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
Ergatis: a web interface and scalable software system for bioinformatics workflows
2010
Bioinformatics
Preserved Fulltext
The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. ...
Ergatis was designed to be accessible to a broad class of users and provides a user friendly, web-based interface. ...
ACKNOWLEDGEMENTS We would like to thank both the developers on the project and the user community who continue to suggest new features and improve the project. ...
doi:10.1093/bioinformatics/btq167
pmid:20413634
pmcid:PMC2881353
fatcat:y3q4bmjwzbddhhsqshjajxuuyi
CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing
2011
BMC Bioinformatics
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 2013; you can also visit the original URL.
The file type is application/pdf.
The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. ...
Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable ...
Acknowledgements and funding ...
doi:10.1186/1471-2105-12-356
pmid:21878105
pmcid:PMC3228541
fatcat:2vs2dcjiarci7jlgxuewujb3x4
Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds
2012
BMC Bioinformatics
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 MapReduce framework enables a scalable processing and analyzing of large datasets by distributing the computational load on connected computer nodes, referred to as a cluster. ...
science and could thus prevent scientists from usage of currently available and useful software solutions. ...
file system image in Bioinformatics including a wide range of biological software, programming libraries as well as data and is therefore an excellent basis for bioinformatic computations in the cloud ...
doi:10.1186/1471-2105-13-200
pmid:22888776
pmcid:PMC3532373
fatcat:tc7jppaw3jc2jh7wwlbbxkzlzm
SMITH: a LIMS for handling next-generation sequencing workflows
2014
BMC Bioinformatics
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.
Methods: SMITH is a web application with a MySQL server at the backend. ...
The workflows are available through an API provided by the workflow management system. ...
This article has been published as part of BMC Bioinformatics Volume 15 Supplement 14, 2014: Semantic, social, mobile applications for bioinformatics and biomedical laboratories: selected works from the ...
doi:10.1186/1471-2105-15-s14-s3
pmid:25471934
pmcid:PMC4255740
fatcat:j4eszvlx2jaj7mt4o77s24dd4e
Web Resources for Metagenomics Studies
2015
Genomics, Proteomics & Bioinformatics
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.
This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. ...
There are at least a dozen such software tools presently available in the public domain. ...
Acknowledgments The authors are thankful to BIT Virtual Centre, Patan Node, Hemchandracharya North Gujarat University, India for providing servers and computational facilities. ...
doi:10.1016/j.gpb.2015.10.003
pmid:26602607
pmcid:PMC4678780
fatcat:uldztj42fbdqvbq55u3poyigeq
Aeromancer: A Workflow Manager for Large-Scale MapReduce-Based Scientific Workflows
2014
2014 IEEE 13th International Conference on Trust, Security and Privacy in Computing and Communications
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 2015; you can also visit the original URL.
The file type is application/pdf.
To address the above challenges, we present Aeromancer, a feature-rich workflow manager for running MapReduce-based workflows that utilizes both client and cloud resources. ...
Managing such workflows, while using such a gamut of computing resources, is an unnecessarily arduous task for domain scientists. ...
Heshan Lin for his guidance and Microsoft for their support in the form of infrastructure and counsel. ...
doi:10.1109/trustcom.2014.97
dblp:conf/trustcom/MohamedMZTF14
fatcat:lsxriwm3pvhpzl673z354me3su
CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline
2017
BMC Genomics
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.
Data up-and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. ...
The benefit of increasing genomic sequence data to the scientific community depends on easy-touse, scalable bioinformatics support. ...
Runtimes were determined based on processing times recorded with the Ergatis workflow system [29] that is part of the CloVR framework and used for process management. ...
doi:10.1186/s12864-017-3717-3
pmid:28449639
pmcid:PMC5408420
fatcat:jrrq57gfyfaplhi6knesdvr2im
A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines
2011
BMC Bioinformatics
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 2011; you can also visit the original URL.
The file type is application/pdf.
Conclusions: PaPy offers a modular framework for the creation and deployment of parallel and distributed dataprocessing workflows. ...
Results: To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). ...
Acknowledgements The Univ of Virginia and the Jeffress Memorial Trust (J-971) are gratefully acknowledged for funding this work. ...
doi:10.1186/1471-2105-12-61
pmid:21352538
pmcid:PMC3051902
fatcat:ijojw42y6jgybi5pwjzajwqhyu