Ergatis: a web interface and scalable software system for bioinformatics workflows
Abstract
Motivation: The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. Software is also needed to simplify data management and make large-scale bioinformatics analysis accessible and reproducible to a wide class of target users. Results: We have developed a workflow management system named Ergatis that enables users to build, execute and monitor pipelines for computational analysis of genomics data. Ergatis contains preconfigured components and template pipelines for a number of common bioinformatics tasks such as prokaryotic genome annotation and genome comparisons. Outputs from many of these components can be loaded into a Chado relational database. Ergatis was designed to be accessible to a broad class of users and provides a user friendly, web-based interface. Ergatis supports highthroughput batch processing on distributed compute clusters and has been used for data management in a number of genome annotation and comparative genomics projects.
- Authors:
-
- Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). Inst. for Genome Sciences
- J. Craig Venter Inst., Inc., Rockville, MD (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- J. Craig Venter Inst., Inc., Rockville, MD (United States); Georgetown Univ., Washington, DC (United States). Dept. of Biology. Computational Genomics Lab.
- Michigan State Univ., East Lansing, MI (United States). Dept. of Plant Biology
- Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). Inst. for Genome Sciences; Univ. of Maryland, College Park, MD (United States). Center for Bioinformatics and Computational Biology
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1625266
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Bioinformatics
- Additional Journal Information:
- Journal Volume: 26; Journal Issue: 12; Journal ID: ISSN 1367-4803
- Publisher:
- International Society for Computational Biology - Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Computer Science; Mathematical & Computational Biology; Mathematics
Citation Formats
Orvis, Joshua, Crabtree, Jonathan, Galens, Kevin, Gussman, Aaron, Inman, Jason M., Lee, Eduardo, Nampally, Sreenath, Riley, David, Sundaram, Jaideep P., Felix, Victor, Whitty, Brett, Mahurkar, Anup, Wortman, Jennifer, White, Owen, and Angiuoli, Samuel V. Ergatis: a web interface and scalable software system for bioinformatics workflows. United States: N. p., 2010.
Web. doi:10.1093/bioinformatics/btq167.
Orvis, Joshua, Crabtree, Jonathan, Galens, Kevin, Gussman, Aaron, Inman, Jason M., Lee, Eduardo, Nampally, Sreenath, Riley, David, Sundaram, Jaideep P., Felix, Victor, Whitty, Brett, Mahurkar, Anup, Wortman, Jennifer, White, Owen, & Angiuoli, Samuel V. Ergatis: a web interface and scalable software system for bioinformatics workflows. United States. https://doi.org/10.1093/bioinformatics/btq167
Orvis, Joshua, Crabtree, Jonathan, Galens, Kevin, Gussman, Aaron, Inman, Jason M., Lee, Eduardo, Nampally, Sreenath, Riley, David, Sundaram, Jaideep P., Felix, Victor, Whitty, Brett, Mahurkar, Anup, Wortman, Jennifer, White, Owen, and Angiuoli, Samuel V. Thu .
"Ergatis: a web interface and scalable software system for bioinformatics workflows". United States. https://doi.org/10.1093/bioinformatics/btq167. https://www.osti.gov/servlets/purl/1625266.
@article{osti_1625266,
title = {Ergatis: a web interface and scalable software system for bioinformatics workflows},
author = {Orvis, Joshua and Crabtree, Jonathan and Galens, Kevin and Gussman, Aaron and Inman, Jason M. and Lee, Eduardo and Nampally, Sreenath and Riley, David and Sundaram, Jaideep P. and Felix, Victor and Whitty, Brett and Mahurkar, Anup and Wortman, Jennifer and White, Owen and Angiuoli, Samuel V.},
abstractNote = {Motivation: The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. Software is also needed to simplify data management and make large-scale bioinformatics analysis accessible and reproducible to a wide class of target users. Results: We have developed a workflow management system named Ergatis that enables users to build, execute and monitor pipelines for computational analysis of genomics data. Ergatis contains preconfigured components and template pipelines for a number of common bioinformatics tasks such as prokaryotic genome annotation and genome comparisons. Outputs from many of these components can be loaded into a Chado relational database. Ergatis was designed to be accessible to a broad class of users and provides a user friendly, web-based interface. Ergatis supports highthroughput batch processing on distributed compute clusters and has been used for data management in a number of genome annotation and comparative genomics projects.},
doi = {10.1093/bioinformatics/btq167},
journal = {Bioinformatics},
number = 12,
volume = 26,
place = {United States},
year = {Thu Apr 22 00:00:00 EDT 2010},
month = {Thu Apr 22 00:00:00 EDT 2010}
}
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