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Ergatis: a web interface and scalable software system for bioinformatics workflows

J. Orvis, J. Crabtree, K. Galens, A. Gussman, J. M. Inman, E. Lee, S. Nampally, D. Riley, J. P. Sundaram, V. Felix, B. Whitty, A. Mahurkar (+3 others)
2010 Bioinformatics  
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

Samuel V Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White, W Florian Fricke
2011 BMC Bioinformatics  
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

Sebastian Schönherr, Lukas Forer, Hansi Weißensteiner, Florian Kronenberg, Günther Specht, Anita Kloss-Brandstätter
2012 BMC Bioinformatics  
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

Francesco Venco, Yuriy Vaskin, Arnaud Ceol, Heiko Muller
2014 BMC Bioinformatics  
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

Pravin Dudhagara, Sunil Bhavsar, Chintan Bhagat, Anjana Ghelani, Shreyas Bhatt, Rajesh Patel
2015 Genomics, Proteomics & Bioinformatics  
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

Nabeel Mohamed, Nabanita Maji, Jing Zhang, Nataliya Timoshevskaya, Wu-Chun Feng
2014 2014 IEEE 13th International Conference on Trust, Security and Privacy in Computing and Communications  
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

Sonia Agrawal, Cesar Arze, Ricky S. Adkins, Jonathan Crabtree, David Riley, Mahesh Vangala, Kevin Galens, Claire M. Fraser, Hervé Tettelin, Owen White, Samuel V. Angiuoli, Anup Mahurkar (+1 others)
2017 BMC Genomics  
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

Marcin Cieślik, Cameron Mura
2011 BMC Bioinformatics  
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