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2016
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2011
Proceedings of the 6th IEEE International Conference on Intelligent Data Acquisition and Advanced Computing Systems
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2015
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2013
American Journal of Pharmaceutical Education
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2019
Figshare
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2009
Computational Methods in Science and Technology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2015
Nature
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2013
DNA Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2017
Molecules
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2015
Quantitative Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2015
Procedia Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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]
2019
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 2,189 results