Emre Brookes

University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States

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Publications (30)39.47 Total impact

  • H. Kim · E.H. Brookes · B. Demeler
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    ABSTRACT: A performance prediction model for the two-dimensional spectrum analysis algorithm of the UltraScan software was developed to aid in the prediction of calculation times on XSEDE supercomputer infrastructure. The efficiency profiles for various analysis types and analysis parameter combinations when used on Lonestar, Trestles and Stampede were determined by mining performance data from past analyses stored in the UltraScan LIMS database. The resulting model was validated against an analytical performance model. The model can be integrated into the existing UltraScan submission infrastructure to provide improved wall time estimates for the XSEDE supercomputer clusters to increase queuing efficiency.
    No preview · Article · Jul 2015
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    ABSTRACT: A new framework (GenApp) for rapid generation of scientific applications running on a variety of systems including science gateways has recently been developed. This framework currently builds a GUI and/or web-based user interface for a variety of target environments on a collection of executable modules. The method for execution of modules has limited framework restrictions: primarily the requirement of wrapping the application to accept input and output formatted in JavaScript Object Notation (JSON). Initial implementation supports direct execution on a user's workstation, a web server, or a compute resource accessible from the web server. After a successful initial workshop utilizing the framework to create a web-based user interface wrapping a scientific software suite, it was discovered that long-running jobs would sometimes fail, because of the loss of a Transmission Control Protocol (TCP) connection. This precipitated an improvement to the execution method with the bonus of easily allowing multiple web clients to attach to the running job. To support a diversity of queue managed compute resources, a Google ‘Summer of Code’ project was completed to integrate the Apache Airavata middleware as an additional execution model within the GenApp framework. New features of file management, job management with progress, and message box support are described. Concurrency and Computation: Practice and Experience, 2015.© 2015 Wiley Periodicals, Inc.
    No preview · Article · May 2015 · Concurrency and Computation Practice and Experience

  • No preview · Article · Jan 2015 · Biophysical Journal

  • No preview · Article · Jan 2015 · Concurrency and Computation Practice and Experience
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    ABSTRACT: A new framework (GenApp) for rapid generation of scientific applications running on a variety of systems including science gateways has recently been developed. This framework builds a user interface for a variety of target environments on a collection of executable modules. The method for execution of the modules is unrestricted by the framework. Initial implementation supports direct execution, and not queue managed submission, on a user's workstation, a web server, or a compute resource accessible from the web server. After a successful workshop, it was discovered that long running jobs would sometimes fail, due to the loss of a TCP connection. This precipitated an improvement to the execution method with the bonus of easily allowing multiple web clients to attach to the running job. Finally, to support a diversity of queue managed compute resources, a Google Summer of Code project was completed to integrate the Apache Airavata middleware as an additional execution model within the GenApp framework.
    Full-text · Conference Paper · Dec 2014
  • Emre H. Brookes
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    ABSTRACT: Combining modules wrapping a diversity of executable codes derived from various scientific research labs with a range of computational and data scales into a sustainable framework requires careful considerations. In the described framework, we have separated the module's executable codes from the user-interface and created an application generation tool which produces all the code necessary to create a web based science gateway simultaneously with a local GUI based application. This work was driven by requirements related to an international collaborative grant. This ongoing development is producing applications and will be in the hands of beta testers at the time of this publication.
    No preview · Article · Jul 2014
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    ABSTRACT: A critical problem in material science is the accurate characterization of the size dependent properties of colloidal inorganic nanocrystals. Due to the intrinsic polydispersity present during synthesis, dispersions of such materials exhibit simultaneous heterogeneity in density ρ, molar mass M, and particle diameter d. The density increments partial of ρ over partial of d and the partial of rho over partial of M of these nanoparticles, if known, can then provide important information about crystal growth and particle size distributions. For most classes of nanocrystals, a mixture of surfactants is added during synthesis to control their shape, size and optical properties. However, it remains a challenge to accurately determine the amount of passivating ligand bound to the particle surface post synthesis. The presence of the ligand shell hampers an accurate determination of the nanocrystal diameter. Using CdSe and PbS semiconductor nanocrystals, and the ultrastable silver nanoparticle (M4Ag44(p-MBA)30) as model systems, we describe a Custom Grid method implemented in UltraScan-III for the characterization of nanoparticles and macromolecules using sedimentation velocity analytical ultracentrifugation. We show that multiple parametrizations are possible, and that the Custom Grid method can be generalized to provide high resolution composition information for mixtures of solutes that are heterogeneous in two out of three parameters. For such cases, our method can simultaneously resolve arbitrary 2-dimensional distributions of hydrodynamic parameters when a third property can be held constant. For example, this method extracts partial specific volume and molar mass from sedimentation velocity data for cases where the anisotropy can be held constant, or provides anisotropy and partial specific volume if the molar mass is known.
    Full-text · Article · Jul 2014 · Analytical Chemistry
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    ABSTRACT: A method for fitting sedimentation velocity experiments using whole boundary Lamm equation solutions is presented. The method, termed parametrically constrained spectrum analysis (PCSA), provides an optimized approach for simultaneously modeling heterogeneity in size and anisotropy of macromolecular mixtures. The solutions produced by PCSA are particularly useful for modeling polymerizing systems, where a single-valued relationship exists between the molar mass of the growing polymer chain and its corresponding anisotropy. The PCSA uses functional constraints to identify this relationship, and unlike other multidimensional grid methods, assures that only a single molar mass can be associated with a given anisotropy measurement. A description of the PCSA algorithm is presented, as well as several experimental and simulated examples that illustrate its utility and capabilities. The performance advantages of the PCSA method in comparison to other methods are documented. The method has been added to the UltraScan-III software suite, which is available for free download from http://www.ultrascan.uthscsa.edu.
    Full-text · Article · Apr 2014 · Biophysical Journal
  • Mattia Rocco · Emre Brookes
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    ABSTRACT: Notwithstanding the continuous technological advancements in the current high-resolution methods (X-ray crystallography/NMR), an exhaustive list of every relevant biological structure and of its complexes with every partner remains a far fetched goal. Furthermore, dynamical aspects, from local or large scale flexibility, to conformational changes following interactions/binding, to supramolecular structures formation, are not easily amenable to high-resolution analysis. A host of intermediate-resolution techniques are, however, available to complement the higher resolution data, like cryo-electron microscopy and electron tomography, while small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are in addition capable to monitor the evolution of structural changes in solution. Since the above-mentioned techniques can provide 3D envelopes at ~10–20 Å resolution, a typical task involves placing the atomic structures of the components inside the envelope or to optimize their arrangement to fit experimental scattering data. Single-valued parameters provided by low-resolution techniques, such as the radius of gyration R g , the translational diffusion coefficient D t , the sedimentation coefficient s, the Stokes radius R s , the rotational correlation time τc , and the intrinsic viscosity (η), can be also utilized to screen/confirm potential spatial arrangements of modules/domains, or to monitor their overall conformational changes. The UltraScan SOlution MOdeler (US-SOMO) suite of computer programs was developed for the computation of the solution properties of biomacromolecules starting from their atomic resolution structures, and their comparison with experimental data. In this brief review, its use with respect to dynamical aspects in multi-resolution modeling, including conformational variation and flexibility issues, is discussed.
    No preview · Chapter · Jan 2014
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    ABSTRACT: Fibrinogen is a large heterogeneous aggregation/degradation-prone protein playing a central role in blood coagulation and associated pathologies, whose structure is not completely resolved. When a high-molecular-weight fraction was analyzed by size-exclusion high-performance liquid chromatography/small-angle X-ray scattering (HPLC-SAXS), several composite peaks were apparent and because of the stickiness of fibrinogen the analysis was complicated by severe capillary fouling. Novel SAS analysis tools developed as a part of the UltraScan Solution Modeler (US-SOMO; http://somo.uthscsa.edu/), an open-source suite of utilities with advanced graphical user interfaces whose initial goal was the hydrodynamic modeling of biomacromolecules, were implemented and applied to this problem. They include the correction of baseline drift due to the accumulation of material on the SAXS capillary walls, and the Gaussian decomposition of non-baseline-resolved HPLC-SAXS elution peaks. It was thus possible to resolve at least two species co-eluting under the fibrinogen main monomer peak, probably resulting from in-column degradation, and two others under an oligomers peak. The overall and cross-sectional radii of gyration, molecular mass and mass/length ratio of all species were determined using the manual or semi-automated procedures available within the US-SOMO SAS module. Differences between monomeric species and linear and sideways oligomers were thus identified and rationalized. This new US-SOMO version additionally contains several computational and graphical tools, implementing functionalities such as the mapping of residues contributing to particular regions of P(r), and an advanced module for the comparison of primary I(q) versus q data with model curves computed from atomic level structures or bead models. It should be of great help in multi-resolution studies involving hydrodynamics, solution scattering and crystallographic/NMR data.
    Preview · Article · Dec 2013 · Journal of Applied Crystallography
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    Full-text · Dataset · Apr 2013
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    ABSTRACT: UltraScan Solution Modeler (US-SOMO) computes hydrodynamic parameters and small-angle scattering data from biological macromolecular structural representations and compares them with experimental data for structural determination and validation. At XSEDE 12, a GUI integrated gateway was introduced to offload large computations to various HPC resources. The gateway was directly integrated into the Qt/GUI based software to allow the users a seamless experience. The software is available as source code or precompiled for Apple Mac OSX, MS-Windows and Linux. Current cluster resources include TACC Lonestar and Stampede, SDSC Trestles and a 256 CPU cluster local to the University of Texas Health Science Center at San Antonio. The simplicity of design allowed the implementation of a new method of modeling small angle scattering data that provided new scientific insights and was presented at the 2012 international small-angle scattering conference. Since introduction, multiple workshops have been taught and users are beginning to utilize the gateway in their biological research.
    Full-text · Conference Paper · Jan 2013
  • Mattia Rocco · Emre Brookes · Olwyn Byron

    No preview · Chapter · Jan 2013
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    ABSTRACT: UltraScan Solution Modeler (US-SOMO) processes atomic and lower-resolution bead model representations of biological and other macromolecules to compute various hydrodynamic parameters, such as the sedimentation and diffusion coefficients, relaxation times and intrinsic viscosity, and small angle scattering curves, that contribute to our understanding of molecular structure in solution. Knowledge of biological macromolecules' structure aids researchers in understanding their function as a path to disease prevention and therapeutics for conditions such as cancer, thrombosis, Alzheimer's disease and others. US-SOMO provides a convergence of experimental, computational, and modeling techniques, in which detailed molecular structure and properties are determined from data obtained in a range of experimental techniques that, by themselves, give incomplete information. Our goal in this work is to develop the infrastructure and user interfaces that will enable a wide range of scientists to carry out complicated experimental data analysis techniques on XSEDE. Our user community predominantly consists of biophysics and structural biology researchers. A recent search on PubMed reports 9,205 papers in the decade referencing the techniques we support. We believe our software will provide these researchers a convenient and unique framework to refine structures, thus advancing their research. The computed hydrodynamic parameters and scattering curves are screened against experimental data, effectively pruning potential structures into equivalence classes. Experimental methods may include analytical ultracentrifugation, dynamic light scattering, small angle X-ray and neutron scattering, NMR, fluorescence spectroscopy, and others. One source of macromolecular models is X-ray crystallography. However, the conformation in solution may not match that observed in the crystal form. Using computational techniques, an initial fixed model can be expanded into a search space utilizing high temperature molecular dynamic approaches or stochastic methods such as Brownian dynamics. The number of structures produced can vary greatly, ranging from hundreds to tens of thousands or more. This introduces a number of cyberinfrastructure challenges. Computing hydrodynamic parameters and small angle scattering curves can be computationally intensive for each structure, and therefore cluster compute resources are essential for timely results. Input and output data sizes can vary greatly from less than 1 MB to 2 GB or more. Although the parallelization is trivial, along with data size variability there is a large range of compute sizes, ranging from one to potentially thousands of cores with compute time of minutes to hours. In addition to the distributed computing infrastructure challenges, an important concern was how to allow a user to conveniently submit, monitor and retrieve results from within the C++/Qt GUI application while maintaining a method for authentication, approval and registered publication usage throttling. Middleware supporting these design goals has been integrated into the application with assistance from the Open Gateway Computing Environments (OGCE) collaboration team. The approach was tested on various XSEDE clusters and local compute resources. This paper reviews current US-SOMO functionality and implementation with a focus on the newly deployed cluster integration.
    No preview · Article · Jul 2012
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    ABSTRACT: The Ultrascan gateway provides a user friendly web interface for evaluation of experimental analytical ultracentrifuge data using the UltraScan modeling software. The analysis tasks are executed on the TeraGrid and campus computational resources. The gateway is highly successful in providing the service to end users and consistently listed among the top five gateway community account usage. This continued growth and challenges of sustainability needed additional support to revisit the job management architecture. In this paper we describe the enhancements to the Ultrascan gateway middleware infrastructure provided through the TeraGrid Advanced User Support program. The advanced support efforts primarily focused on a) expanding the TeraGrid resources incorporate new machines; b) upgrading UltraScan's job management interfaces to use GRAM5 in place of the deprecated WS-GRAM; c) providing realistic usage scenarios to the GRAM5 and INCA resource testing and monitoring teams; d) creating general-purpose, resource-specific, and UltraScan-specific error handling and fault tolerance strategies; and e) providing forward and backward compatibility for the job management system between UltraScan's version 2 (currently in production) and version 3 (expected to be released mid-2011).
    No preview · Conference Paper · Jan 2011
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    ABSTRACT: We compare here the utility of sedimentation velocity (SV) to sedimentation equilibrium (SE) analysis for the characterization of reversible systems. Genetic algorithm optimization in UltraScan is used to optimize the model and to obtain solution properties of all components present in the system. We apply our method to synthetic and experimental data, and suggest limits for the accessible kinetic range. We conclude that equilibrium constants obtained from SV and SE analysis are equivalent, but that SV experiments provide better confidence for the K(d), can better account for the presence of contaminants and provide additional information including rate constants and shape parameters.
    No preview · Article · Jul 2010 · Macromolecular Bioscience
  • Emre Brookes · Borries Demeler · Mattia Rocco
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    ABSTRACT: The US-SOMO suite provides a flexible interface for accurately computing solution parameters from 3D structures of biomacromolecules through bead-modeling approaches. We present an extended analysis of the influence of accessible surface area screening, overlap reduction routines, and approximations for non-coded residues and missing atoms on the computed parameters for models built by the residue-to-bead direct correspondence and the cubic grid methods. Importantly, by taking the theoretical hydration into account at the atomic level, the performance of the grid-type models becomes comparable or exceeds that of the corresponding hydrated residue-to-bead models.
    No preview · Article · Jul 2010 · Macromolecular Bioscience
  • Emre H. Brookes · Borries Demeler
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    ABSTRACT: Solving large non-negatively constrained least squares systems is frequently used in the physical sciences to estimate model parameters which best fit experimental data. Analytical Ultracentrifugation (AUC) is an important hydrodynamic experimental technique used in biophysics to characterize macromolecules and to determine parameters such as molecular weight and shape. We previously developed a parallel divide and conquer method to facilitate solving the large systems obtained from AUC experiments. New AUC instruments equipped with multi-wavelength (MWL) detectors have recently increased the data sizes by three orders of magnitude. Analyzing the MWL data requires significant compute resources. To better utilize these resources, we introduce a procedure allowing the researcher to optimize the divide and conquer scheme along a continuum from minimum wall time to minimum compute service units. We achieve our results by implementing a preprocessing stage performed on a local workstation before job submission.
    No preview · Article · Jan 2010
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    ABSTRACT: Progress in analytical ultracentrifugation (AUC) has been hindered by obstructions to hardware innovation and by software incompatibility. In this paper, we announce and outline the Open AUC Project. The goals of the Open AUC Project are to stimulate AUC innovation by improving instrumentation, detectors, acquisition and analysis software, and collaborative tools. These improvements are needed for the next generation of AUC-based research. The Open AUC Project combines on-going work from several different groups. A new base instrument is described, one that is designed from the ground up to be an analytical ultracentrifuge. This machine offers an open architecture, hardware standards, and application programming interfaces for detector developers. All software will use the GNU Public License to assure that intellectual property is available in open source format. The Open AUC strategy facilitates collaborations, encourages sharing, and eliminates the chronic impediments that have plagued AUC innovation for the last 20 years. This ultracentrifuge will be equipped with multiple and interchangeable optical tracks so that state-of-the-art electronics and improved detectors will be available for a variety of optical systems. The instrument will be complemented by a new rotor, enhanced data acquisition and analysis software, as well as collaboration software. Described here are the instrument, the modular software components, and a standardized database that will encourage and ease integration of data analysis and interpretation software. Electronic supplementary material The online version of this article (doi:10.1007/s00249-009-0438-9) contains supplementary material, which is available to authorized users.
    Full-text · Article · Apr 2009 · Biophysics of Structure and Mechanism
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    Emre Brookes · Weiming Cao · Borries Demeler
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    ABSTRACT: We report a model-independent analysis approach for fitting sedimentation velocity data which permits simultaneous determination of shape and molecular weight distributions for mono- and polydisperse solutions of macromolecules. Our approach allows for heterogeneity in the frictional domain, providing a more faithful description of the experimental data for cases where frictional ratios are not identical for all components. Because of increased accuracy in the frictional properties of each component, our method also provides more reliable molecular weight distributions in the general case. The method is based on a fine grained two-dimensional grid search over s and f/f 0, where the grid is a linear combination of whole boundary models represented by finite element solutions of the Lamm equation with sedimentation and diffusion parameters corresponding to the grid points. A Monte Carlo approach is used to characterize confidence limits for the determined solutes. Computational algorithms addressing the very large memory needs for a fine grained search are discussed. The method is suitable for globally fitting multi-speed experiments, and constraints based on prior knowledge about the experimental system can be imposed. Time- and radially invariant noise can be eliminated. Serial and parallel implementations of the method are presented. We demonstrate with simulated and experimental data of known composition that our method provides superior accuracy and lower variance fits to experimental data compared to other methods in use today, and show that it can be used to identify modes of aggregation and slow polymerization.
    Full-text · Article · Mar 2009 · Biophysics of Structure and Mechanism