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NMR in the Cloud
Resources for Moving Biomolecular NMR Research to the cloud
- 1st Edition - March 1, 2099
- Editor: Jeffrey Hoch
- Language: English
- Paperback ISBN:9 7 8 - 0 - 3 2 3 - 9 0 5 5 9 - 6
- eBook ISBN:9 7 8 - 0 - 3 2 3 - 9 0 6 7 9 - 1
NMR in the Cloud: Resources for Moving Biomolecular NMR Research to the cloud is the ideal reference for Biomolecular researchers to explore and incorporate cloud-based tools to… Read more
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Request a sales quoteNMR in the Cloud: Resources for Moving Biomolecular NMR Research to the cloud is the ideal reference for Biomolecular researchers to explore and incorporate cloud-based tools to increase productivity of their projects. The COVID-19 pandemic, by forcing social distancing and work-from-home, has accelerated these trends and increased the demand for online resources for data processing and analysis, data storage, and remote collaboration and training tools. The trend toward online research will continue well after the pandemic subsides, because online resources remain valuable even in the absence of restrictions on in-person work. They increase the efficiency of the research enterprise and make it more robust in the face of disruptions of all sorts, environmental as well as public health.
The book is structured around four parts. The first introduces reproducible computing for Bio-NMR, and collaborative computing tools. Part two presents online NMR platforms, including WeNMR, SB Grid, BMBR, Scientific Cloud Computing tools, and data Stewardship. The third part covers NMR specific online tools, including NMRfx, NMRPipe, NMRFAM-SPARKY, MNova, Chemical Shift Prediction, Peak Assignment, SPINACH, GISSMO, CSRosetta, NMR Metabolomics, Protein Structure Prediction, and reproducibility in the cloud environment. Part four presents case studies that help researchers envision how to select and deploy these tools to make their biological quest more productive and impactful.
Biomolecular researchers will benefit from this book by gaining insights into selecting and using these analytical tools in the most productive way. Core Bio-NMR Managers may as well benefit from offering the book as reference for their customers.
- Provides an overview of the most current and powerful cloud-based analytical tools
- Presents case studies of research projects that incorporated the tools successfully
- Discusses research data stewardship and governance
- Provides an extensive list of tools with key decision factors in its adoption
Bioscience researchers at PhD level and above, Core NMR facility managers, Biochemistry and Biomaterials researchers at PhD level and above, Chemistry researchers
Part I - Introduction1. Reproducible Computing for Bio-NMR: NMRboxNMRbox Team, UConn Health2. Collaborative Computing Project for NMRGeerten Vuister, University of Leicester
Part II – Online Platforms3. WeNMRAlexander Bonvin, University of Utrecht4. SB-GridPiotr Sliz., Harvard Medical School5. Biological Magnetic Resonance Data BankBMRB Team, UConn Health and Osaka Universitya. BMRB, BMRBj, BMRbig6. Resources for Online TrainingAdam Schuyler, UConn Health7. Resources for Remote CollaborationMark Maciejewski, UConn Health8. Scientific Cloud ComputingMiron Livny, University of Wisconsin9. Data StewardshipMichael Gryk, UConn Health
Part III – NMR Online Tools10. NMRfxBruce Johnson, CUNY11. NMRPipeFrank Delaglio, NIST12. NMRFAM-SPARKYWoonghee Lee, University of Colorado13. MNova14. Chemical Shift Prediction (possible contributors)a. David Wishart, University of Albertab. Ad Bax, NIHc. David Case, Rutgers15. Peak AssignmentHamid Eghbalnia, UConn Health16. Spin Simulation Using SPINACHIlya Kuprov, University of Southampton17. Spin Modeling with GISSMOHesam Dashti, Broad Insitute18. Deconvolving 2D Spectra for Complex MixturesRaphael Brüschweiler, Ohio State University19. Relaxation and Rate Analysis (possible contributors)a. Art Palmer, Columbia Universityb. Pat Loria, Yalec. Mark Foster, Ohio State20. CS-RosettaRosetta and BMRB teams, Ad Bax, Yang Shen, NIH, Universities of Washington and Wisconsin21. NMR MetabolomicsDavid Wishart, University of Alberta22. Protein Structure PredictionGoogle Alpha Team23. Reproducibility in the CloudBertram Ludäscher, University of Illinois
Part IV – Case Studies24. Case Study: Covid-19 NMR ConsortiumHarald Schwalbe, University of Frankfurt; Signals Team25. Case Study: NUSconAdam Schuyler, UConn Health26. Case Study: NMRFAM WorkshopMilo Westler, UW-Madison27. Case Study: ICMRBS virtual seminarsMarkus Zweckstetter, Max Planck Institute for Biophysical
- No. of pages: 266
- Language: English
- Edition: 1
- Published: March 1, 2099
- Imprint: Academic Press
- Paperback ISBN: 9780323905596
- eBook ISBN: 9780323906791
JH
Jeffrey Hoch
Jeffrey C. Hoch, Ph.D.
Director, Gregory P. Mullen NMR Structural Biology Facility
Professor, Department of Molecular Biology and Biophysics
Molecular, Microbial and Structural Biology
UConn Health
Farmington, CT 06030
Dr. Hoch received his Masters and PhD degrees in Physical Chemistry from Harvard University. His laboratory works on problems related to the physical basis for the biological activity of proteins. Broadly, this includes their structure, dynamics, stability, and interactions with other molecules. He is a leader in NMR data processing and analysis for biomolecular applications: he chaired a 1990 NATO Advanced Research Workshop on Computational Aspects of Biomolecular NMR, chaired the inaugural Gordon Research Conference on the same topic in 1999, co-authored the book “NMR Data Processing” with Dr. Alan Stern (1996), and currently directs two international online NMR resources: the National Center for Biomolecular NMR Data Processing and Analysis (nmrbox.org) and the Biological Magnetic Resonance Data Bank (bmrb.io).
He and his group have extensive experience in operating UConn Health’s Gregory P. Mullen NMR Structural Biology Facility (which Dr. Hoch directs) that includes spectrometers operating at 400, 500, 600, and 800 MHz. The latter three instruments are equipped with state-of-the-art cryogenically cooled probes. Computational resources include a power 1000-node cluster.
Affiliations and expertise
Director, Gregory P. Mullen NMR Structural Biology Facility and Professor, Department of Molecular Biology and Biophysics Molecular, Microbial and Structural Biology, UConn Health, Farmington, CT, USA