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Creators/Authors contains: "Brookes, Emre H"

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  1. Abstract Science Gateways provide an easily accessible and powerful computing environment for researchers. These are built around a set of software tools that are frequently and heavily used by large number of researchers in specific domains. Science Gateways have been catering to a growing need of researchers for easy to use computational tools, however their usage model is typically single user-centric. As scientific research becomes ever more team oriented, the need driven by user-demand to support integrated collaborative capabilities in Science Gateways is natural progression. Ability to share data/results with others in an integrated manner is an important and frequentlymore »requested capability. In this article we will describe and discuss our work to provide a rich environment for data organization and data sharing by integrating the SeedMeLab (formerly SeedMe2) platform with two Science Gateways: CIPRES and GenApp. With this integration we also demonstrate SeedMeLab’s extensible features and how Science Gateways may incorporate and realize FAIR data principles in practice and transform into community data hubs.« less
    Free, publicly-accessible full text available September 23, 2020
  2. Proteins and nucleic acids participate in essentially every biochemical process in living organisms, and the elucidation of their structure and motions is essential for our understanding how these molecular machines perform their function. Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful versatile technique that provides critical information on the molecular structure and dynamics. Spin-relaxation data are used to determine the overall rotational diffusion and local motions of biological macromolecules, while residual dipolar couplings (RDCs) reveal local and long-range structural architecture of these molecules and their complexes. This information allows researchers to refine structures of proteins and nucleic acids and providesmore »restraints for molecular docking. Several software packages have been developed by NMR researchers in order to tackle the complicated experimental data analysis and structure modeling. However, many of them are offline packages or command-line applications that require users to set up the run time environment and also to possess certain programming skills, which inevitably limits accessibility of this software to a broad scientific community. Here we present new science gateways designed for NMR/structural biology community that address these current limitations in NMR data analysis. Using the GenApp technology for scientific gateways (https://genapp.rocks), we successfully transformed ROTDIF and ALTENS, two offline packages for bio-NMR data analysis, into science gateways that provide advanced computational functionalities, cloud-based data management, and interactive 2D and 3D plotting and visualizations. Furthermore, these gateways are integrated with molecular structure visualization tools (Jmol) and with gateways/engines (SASSIE-web) capable of generating huge computer-simulated structural ensembles of proteins and nucleic acids. This enables researchers to seamlessly incorporate conformational ensembles into the analysis in order to adequately take into account structural heterogeneity and dynamic nature of biological macromolecules. ROTDIF-web offers a versatile set of integrated modules/tools for determining and predicting molecular rotational diffusion tensors and model-free characterization of bond dynamics in biomacromolecules and for docking of molecular complexes driven by the information extracted from NMR relaxation data. ALTENS allows characterization of the molecular alignment under anisotropic conditions, which enables researchers to obtain accurate local and long-range bond-vector restraints for refining 3-D structures of macromolecules and their complexes. We will describe our experience bringing our programs into GenApp and illustrate the use of these gateways for specific examples of protein systems of high biological significance. We expect these gateways to be useful to structural biologists and biophysicists as well as NMR community and to stimulate other researchers to share their scientific software in a similar way.« less
    Free, publicly-accessible full text available September 23, 2020
  3. Free, publicly-accessible full text available August 1, 2020
  4. Science gateways, also known as advanced web portals, virtual research environments, and more, have changed the face of research and scholarship over the last two decades. Scholars world-wide leverage science gateways for a wide variety of individual research endeavors spanning diverse scientific fields. Evaluating the value of a given gateway to its constituent community is critical in obtaining the financial and human resources to sustain gateway operations. Accordingly, those who run gateways must routinely measure and communicate impact. Just as gateways are varied, their success metrics vary as well. In this survey paper, a variety of different gateways briefly sharemore »their approaches.« less
    Free, publicly-accessible full text available September 23, 2020
  5. Science gateways, also known as advanced web portals, virtual research environments, and more, have changed the face of research and scholarship over the last two decades. Scholars world-wide leverage science gateways for a wide variety of individual research endeavors spanning diverse scientific fields. Evaluating the value of a given gateway to its constituent community is critical in obtaining the financial and human resources to sustain gateway operations. Accordingly, those who run gateways must routinely measure and communicate impact. Just as gateways are varied, their success metrics vary as well. In this survey paper, a variety of different gateways briefly sharemore »their approaches.« less
    Free, publicly-accessible full text available September 23, 2020
  6. Science gateways, also known as advanced web portals, virtual research environments, and more, have changed the face of research and scholarship over the last two decades. Scholars world-wide leverage science gateways for a wide variety of individual research endeavors spanning diverse scientific fields. Evaluating the value of a given gateway to its constituent community is critical in obtaining the financial and human resources to sustain gateway operations. Accordingly, those who run gateways must routinely measure and communicate impact. Just as gateways are varied, their success metrics vary as well. In this survey paper, a variety of different gateways briefly sharemore »their approaches.« less
    Free, publicly-accessible full text available September 23, 2020
  7. Free, publicly-accessible full text available September 23, 2020