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

Performing Two-Way Analysis of Variance Under Variance Heterogeneity

Small sample properties of the method proposed by Brunner et al. (1997) for performing two-way analysis of variance are compared to those of the normal based ANOVA method for factorial arrangements. Different effect sizes, sample sizes, and error structures are utilized in a simulation study to compare type I error rates and power of the two methods. An SAS program is also presented to assist those wishing to implement the Brunner method to real data

DELAYED ONSET MUSCLE SORENESS AND PROPRIOCEPTION

J. Rupp, E. Payton, & S. O. Henry Pacific University, Forest Grove, OR Although some effects of delayed onset muscle soreness (DOMS) are well documented, the impact of DOMS on proprioception – awareness of body and limb position in space and time has not yet been investigated. Delayed onset muscle soreness may affect neuromuscular sensory receptors and neural pathways due to microtears in the muscle, which could reduce proprioceptive abilities. PURPOSE: Investigate effects of DOMS on three selected measures of proprioception. METHODS: Using digital inclinometers, and data acquisition system; proprioception was assessed by participants’ (n = 19) ability to actively replicate a target angle (actively-determined reference) and ability to replicate joint angle velocity of knee flexion and extension. Force gradation, the ability to produce a target sub-maximal isometric force (25%, 50%, or 75% maximal voluntary isometric contraction), was assessed via force transducer. All testing trials were conducted in a random and repeated design and without immediate visual or auditory augmented feedback. After establishing baseline sensitivity and proprioceptive abilities, one leg was chosen at random to undergo a customized resistance training regimen, to induce DOMS, using the contralateral leg as the control. Post-testing followed approximately 48hrs post exercise regimen. For each set of proprioceptive test absolute error and percent error (from reference value) were calculated; percent error was used for analysis. RESULTS: Two-way repeated measures ANOVA (α=0.05) revealed no differences amongst the PrePost, ConExp, or PrePost* ContExp main effects for joint angle replication, joint movement velocity replication, or force gradation. **Table can be found in the downloadable pdf version** CONCLUSION: Delayed onset muscle soreness had no effect on ability to replicate a target joint angle, joint velocity, or ability to scale submaximal force

USING RANKS TO PERFORM EXACT AND ESTIMATED EXACT TESTS IN DESIGNED EXPERIMENTS

A procedure is studied that uses rank transformed data to perform exact and estimated exact tests which is an alternative to the commonly used F-ratio test procedure. First, a common parametric test statistic is computed using rank transformed data, where two methods of ranking - ranks taken of the original observations, and ranks taken after aligning the observations - are studied. Significance is then determined using either the exact permutation distribution of the statistic or an estimate of this distribution based on a random sample of all possible permutations. Simulation studies compare the performance of this method to both the normal theory parametric F-test and the traditional rank transform procedure. Power and nominal type-I error rates are compared under conditions when normal theory assumptions are satisfied as well as when these assumptions are violated. The method is studied for a two factor factorial arrangement of treatments in a completely randomized design and also for a split-unit experiment

JMASM8: Using SAS To Perform Two-Way Analysis Of Variance Under Variance Heterogeneity

We present SAS code to implement the method proposed by Brunner et al. (1997) for performing two-way analysis of variance under variance heterogeneity

Failure of the ERBE scanner instrument aboard NOAA 10 spacecraft and results of failure analysis

The Earth Radiation Budget Experiment (ERBE) scanner instrument on the NOAA 10 spacecraft malfunctioned on May 22, 1989, after more than 4 years of in-flight operation. After the failure, all instrument operational mode commands were tested and the resulting data analyzed. Details of the tests and analysis of output data are discussed therein. The radiometric and housekeeping data appear to be valid. However, the instrument will not correctly execute operational scan mode commands or the preprogrammed calibration sequences. The data indicate the problem is the result of a failure in the internal address decoding circuity in one of the ROM (read only memory) chips of the instrument computer