Practical Recommendations for Supporting a Systems Biology Cyberinfrastructure

Jeremy D. DeBarry; Jessica C. Kissinger; Mustafa V. Nural; Suman B. Pakala; Jay C. Humphrey; Esmeralda V. S. Meyer; Regina Joice Cordy; Monica Cabrera-Mora; Elizabeth D. Trippe; Jacob B. Aguilar; Ebru Karpuzoglu; Yi H. Yan; Jessica A. Brady; Allison N. Hankus; Nicolas Lackman; Alan R. Gingle; Vishal Nayak; Alberto Moreno; Chester J. Joyner; Juan B. Gutierrez; Mary R. Galinski; the MaHPIC Consortium

doi:10.5334/dsj-2020-024

Data Science Journal (Jun 2020)

Practical Recommendations for Supporting a Systems Biology Cyberinfrastructure

Jeremy D. DeBarry,
Jessica C. Kissinger,
Mustafa V. Nural,
Suman B. Pakala,
Jay C. Humphrey,
Esmeralda V. S. Meyer,
Regina Joice Cordy,
Monica Cabrera-Mora,
Elizabeth D. Trippe,
Jacob B. Aguilar,
Ebru Karpuzoglu,
Yi H. Yan,
Jessica A. Brady,
Allison N. Hankus,
Nicolas Lackman,
Alan R. Gingle,
Vishal Nayak,
Alberto Moreno,
Chester J. Joyner,
Juan B. Gutierrez,
Mary R. Galinski,
the MaHPIC Consortium

Affiliations

Jeremy D. DeBarry: Institute of Bioinformatics, University of Georgia, Athens
Jessica C. Kissinger: Institute of Bioinformatics, University of Georgia, Athens; Department of Genetics, University of Georgia, Athens; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens
Mustafa V. Nural: Institute of Bioinformatics, University of Georgia, Athens; Department of Computer Science, University of Georgia, Athens
Suman B. Pakala: Institute of Bioinformatics, University of Georgia, Athens
Jay C. Humphrey: Institute of Bioinformatics, University of Georgia, Athens
Esmeralda V. S. Meyer: International Center for Malaria Research, Education and Development, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta
Regina Joice Cordy: International Center for Malaria Research, Education and Development, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta; Environmental Health and Safety Office, Emory University, Atlanta
Monica Cabrera-Mora: International Center for Malaria Research, Education and Development, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta; Department of Biology, Wake Forest University, Winston-Salem
Elizabeth D. Trippe: Institute of Bioinformatics, University of Georgia, Athens
Jacob B. Aguilar: Department of Mathematics, University of Georgia, Athens
Ebru Karpuzoglu: International Center for Malaria Research, Education and Development, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta
Yi H. Yan: Institute of Bioinformatics, University of Georgia, Athens
Jessica A. Brady: School of Chemical, Materials, and Biomedical Engineering, University of GA, Athens
Allison N. Hankus: International Center for Malaria Research, Education and Development, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta
Nicolas Lackman: Institute of Bioinformatics, University of Georgia, Athens
Alan R. Gingle: Institute of Bioinformatics, University of Georgia, Athens
Vishal Nayak: Institute of Bioinformatics, University of Georgia, Athens; CSRA Inc., 2 Corporate Blvd Suite 100, Atlanta
Alberto Moreno: International Center for Malaria Research, Education and Development, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta; Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta
Chester J. Joyner: International Center for Malaria Research, Education and Development, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta
Juan B. Gutierrez: Institute of Bioinformatics, University of Georgia, Athens; Department of Mathematics, University of Georgia, Athens; Department of Mathematics, University of Texas, San Antonio
Mary R. Galinski: International Center for Malaria Research, Education and Development, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta; Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta
the MaHPIC Consortium: Membership of the MaHPIC Consortium is provided in the Acknowledgments

DOI: https://doi.org/10.5334/dsj-2020-024
Journal volume & issue: Vol. 19, no. 1

Abstract

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Projects in the life sciences continue to increase in complexity as they scale to answer deeper and more diverse questions. They employ technologies that generate increasingly large ‘omic’ datasets and research teams regularly include experts ranging from animal care technicians, veterinarians, human health clinicians, geneticists, immunologists, and biochemists to computer scientists, mathematical modelers, and data scientists, often located at different institutions. Providing the cyberinfrastructure support framework (IT, data management, communication, documentation, and aspects of project management related to these areas) for these projects requires a diverse set of technical tools and soft skills. These skills must be able to meet both the broad needs of data generators and consumers within the project and the needs of the larger scientific community. Here we describe recommendations for cyberinfrastructure support teams responsible for systems biology research programs. Recommendations are based on lessons learned while establishing and leading a complex, transdisciplinary, host-pathogen malaria systems biology consortium involving many institutions, a variety of disciplines, animal infectious disease models, and clinical studies. While some technical suggestions are included, the primary foci are situational and sociological challenges and tips for handling them.

Published in Data Science Journal

ISSN: 1683-1470 (Online)
Publisher: Ubiquity Press
Country of publisher: United Kingdom
LCC subjects: Science: Science (General)
Website: http://datascience.codata.org/

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