Practical Recommendations for Supporting a Systems Biology Cyberinfrastructure

Authors

  • 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

Keywords:

Transdisciplinary, Cyberinfrastructure, Team science, Team communication, Systems biology, MaHPIC

Abstract

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.

Downloads

Published

2020-06-09

Issue

Vol. 19 (2020)

Section

Practice Papers

License

Copyright (c) 2020 The Author(s)

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Authors who publish with this journal agree to the following terms.  If a submission is rejected or withdrawn prior to publication, all rights return to the author(s):

  • Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.

  • Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.

  • Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work.

Submitting to the journal implicitly confirms that all named authors and rights holders have agreed to the above terms of publication. It is the submitting author's responsibility to ensure all authors and relevant institutional bodies have given their agreement at the point of submission.

Note: some institutions require authors to seek written approval in relation to the terms of publication. Should this be required, authors can request a separate licence agreement document from the editorial team (e.g. authors who are Crown employees).