extended-abstract

Public Access

LSU Computational System Biology Gateway for Education

Authors:

Eroma Abeysinghe,

Michal Brylinski,

Marcus Christie,

Marlon PierceAuthors Info & Claims

PEARC '19: Practice and Experience in Advanced Research Computing 2019: Rise of the Machines (learning)

Article No.: 112, Pages 1 - 4

https://doi.org/10.1145/3332186.3333259

Published: 28 July 2019 Publication History

Abstract

Science gateways are a mechanism for delivering scientific software as a service, especially when the software requires high performance computing (HPC) resources to run effectively. The existence of a science gateway eliminates the user's need to learn to work with HPC systems and to manage software installations and updates. With well-designed user interfaces, users can more quickly become effective users of scientific applications and can manage information needed for replicating, modifying, and sharing results. All of these efficiency gains enable users to focus more on their research. In addition, science gateways are being identified as an effective educational tool, a tool to be used in classroom environments as a method to get students quickly into research on domain specific questions. In the absence of a science gateway, students are likely to need a considerable time to learn to work with HPC systems, and any time spent on such will reduce their time on the actual science. This poster presents how the Louisiana State University (LSU) gateway for the Computational System Biology Group (CSBG) - (www.brylinski.org) was updated and improved to be a classroom teaching tool. This work makes extensive use of Apache Airavata's group management capabilities.

References

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Digital Library

[2]

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Suresh Marru, Lahiru Gunathilake, Chathura Herath, Patanachai Tangchaisin, Marlon Pierce, Chris Mattmann, Raminder Singh, Thilina Gunarathne, Eran Chinthaka, Ross Gardler, et al. Apache airavata: a framework for distributed applications and computational workflows. In Proceedings of the 2011 ACM workshop on Gateway computing environments, pages 21--28. ACM, 2011.

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Supun Nakandala, Suresh Marru, Marlon Piece, Sudhakar Pamidighantam, Kenneth Yoshimoto, Terri Schwartz, Subhashini Sivagnanam, Amit Majumdar, and Mark A Miller. Apache airavata sharing service: A tool for enabling user collaboration in science gateways. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact, page 20. ACM, 2017.

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Thejaka Amila Kanewala, Suresh Marru, Jim Basney, and Marlon Pierce. A credential store for multi-tenant science gateways. In Cluster, Cloud and Grid Computing (CCGrid), 2014 14th IEEE/ACM International Symposium on, pages 445--454. IEEE, 2014.

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Stephen Paul Adithela, Marcus Christie, Suresh Marru, and Marlon Pierce. Django content management system evaluation and integration with apache airavata. PEARC âĂ&Zacute;18, pages 86:1--86:4, New York, NY, USA, 2018. ACM.

Cited By

Madamanchi AThomas MMagana AHeiland RMacklin P(2021) Supporting Computational Apprenticeship Through Educational and Software Infrastructure: A Case Study in a Mathematical Oncology Research Lab PRIMUS10.1080/10511970.2021.188184932:3(446-467)Online publication date: 18-Feb-2021
https://doi.org/10.1080/10511970.2021.1881849
Choi IAbeysinghe ECoulter EMarru SPierce MLiu X(2020)TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data InterpretationPractice and Experience in Advanced Research Computing 2020: Catch the Wave10.1145/3311790.3400853(461-464)Online publication date: 26-Jul-2020
https://dl.acm.org/doi/10.1145/3311790.3400853
Christie MMarru SAbeysinghe EUpeksha DPamidighantam SPaul Adithela SMathulla EBisht ARastogi SPierce M(2020)An extensible Django-based web portal for Apache AiravataPractice and Experience in Advanced Research Computing 2020: Catch the Wave10.1145/3311790.3396650(160-167)Online publication date: 26-Jul-2020
https://dl.acm.org/doi/10.1145/3311790.3396650

Index Terms

LSU Computational System Biology Gateway for Education
1. Computing methodologies
  1. Modeling and simulation
    1. Model development and analysis
      1. Model verification and validation
      2. Modeling methodologies
    2. Simulation support systems
      1. Simulation environments
      2. Simulation tools
2. Software and its engineering
  1. Software notations and tools
    1. Development frameworks and environments
      1. Software as a service orchestration system

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Published In

cover image ACM Other conferences

PEARC '19: Practice and Experience in Advanced Research Computing 2019: Rise of the Machines (learning)

July 2019

775 pages

ISBN:9781450372275

DOI:10.1145/3332186

General Chair:
Tom Furlani
Roswell Park Comprehensive Cancer Center

Copyright © 2019 Owner/Author.

Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author.

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 28 July 2019

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Extended-abstract
Research
Refereed limited

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NSF

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PEARC '19

PEARC '19: Practice and Experience in Advanced Research Computing

July 28 - August 1, 2019

IL, Chicago, USA

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Overall Acceptance Rate 133 of 202 submissions, 66%

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Cited By

Madamanchi AThomas MMagana AHeiland RMacklin P(2021) Supporting Computational Apprenticeship Through Educational and Software Infrastructure: A Case Study in a Mathematical Oncology Research Lab PRIMUS10.1080/10511970.2021.188184932:3(446-467)Online publication date: 18-Feb-2021
https://doi.org/10.1080/10511970.2021.1881849
Choi IAbeysinghe ECoulter EMarru SPierce MLiu X(2020)TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data InterpretationPractice and Experience in Advanced Research Computing 2020: Catch the Wave10.1145/3311790.3400853(461-464)Online publication date: 26-Jul-2020
https://dl.acm.org/doi/10.1145/3311790.3400853
Christie MMarru SAbeysinghe EUpeksha DPamidighantam SPaul Adithela SMathulla EBisht ARastogi SPierce M(2020)An extensible Django-based web portal for Apache AiravataPractice and Experience in Advanced Research Computing 2020: Catch the Wave10.1145/3311790.3396650(160-167)Online publication date: 26-Jul-2020
https://dl.acm.org/doi/10.1145/3311790.3396650

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