Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum

Multi-camera complexity assessment system for assembly line work stations

In the last couple of years, the market demands an increasing number of product variants. This leads to an inevitable rise of the complexity in manufacturing systems. A model to quantify the complexity in a workstation has been developed, but part of the analysis is done manually. Thereto, this paper presents the results of an industrial proof-of-concept in which the possibility of automating the complexity analysis using multi camera video images, was tested

Multi-objective discrete particle swarm optimisation algorithm for integrated assembly sequence planning and assembly line balancing

In assembly optimisation, assembly sequence planning and assembly line balancing have been extensively studied because both activities are directly linked with assembly efficiency that influences the final assembly costs. Both activities are categorised as NP-hard and usually performed separately. Assembly sequence planning and assembly line balancing optimisation presents a good opportunity to be integrated, considering the benefits such as larger search space that leads to better solution quality, reduces error rate in planning and speeds up time-to-market for a product. In order to optimise an integrated assembly sequence planning and assembly line balancing, this work proposes a multi-objective discrete particle swarm optimisation algorithm that used discrete procedures to update its position and velocity in finding Pareto optimal solution. A computational experiment with 51 test problems at different difficulty levels was used to test the multi-objective discrete particle swarm optimisation performance compared with the existing algorithms. A statistical test of the algorithm performance indicates that the proposed multi-objective discrete particle swarm optimisation algorithm presents significant improvement in terms of the quality of the solution set towards the Pareto optimal set

Interactive Visualization of the Largest Radioastronomy Cubes

3D visualization is an important data analysis and knowledge discovery tool, however, interactive visualization of large 3D astronomical datasets poses a challenge for many existing data visualization packages. We present a solution to interactively visualize larger-than-memory 3D astronomical data cubes by utilizing a heterogeneous cluster of CPUs and GPUs. The system partitions the data volume into smaller sub-volumes that are distributed over the rendering workstations. A GPU-based ray casting volume rendering is performed to generate images for each sub-volume, which are composited to generate the whole volume output, and returned to the user. Datasets including the HI Parkes All Sky Survey (HIPASS - 12 GB) southern sky and the Galactic All Sky Survey (GASS - 26 GB) data cubes were used to demonstrate our framework's performance. The framework can render the GASS data cube with a maximum render time < 0.3 second with 1024 x 1024 pixels output resolution using 3 rendering workstations and 8 GPUs. Our framework will scale to visualize larger datasets, even of Terabyte order, if proper hardware infrastructure is available.Comment: 15 pages, 12 figures, Accepted New Astronomy July 201

Leveraging legacy codes to distributed problem solving environments: A web service approach

This paper describes techniques used to leverage high performance legacy codes as CORBA components to a distributed problem solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user’s desktop computing environment can be extended to a high performance computing environment using a cluster of workstations or a parallel computer

Three Dimensional Software Modelling

Traditionally, diagrams used in software systems modelling have been two dimensional (2D). This is probably because graphical notations, such as those used in object-oriented and structured systems modelling, draw upon the topological graph metaphor, which, at its basic form, receives little benefit from three dimensional (3D) rendering. This paper presents a series of 3D graphical notations demonstrating effective use of the third dimension in modelling. This is done by e.g., connecting several graphs together, or in using the Z co-ordinate to show special kinds of edges. Each notation combines several familiar 2D diagrams, which can be reproduced from 2D projections of the 3D model. 3D models are useful even in the absence of a powerful graphical workstation: even 2D stereoscopic projections can expose more information than a plain planar diagram

Transportable Applications Environment (TAE) Plus: A NASA user interface development and management system

The transportable Applications Environment Plus (TAE Plus), developed at the NASA Goddard Space FLight Center, is a portable, What you see is what you get (WYSIWYG) user interface development and management system. Its primary objective is to provide an integrated software environment that allows interactive prototyping and development of graphical user interfaces, as well as management of the user interface within the operational domain. TAE Plus is being applied to many types of applications, and what TAE Plus provides, how the implementation has utilizes state-of-the-art technologies within graphic workstations, and how it has been used both within and without NASA are discussed

TARGET: Rapid Capture of Process Knowledge

TARGET (Task Analysis/Rule Generation Tool) represents a new breed of tool that blends graphical process flow modeling capabilities with the function of a top-down reporting facility. Since NASA personnel frequently perform tasks that are primarily procedural in nature, TARGET models mission or task procedures and generates hierarchical reports as part of the process capture and analysis effort. Historically, capturing knowledge has proven to be one of the greatest barriers to the development of intelligent systems. Current practice generally requires lengthy interactions between the expert whose knowledge is to be captured and the knowledge engineer whose responsibility is to acquire and represent the expert's knowledge in a useful form. Although much research has been devoted to the development of methodologies and computer software to aid in the capture and representation of some types of knowledge, procedural knowledge has received relatively little attention. In essence, TARGET is one of the first tools of its kind, commercial or institutional, that is designed to support this type of knowledge capture undertaking. This paper will describe the design and development of TARGET for the acquisition and representation of procedural knowledge. The strategies employed by TARGET to support use by knowledge engineers, subject matter experts, programmers and managers will be discussed. This discussion includes the method by which the tool employs its graphical user interface to generate a task hierarchy report. Next, the approach to generate production rules for incorporation in and development of a CLIPS based expert system will be elaborated. TARGET also permits experts to visually describe procedural tasks as a common medium for knowledge refinement by the expert community and knowledge engineer making knowledge consensus possible. The paper briefly touches on the verification and validation issues facing the CLIPS rule generation aspects of TARGET. A description of efforts to support TARGET's interoperability issues on PCs, Macintoshes and UNIX workstations concludes the paper