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Physiological measurements in neuroscience experiments often involve complex stimulus paradigms and multiple data channels. Ephus (http://www.ephus.org) is an open-source software package designed for general-purpose data acquisition and instrument control. Ephus operates as a collection of modular programs, including an ephys program for standard(More)
MOTIVATION Multiple sequence alignments (MSAs) are at the heart of bioinformatics analysis. Recently, a number of multiple protein sequence alignment benchmarks (i.e. BAliBASE, OXBench, PREFAB and SMART) have been released to evaluate new and existing MSA applications. These databases have been well received by researchers and help to quantitatively(More)
—The performance of maximum likelihood searches can be boosted by using the most parsimonious tree as a starting point for the search. The time spent in performing the parsimony search to find this starting tree is insignificant compared to the time spent in the maximum likelihood search, leading to an overall gain in search time. These parsimony boosted(More)
The CYP2D6 gene is responsible for metabolising a large portion of the commonly prescribed drugs. Because of its importance, various approaches have been taken to analyse CYP2D6 and Single Nucleotide Polymorphisms (SNPs) throughout its sequence. This study introduces a novel method to analyse the effects of SNPs on encoded protein complexes by focusing on(More)
Phylogenetic search is a key tool used in a variety of biological research endeavours. However, this search problem is known to be computationally difficult, due to the astronomically large search space, making the use of heuristic methods necessary. The performance of heuristic methods for finding Maximum Likelihood (ML) trees can be improved by using(More)
A number of electronic devices have been tested for sensitivity to single event effects for space applications by Ball Aerospace & Technologies Corp. and collaborators. Test conditions and results are presented for each device.
In this paper, we present an effective algorithm for reassembling three-dimensional apictorial jigsaw puzzles obtained by dividing a curved surface into a finite number of interlocking pieces. As such, our algorithm does not make use of any picture or design that may be painted on the surface; nor does it require a priori knowledge of the overall shape of(More)
—Long branch attraction is a problem that afflicts phylogenetic methods and a procedure to detect a data set suffering from this problem is the long branch extraction method[1]. This method has been well cited and used by many authors for their analysis but no strong validation has been performed as to its accuracy. We performed such an analysis by an(More)
Throughout the 1990s, Jaegwon Kim developed a line of argument that what purport to be nonreductive forms of physicalism are ultimately untenable, since they cannot accommodate the causal efficacy of mental states. His argument has received a great deal of discussion, much of it critical. We believe that, while the argument needs some tweaking, its basic(More)