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Genome-scale expression of proteins from Bacillus subtilis

Journal of Structural and Functional Genomics 2004年第1-2期5卷 103-109页

作者： Moy, S. Dieckman, L. Schiffer, M. Maltsev, N. Yu, G.-X. Collart, F.R. Biosciences Argonne IL 60439 United States Math. and Computer Science Division Argonne National Laboratory Argonne IL 60439 United States Oak Ridge National Laboratory Oak Ridge TN 37831 United States

We have applied high throughput methods for cloning and expression of more than 850 genes from the Bacillus subtilis genome. The process uses 96-well plates and is automated from the level of primer design to the detection of soluble protein by a tag detection screen. This process was applied to a set of cytoplasmic targets from Bacillus subtilis to produce clones expressing soluble protein for incorporation into the structure determination pipeline of the Midwest Center for Structural Genomics. We also evaluated the feasibility of these plate-based methods for domain-based cloning and expression of secretory proteins and putative soluble domains of membrane proteins. This approach shows promise for implementation in a high throughput format and could provide additional target resources for structure determination. The continued development of new technologies that can be implemented in an automated format will be essential for continued success in the structural genomic programs.

关键词： Bacillus subtilis High-throughput Protein expression Structural genomics

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On lines avoiding unit balls in three dimensions

On lines avoiding unit balls in three dimensions

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Proceedings of the Twentieth Annual Symposium on Computational Geometry (SCG'04)

作者： Agarwal, Pankaj K. Aronov, Boris Koltun, Vladlen Sharir, Micha Department of Computer Science Duke University Durham NC 27708-0129 United States Department of Computer Science Polytechnic University Brooklyn NY 11201-3840 United States Computer Science Division University of California Berkeley CA 94720-1776 United States School of Computer Science Tel Aviv University Tel Aviv 69978 Israel Courant Inst. of Math. Sciences New York University New York NY 10012 United States

Let B be a set of n unit balls in 3. We show that the combinatorial complexity of the space of lines in 3 that avoid all the balls of B is O(n3+Ε), for any Ε > 0. This result has connections to problems in visibi... 详细信息

关键词： Computational geometry

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Reconstruction of 2D PET data with monte carlo generated natural pixels

Reconstruction of 2D PET data with monte carlo generated nat...

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2004 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano

作者： Vandenberghe, S. Byrne, C.L. Soares, E.J. Lemahieu, I. Glick, S. FWO Flanders MEDISIP Ghent University University of Massachusetts Medical School Worcester MA Dept. of Mathematical Sciences University of Massachussetts Lowell Lowell MA Dept. of Math. and Computer Science College of the Holy Cross Worcester MA ELIS Department MEDISIP Ghent University Ghent Belgium Division of Nuclear Medicine University of Massachussetts Medical School Worcester MA

ISBN: (纸本)0780383885

In discrete detector PET, natural pixels are image basis functions calculated from responses of detector pairs. By using reconstruction with natural pixels the discretization of the object into a predefined grid can be avoided. Instead of trying to find the object x from system matrix A and measured data p by solving Ax = p, one solves Mq = AATq = p. The backprojection of the final q results in the estimated image of the object xˆ. In previous work natural pixels were calculated by intersections of strip functions or combinations of strip functions. However, in PET systems the detector response is not correctly described by a strip function. In PET the detector response is better described by a gaussian tube. It is quite difficult to calculate the intersections of all possible Lines Of Response (LOR) in the scanner. This paper proposes an easy and efficient way to generate the matrix M directly by Monte Carlo simulation. Using the natural pixel matrix M has several advantages over using the conventional system matrix A. The discretisation of the object into pixels, which requires an angular dependent projector and backprojector, is avoided. Due to rotational symmetry in the PET scanner the matrix M is block circulant and only the first block row needs to be stored. The block circulant property of the matrix allows use of fast direct methods to calculate the solution. Iterative methods to solve the system are preferred because of numerical stability. ©2004 IEEE.

关键词： Image reconstruction

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On the queueing behavior of multiple first-order autoregressive sources

On the queueing behavior of multiple first-order autoregress...

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IEEE Conference and Exhibition on Global Telecommunications (GLOBECOM)

作者： Gang Uk Hwan K. Sohraby Div. of Appl. Math. Korea Adv. Inst. of Sci. & Technol. Taejeon South Korea School of Computing and Engineering Department of Computer Science and Electrical Engineering University of Missouri Kansas City Kansas City MO USA Division of Applied Mathematics Korea Advanced Institute of Science and Technology Yuseong-gu Taejeon South Korea

It is generally believed that the queueing behavior of an arrival process is most sensitive to its first and second order statistics. In this paper, we show that this is not generally true. We consider the queueing behavior of two classes of sources. The first class is the superposition of multiple discrete autoregressive sources of order 1 (referred to as DAR(1) sources), and the second class is a single DAR(1) source having the same first and second order statistics as the superposed source. In particular, we show that in the homogeneous case, the mean queue lengths of the two models are identical, but the queue length variances of the two models are significantly different depending on the correlation of individual sources.

关键词： Random variables Cities and towns Statistics math.matical model Equations math.matics computer science Teleconferencing Traffic control Steady-state

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Simulation studies of computation and data scheduling algorithms for data grids

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Journal of Grid Computing 2003年第1期1卷 53-62页

作者： Ranganathan, Kavitha Foster, Ian Department of Computer Science University of Chicago Chicago IL 60637 United States Math. and Computer Science Division Argonne National Laboratory Argonne IL 60439 United States

Data Grids seek to harness geographically distributed resources for large-scale data-intensive problems. Such problems, involving loosely coupled jobs and large data-sets, are found in fields like high-energy physics, astronomy and bioinformatics. A variety of factors need to be considered for effective scheduling of resources in such environments: e.g., resource utilization, response time, global and local allocation policies and scalability. We propose a general and extensible scheduling architecture that addresses these issues. Within this architecture we develop a suite of job scheduling and data replication algorithms that we evaluate using simulations for a wide range of parameters. Our results show that it is important to evaluate the combined effectiveness of replication and scheduling strategies, rather than study them *** specifically, we find that scheduling jobs to locations that contain the data they need and asynchronously replicating popular data-sets to remote sites, works rather well. © 2003 Kluwer Academic Publishers.

关键词： Grid computing

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Improving the performance of MPI derived datatypes by optimizing memory-access cost

Improving the performance of MPI derived datatypes by optimi...

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IEEE International Conference on Cluster Computing, CLUSTER 2003

作者： Byna, Surendra Gropp, William Sun, Xian-He Thakur, Rajeev Department of Computer Science Illinois Institute of Technology ChicagoIL60616 United States Math. and Comp. Science Division Argonne National Laboratory ArgonneIL60439 United States

ISBN: (纸本)0769520669

The MPI Standard supports derived datatypes, which allow users to describe noncontiguous memory layout and communicate noncontiguous data with a single communication function. This feature enables an MPI implementation to optimize the transfer of noncontiguous data. In practice, however, few MPI implementations implement derived datatypes in a way that performs better than what the user can achieve by manually packing data into a contiguous buffer and then calling an MPI function. In this paper, we present a technique for improving the performance of derived datatypes by automatically using packing algorithms that are optimized for memory-access cost. The packing algorithms use memory-optimization techniques that the user cannot apply easily without advanced knowledge of the memory architecture. We present performance results for a matrix-transpose example that demonstrate that our implementation of derived datatypes significantly outperforms both manual packing by the user and the existing derived-datatype code in the MPI implementation (MPICH). © 2003 IEEE.

关键词： Memory architecture

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Curve-sensitive cuttings

Curve-sensitive cuttings

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Nineteenth Annual Symposium on Computational Geometry

作者： Koltun, Vladlen Sharir, Micha Computer Science Division University of California Berkeley CA 94720-1776 United States School of Computer Science Tel Aviv University Tel-Aviv 69978 Israel Courant Inst. of Math. Sciences New York University New York NY 10012 United States

We introduce (1/r)-cuttings for collections of surfaces in 3-space that are sensitive to an additional collection of curves. Specifically, let S be a set of n surfaces in 3 of constant description complexity, and let C be a set of m curves in 3 of constant description complexity. Let 1 ≤ r ≤ min{m, n} be a given parameter. We show the existence of a (1/r)-cutting Ξ of S of size O(r3+Ε), for any Ε > 0, such that the number of crossings between the curves of C and the cells of Ξ is O(m1+Εr). The latter bound improves, by roughly a factor of r, the bound that can be obtained for cuttings based on vertical decompositions. We view curve-sensitive cuttings as a powerful tool that is potentially useful in various scenarios that involve curves and surfaces in three dimensions. As a preliminary application, we use the construction to obtain a bound of O(m1/2+Εn2+Ε), for any Ε > 0, on the complexity of the multiple zone of m curves in the arrangement of n surfaces in 3-space.

关键词： Boolean algebra

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Cutting triangular cycles of lines in space

Cutting triangular cycles of lines in space

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35th Annual ACM Symposium on Theory of Computing

作者： Aronov, Boris Koltun, Vladlen Sharir, Micha Department of Computer Science Polytechnic University Brooklyn NY 11201-3840 United States Computer Science Division University of California Berkeley CA 94720-1776 United States School of Computer Science Tel Aviv University Tel-Aviv 69978 Israel Courant Inst. of Math. Sciences New York University New York NY 10012 United States

The cutting triangular cycles of lines in space were investigated. It was shown that a collection of lines in 3-space can be cut into a subquadratic number of pieces, such that all depth cycles defined by triples of lines are eliminated. A long-standing open problem in computational geometry, motivated by hidden-surface removal in computer graphics, was solved.

关键词： Computational geometry

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Calculated effect of alloy additions on the saturation magnetization of Fe0.80B0.20

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Materials Research Society Symposium - Proceedings 2003年 754卷 451-456页

作者： Nicholson, D.M.C. Wang, Yang Widom, Mike Computer Science and Math. Division Oak Ridge National Laboratory Oak Ridge TN 37830 United States Pittsburgh Supercomputing Center Pittsburgh PA 15213 United States Department of Physics Carnegie Mellon University Pittsburgh PA 15213 United States

The great number of different local environments in amorphous alloys leads to the evolution of complicated non collinear magnetic structures. Alloy additions can affect the magnetic structure in surprising ways. For example, replacement of a small amount of Fe with Co increases the saturation magnetization even though Co has a much smaller moment than Fe. The calculated behavior of the magnetic structure of (Fe(1-x)Mx)0.8B0.2 with M=Co, Cr, Zr, and Mn2Zr are presented.

关键词： Iron compounds

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Parallel components for PDEs and optimization: Some issues and experiences

Parallel components for PDEs and optimization: Some issues a...

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作者： Norris, Boyana Balay, Satish Benson, Steven Freitag, Lori Hovland, Paul McInnes, Lois Smith, Barry Math. and Computer Science Division Argonne National Laboratory 9700 S. Cass Avenue Argonne IL 60439 United States

High-performance simulations in computational science often involve the combined software contributions of multidisciplinary teams of scientists, engineers, math.maticians, and computer scientists. One goal of component-based software engineering in large-scale scientific simulations is to help manage such complexity by enabling better interoperability among codes developed by different groups. This paper discusses recent work on building component interfaces and implementations in parallel numerical toolkits for mesh manipulations, discretization, linear algebra, and optimization. We consider several motivating applications involving partial differential equations and unconstrained minimization to demonstrate this approach and evaluate performance. © 2002 Elsevier science B.V. All rights reserved.

关键词： Parallel processing systems

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