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Karim MR, Michel A, Zappa A, Baranov P, Sahay R, Rebholz-Schuhmann D. Improving data workflow systems with cloud services and use of open data for bioinformatics research. Brief Bioinform 2019; 19:1035-1050. [PMID: 28419324 PMCID: PMC6169675 DOI: 10.1093/bib/bbx039] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Indexed: 11/22/2022] Open
Abstract
Data workflow systems (DWFSs) enable bioinformatics researchers to combine components for data access and data analytics, and to share the final data analytics approach with their collaborators. Increasingly, such systems have to cope with large-scale data, such as full genomes (about 200 GB each), public fact repositories (about 100 TB of data) and 3D imaging data at even larger scales. As moving the data becomes cumbersome, the DWFS needs to embed its processes into a cloud infrastructure, where the data are already hosted. As the standardized public data play an increasingly important role, the DWFS needs to comply with Semantic Web technologies. This advancement to DWFS would reduce overhead costs and accelerate the progress in bioinformatics research based on large-scale data and public resources, as researchers would require less specialized IT knowledge for the implementation. Furthermore, the high data growth rates in bioinformatics research drive the demand for parallel and distributed computing, which then imposes a need for scalability and high-throughput capabilities onto the DWFS. As a result, requirements for data sharing and access to public knowledge bases suggest that compliance of the DWFS with Semantic Web standards is necessary. In this article, we will analyze the existing DWFS with regard to their capabilities toward public open data use as well as large-scale computational and human interface requirements. We untangle the parameters for selecting a preferable solution for bioinformatics research with particular consideration to using cloud services and Semantic Web technologies. Our analysis leads to research guidelines and recommendations toward the development of future DWFS for the bioinformatics research community.
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Affiliation(s)
- Md Rezaul Karim
- Semantics in eHealth and Life Sciences (SeLS), Insight Centre for Data Analytics, National University of Ireland, Galway, Ireland
| | - Audrey Michel
- School of Biochemistry and Cell Biology, University College Cork, Ireland
| | - Achille Zappa
- Insight Centre for Data Analytics, National University of Ireland Galway, Dangan, Galway, Ireland
| | - Pavel Baranov
- School of Biochemistry and Cell Biology, University College Cork, Ireland
| | - Ratnesh Sahay
- Semantics in eHealth and Life Sciences (SeLS), Insight Centre for Data Analytics, National University of Ireland, Galway, Ireland
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Schiffer J, Mael LE, Prather KA, Amaro RE, Grassian VH. Sea Spray Aerosol: Where Marine Biology Meets Atmospheric Chemistry. ACS CENTRAL SCIENCE 2018; 4:1617-1623. [PMID: 30648145 PMCID: PMC6311946 DOI: 10.1021/acscentsci.8b00674] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Indexed: 05/25/2023]
Abstract
Atmospheric aerosols have long been known to alter climate by scattering incoming solar radiation and acting as seeds for cloud formation. These processes have vast implications for controlling the chemistry of our environment and the Earth's climate. Sea spray aerosol (SSA) is emitted over nearly three-quarters of our planet, yet precisely how SSA impacts Earth's radiation budget remains highly uncertain. Over the past several decades, studies have shown that SSA particles are far more complex than just sea salt. Ocean biological and physical processes produce individual SSA particles containing a diverse array of biological species including proteins, enzymes, bacteria, and viruses and a diverse array of organic compounds including fatty acids and sugars. Thus, a new frontier of research is emerging at the nexus of chemistry, biology, and atmospheric science. In this Outlook article, we discuss how current and future aerosol chemistry research demands a tight coupling between experimental (observational and laboratory studies) and computational (simulation-based) methods. This integration of approaches will enable the systematic interrogation of the complexity within individual SSA particles at a level that will enable prediction of the physicochemical properties of real-world SSA, ultimately illuminating the detailed mechanisms of how the constituents within individual SSA impact climate.
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Affiliation(s)
- Jamie
M. Schiffer
- Department of Chemistry and Biochemistry and Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Liora E. Mael
- Department of Chemistry and Biochemistry and Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Kimberly A. Prather
- Department of Chemistry and Biochemistry and Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
- Scripps
Institution of Oceanography, University
of California, San Diego, La Jolla, California 92093, United States
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry and Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Vicki H. Grassian
- Department of Chemistry and Biochemistry and Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
- Scripps
Institution of Oceanography, University
of California, San Diego, La Jolla, California 92093, United States
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Amaro RE, Mulholland AJ. Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures. Nat Rev Chem 2018; 2:0148. [PMID: 30949587 PMCID: PMC6445369 DOI: 10.1038/s41570-018-0148] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Drug action is inherently multiscale: it connects molecular interactions to emergent properties at cellular and larger scales. Simulation techniques at each of these different scales are already central to drug design and development, but methods capable of connecting across these scales will extend understanding of complex mechanisms and the ability to predict biological effects. Improved algorithms, ever-more-powerful computing architectures and the accelerating growth of rich datasets are driving advances in multiscale modeling methods capable of bridging chemical and biological complexity from the atom to the cell. Particularly exciting is the development of highly detailed, structure-based, physical simulations of biochemical systems, which are now able to access experimentally relevant timescales for large systems and, at the same time, achieve unprecedented accuracy. In this Perspective, we discuss how emerging data-rich, physics-based multiscale approaches are of the cusp of realizing long-promised impact in the discovery, design and development of novel therapeutics. We highlight emerging methods and applications in this growing field, and outline how different scales can be combined in practical modelling and simulation strategies.
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Affiliation(s)
- Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0304
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts. Sci Rep 2016; 6:26536. [PMID: 27216779 PMCID: PMC4877583 DOI: 10.1038/srep26536] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/03/2016] [Indexed: 12/22/2022] Open
Abstract
The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services.
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Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol 2016; 12:e1004619. [PMID: 27124275 PMCID: PMC4849799 DOI: 10.1371/journal.pcbi.1004619] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.
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Affiliation(s)
- Tatiana Maximova
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Ryan Moffatt
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
- Department of Biongineering, George Mason University, Fairfax, Virginia, United States of America
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
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Chen CB, Chen J, Wang J, Zhu YY, Shi JH. Combined spectroscopic and molecular docking approach to probing binding interactions between lovastatin and calf thymus DNA. LUMINESCENCE 2015; 30:1004-10. [DOI: 10.1002/bio.2851] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 12/03/2014] [Accepted: 12/29/2014] [Indexed: 01/21/2023]
Affiliation(s)
- C.-B. Chen
- College of Pharmaceutical Science; Zhejiang University of Technology; Hangzhou 310032 China
| | - J. Chen
- College of Pharmaceutical Science; Zhejiang University of Technology; Hangzhou 310032 China
| | - J. Wang
- College of Pharmaceutical Science; Zhejiang University of Technology; Hangzhou 310032 China
| | - Y.-Y. Zhu
- College of Pharmaceutical Science; Zhejiang University of Technology; Hangzhou 310032 China
| | - J.-H. Shi
- College of Pharmaceutical Science; Zhejiang University of Technology; Hangzhou 310032 China
- State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology; Zhejiang University of Technology; Hangzhou 310032 China
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