Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the "multiple segment Viterbi" (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call "sparse rescaling". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.

/pdf/accelerated-profile-hmm-searches-5f0frwnmca.pdf

Accelerated Profile HMM Searches

Aspect] is a simple and practical aspect-oriented extension to Java With just a few new constructs, AspectJ provides support for modular implementation of a range of crosscutting concerns. In AspectJ's dynamic join point model, join points are well-defined points in the execution of the program; pointcuts are collections of join points; advice are special method-like constructs that can be attached to pointcuts; and aspects are modular units of crosscutting implementation, comprising pointcuts, advice, and ordinary Java member declarations. AspectJ code is compiled into standard Java bytecode. Simple extensions to existing Java development environments make it possible to browse the crosscutting structure of aspects in the same kind of way as one browses the inheritance structure of classes. Several examples show that AspectJ is powerful, and that programs written using it are easy to understand.

An overview of AspectJ

The Object Management Group's (OMG) Model Driven Architecture (MDA) strategy envisages a world where models play a more direct role in software production, being amenable to manipulation and transformation by machine. Model Driven Engineering (MDE) is wider in scope than MDA. MDE combines process and analysis with architecture. This article sets out a framework for model driven engineering, which can be used as a point of reference for activity in this area. It proposes an organisation of the modelling 'space' and how to locate models in that space. It discusses different kinds of mappings between models. It explains why process and architecture are tightly connected. It discusses the importance and nature of tools. It identifies the need for defining families of languages and transformations, and for developing techniques for generating/configuring tools from such definitions. It concludes with a call to align metamodelling with formal language engineering techniques.

Model Driven Engineering

Originating from basic research conducted in the 1970's and 1980's, the parallel and distributed simulation field has matured over the last few decades. Today, operational systems have been fielded for applications such as military training, analysis of communication networks, and air traffic control systems, to mention a few. The article gives an overview of technologies to distribute the execution of simulation programs over multiple computer systems. Particular emphasis is placed on synchronization (also called time management) algorithms as well as data distribution techniques.

/pdf/parallel-and-distributed-simulation-systems-2ovm9qn1cd.pdf

Parallel and Distributed Simulation Systems

コンピュータ・サイエンス : ACM computing surveys

A data storage and retrieval device and method is disclosed. The device includes at least one magnetic storage medium configured to store target data and at least one re-configurable logic device comprising an FPGA coupled to the at least one magnetic storage medium and configured to read a continuous stream of target data therefrom, having been configured with a template or as otherwise desired to fit the type of search and data being searched. The re-configurable logic device is configured to receive at least one search inquiry in the form of a data key and to determine a match between the data key and the target data as it is being read from the at least one magnetic storage medium. This device and method can perform a variety of searches on the target data including without limitation exact and approximate match searches, sequence match searches, image match searches and data reduction searches. This device and method may be provided as part of a stand-alone computer system, embodied in a network attached storage device, or can otherwise be provided as part of a computer LAN or WAN. In addition to performing search and data reduction operations, this device may also be used to perform a variety of other processing operations including encryption, decryption, compression, decompression, and combinations thereof.

Intelligent data storage and processing using fpga devices

Methods and systems for processing financial market data using reconfigurable logic are disclosed. Various functional operations to be performed on the financial market data can be implemented in firmware pipelines to accelerate the speed of processing. Also, a combination of software logic and firmware logic can be used to efficiently control and manage the high speed flow of financial market data to and from the reconfigurable logic.

High Speed Processing of Financial Information Using FPGA Devices

An encryption technique is disclosed for encrypting a plurality of data blocks of a data segment where the encryption selectively switches between a blockwise independent randomized (BIR) encryption mode and a cipher block chaining (CBC) encryption mode based on a configurable feedback stride. A corresponding decryption technique is also disclosed.

Method and System for High Throughput Blockwise Independent Encryption/Decryption

A parallel simulated annealing algorithm that is problem-independent, maintains the serial decision sequence, and obtains speedup which can exceed log/sub 2/P on P processors is discussed. The algorithm achieves parallelism by using the concurrency technique of speculative computation. Implementation of the parallel algorithm on a hypercube multiprocessor and application to a task assignment problem are described. The simulated annealing solutions are shown to be, on average, 28% better than the solutions produced by a random task assignment algorithm and 2% better than the solutions produced by a heuristic. >

Parallel simulated annealing using speculative computation

A capacitive sensor array is adapted to be disposed in a reservoir containing fluid or material along an axis of measurement of the fluid or material to determine the level of fluid or material contained within the reservoir. The sensor array includes a plurality of reference electrodes, wherein the capacitance of each of the electrodes varies in accordance both with the extent of the array's immersion in the fluid or material and the dielectric constant of the fluid or material. The plurality of reference electrodes preferably includes a lower electrode adapted to be immersed within the fluid or material in the reservoir and whose capacitance provides an estimate of the dielectric constant of the fluid or material contained within the reservoir. The reference electrodes also include an upper electrode adapted to be positioned above the fluid or material level that provides an estimate of the dielectric constant above the level of the fluid or material in the reservoir, and a middle electrode whose capacitance varies from a calibrated initial value to a value that is dependent on the level of and the dielectric constant of the fluid or material contained within the reservoir as determined from the capacitance of the lower electrode.

Roger D. Chamberlain

Papers

Intelligent data storage and processing using fpga devices

High Speed Processing of Financial Information Using FPGA Devices

Method and System for High Throughput Blockwise Independent Encryption/Decryption

Parallel simulated annealing using speculative computation

Auto-compensating capacitive level sensor