Measuring Software Timing Errors in the Presentation of Visual Stimuli in Cognitive Neuroscience Experiments

Because of the features provided by an abundance of specialized experimental software packages, personal computers have become prominent and powerful tools in cognitive research. Most of these programs have mechanisms to control the precision and accuracy with which visual stimuli are presented as well as the response times. However, external factors, often related to the technology used to display the visual information, can have a noticeable impact on the actual performance and may be easily overlooked by researchers. The aim of this study is to measure the precision and accuracy of the timing mechanisms of some of the most popular software packages used in a typical laboratory scenario in order to assess whether presentation times configured by researchers do not differ from measured times more than what is expected due to the hardware limitations. Despite the apparent precision and accuracy of the results, important issues related to timing setups in the presentation of visual stimuli were found, and they should be taken into account by researchers in their experiments.     

A note on the selection of priority rules in software packages for project management

Various software packages for project management include a procedure for resource-constrained scheduling. In several packages, the user can influence this procedure by selecting a priority rule. However, the resource-allocation methods that are implemented in the procedures are proprietary information; therefore, the question of how the priority-rule selection impacts the performance of the procedures arises. We experimentally evaluate the resource-allocation methods of eight recent software packages using the 600 instances of the PSPLIB J120 test set. The results of our analysis indicate that applying the default rule tends to outperform a randomly selected rule, whereas applying two randomly selected rules tends to outperform the default rule. Applying a small set of more than two rules further improves the project durations considerably. However, a large number of rules must be applied to obtain the best possible project durations.     

Innovative Multimedia for Teaching Nematology

The availability of interactive multimedia authoring software programs promises to revolutionize the teaching of nematology. These programs integrate text, hypertext, graphics, animations, video, and sound. The user interacts with the information on demand in a nonlinear fashion. Beginning students can limit themselves to the general outlines of the subject, and advanced students can explore the information to the limits of their ability. Use of interactive multimedia does not eliminate the need for effective, enthusiastic teachers but provides a mechanism for the efficient transfer of information. An interactive multimedia presentation that supplements lectures in an introductory course is presented as an example of the application of this technology for teaching nematology.     

Sperm package morphology in scorpions and its relation to phylogeny

Sperm packages are widespread in the order Scorpiones, but absent in the family Buthidae. The morphology of sperm packages is diverse and apparently has phylogenetic information. The objectives of this work were to show diversity of sperm packages and to provide a quantitative basis for using sperm packages’ morphology as a taxonomic character. For this, we conducted a morphological analysis and comparison of the different sperm packages of species of the family Bothriuridae. The seminal content from males of species of Bothriuridae was studied. Specimens from Iuridae, Buthidae, Euscorpiidae, Liochelidae, Scorpionidae, Vaejovidae, Chaerilidae, and Chactidae were used for comparison. Digital images of sperm packages were measured and statistically analysed based on the following variables: total length, head width, head–body angle, total area, and head length. Pairs of variables were also contrasted, and all the variables were correlated with the current phylogenetic hypothesis for Bothriuridae. High morphological diversity and variability in measures was observed. In general, measurements were similar within each genus, but differed amongst genera. Cane‐like sperm packages are very common in species of the family Bothriuridae. Species from Bothriurus show a wide range of sperm package shapes, some of them shared with Timogenes and Vachonia species, supporting the idea of nonmonophyly of the genus. Many species showed sperm package dimorphism inside a single male. Some of the analysed features fit well with the phylogenetic hypothesis in Bothriuridae, and the general package shape shows high correlation with scorpion phylogeny in other families. Bent and round packages are the most common amongst the different families. Sperm packages are not developed in Chaerilidae, as in Buthidae. This is the first morphological and comparative analysis of sperm packages in scorpions, and reveals much greater diversity in this trait than previously known. Our results reinforce the idea that the study of morphology of sperm packages would contribute characters for scorpion phylogeny at different levels. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 463–483.     

REBASE--restriction enzymes and methylases.

REBASE is a comprehensive database of information about restriction enzymes and their associated methylases, including their recognition and cleavage sites and their commercial availability. Information from REBASE is available via monthly electronic mailings as well as via WAIS and anonymous ftp. Specialized files are available that can be used directly by many software packages.     

Impact of DNA microarray data transformation on gene expression analysis - comparison of two normalization methods

Two-color DNA microarrays are commonly used for the analysis of global gene expression. They provide information on relative abundance of thousands of mRNAs. However, the generated data need to be normalized to minimize systematic variations so that biologically significant differences can be more easily identified. A large number of normalization procedures have been proposed and many softwares for microarray data analysis are available. Here, we have applied two normalization methods (median and loess) from two packages of microarray data analysis softwares. They were examined using a sample data set. We found that the number of genes identified as differentially expressed varied significantly depending on the method applied. The obtained results, i.e. lists of differentially expressed genes, were consistent only when we used median normalization methods. Loess normalization implemented in the two software packages provided less coherent and for some probes even contradictory results. In general, our results provide an additional piece of evidence that the normalization method can profoundly influence final results of DNA microarray-based analysis. The impact of the normalization method depends greatly on the algorithm employed. Consequently, the normalization procedure must be carefully considered and optimized for each individual data set.     

Information retrieval for patient care.

Doctors need clinical information during most consultations with patients, and much of this need could be satisfied by material from online sources. Advances in data communication technologies mean that multimedia information can be transported rapidly to various clinical care locations. However, selecting the few items of information likely to be useful in a particular clinical situation from the mass of information available is a major problem. Current information retrieval systems are designed primarily for use in research rather than clinical care. The design, implementation, and critical evaluation of new information retrieval systems for clinical care should be guided by knowledgeable clinical users.     

Multimedia information retrieval and environmental monitoring: Shared perspectives on data fusion

Computer-based remote monitoring of our environment is increasingly based on combining data derived from in-situ-sensors with data derived from remote sources, such as satellite images or CCTV. In such deployments it is necessary to continuously monitor the accuracy of each of the sensor data streams so that we can account for sudden failures of sensors, or errors due to calibration drive or biofouling. In multimedia information retrieval (MMIR), we search through archives of multimedia artefacts like video programs, by implementing several independent retrieval systems or agents, and we combine the outputs of each retrieval agent in order to generate an overall ranking. In this paper we draw parallels between these seemingly very different applications and show how they share several similarities. In the case of environmental monitoring we also need some mechanism by which we can establish the trust and reputation of each contributing sensor, though this is something we do not need in MMIR. In this paper we present an outline of a trust and reputation framework we have developed and deployed for monitoring the performance of sensors in a heterogeneous sensor network.     

Fast,scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high‐quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high‐quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.     

Bayesian approaches in evolutionary quantitative genetics

The study of evolutionary quantitative genetics has been advanced by the use of methods developed in animal and plant breeding. These methods have proved to be very useful, but they have some shortcomings when used in the study of wild populations and evolutionary questions. Problems arise from the small size of data sets typical of evolutionary studies, and the additional complexity of the questions asked by evolutionary biologists. Here, we advocate the use of Bayesian methods to overcome these and related problems. Bayesian methods naturally allow errors in parameter estimates to propagate through a model and can also be written as a graphical model, giving them an inherent flexibility. As packages for fitting Bayesian animal models are developed, we expect the application of Bayesian methods to evolutionary quantitative genetics to grow, particularly as genomic information becomes more and more associated with environmental data.     

Protein sequence comparison and fold recognition: progress and good-practice benchmarking

Protein sequence comparison methods have grown increasingly sensitive during the last decade and can often identify distantly related proteins sharing a common ancestor some 3 billion years ago. Although cellular function is not conserved so long, molecular functions and structures of protein domains often are. In combination with a domain-centered approach to function and structure prediction, modern remote homology detection methods have a great and largely underexploited potential for elucidating protein functions and evolution. Advances during the last few years include nonlinear scoring functions combining various sequence features, the use of sequence context information, and powerful new software packages. Since progress depends on realistically assessing new and existing methods and published benchmarks are often hard to compare, we propose 10 rules of good-practice benchmarking.     

Reviewing the curriculum

The potential use of IT in secondary biology teaching is enormous, although it is a huge undertaking and fairly daunting to newcomers. Computer learning packages and the web can offer a variety of opportunities for learning, ranging from non-interactive content provision to highly interactive student-centred learning experiences. The learning materials in use in New South Wales (NSW) schools include information web sites, computer learning packages as tutorial or revision material, computer learning packages made by the students, virtual field trips, simulations, and virtual laboratories. In addition, students and teachers are using the web for communicating amongst themselves via email, newsgroups and discussion lists, videoconferencing for both local and global communications, and telecollaborative projects. This article will focus on materials used in student learning, and on the forms of electronic communication in use within the school system. A list of resources is provided.     

Comparison of two academic software packages for analyzing two-dimensional gel images

One of the key limitations for proteomic studies using two-dimensional (2D) gel is the lack of automatic, fast, robust, and reliable methods for detecting, matching, and quantifying protein spots. Although there are commercial software packages for 2D gel image analysis, extensive human intervention is still needed for spot detection and matching, which is time-consuming and error-prone. Moreover, the commercial software packages are usually expensive and non-open source. Thus, it is very beneficial for researchers to have free software that is fast, fully automatic, and robust. In this paper, we review and compare two recently developed and publicly available software packages, RegStatGel and Pinnacle, for analyzing 2D gel images. These two software packages share some common features and also have some fundamental difference in the aspects of spot detection and quantification. Based on our experience, RegStatGel is much better in terms of spot detection and matching. It also contains more advanced statistical tools and is more user-friendly. In contrast, Pinnacle is quite sensitive to background noise and relies on external statistical software packages for statistical analysis.     

REBASE--restriction enzymes and methylases.

REBASE is a comprehensive database of information about restriction enzymes and their associated methylases, including their recognition and cleavage sites and their commercial availability. Information from REBASE is available via monthly electronic mailings as well as via WAIS, anonymous ftp and through the World Wide Web (http://www.neb.com/rebase). Specialized files are available that can be used directly by many software packages.     

MLEP: an R package for exploring the maximum likelihood estimates of penetrance parameters

ABSTRACT: BACKGROUND: Linkage analysis is a useful tool for detecting genetic variants that regulate a trait of interest, especially genes associated with a given disease. Although penetrance parameters play an important role in determining gene location, they are assigned arbitrary values according to the researcher's intuition or as estimated by the maximum likelihood principle. Several methods exist by which to evaluate the maximum likelihood estimates of penetrance, although not all of these are supported by software packages and some are biased by marker genotype information, even when disease development is due solely to the genotype of a single allele. FINDINGS: Programs for exploring the maximum likelihood estimates of penetrance parameters were developed using the R statistical programming language supplemented by external C functions. The software returns a vector of polynomial coefficients of penetrance parameters, representing the likelihood of pedigree data. From the likelihood polynomial supplied by the proposed method, the likelihood value and its gradient can be precisely computed. To reduce the effect of the supplied dataset on the likelihood function, feasible parameter constraints can be introduced into maximum likelihood estimates, thus enabling flexible exploration of the penetrance estimates. An auxiliary program generates a perspective plot allowing visual validation of the model's convergence. The functions are collectively available as the MLEP R package. CONCLUSIONS: Linkage analysis using penetrance parameters estimated by the MLEP package enables feasible localization of a disease locus. This is shown through a simulation study and by demonstrating how the package is used to explore maximum likelihood estimates. Although the input dataset tends to bias the likelihood estimates, the method yields accurate results superior to the analysis using intuitive penetrance values for disease with low allele frequencies. MLEP is part of the Comprehensive R Archive Network and is freely available at http://cran.r-project.org/web/packages/MLEP/index.html.     

Ryanodine receptors, a family of intracellular calcium ion channels, are expressed throughout early vertebrate development

Background

We developed a new version of the open source software package Peptrix that can yet compare large numbers of Orbitrap? LC-MS data. The peptide profiling results for Peptrix on MS1 spectra were compared with those obtained from a small selection of open source and commercial software packages: msInspect, Sieve? and Progenesis?. The properties compared in these packages were speed, total number of detected masses, redundancy of masses, reproducibility in numbers and CV of intensity, overlap of masses, and differences in peptide peak intensities. Reproducibility measurements were taken for the different MS1 software applications by measuring in triplicate a complex peptide mixture of immunoglobulin on the Orbitrap? mass spectrometer. Values of peptide masses detected from the high intensity peaks of the MS1 spectra by peptide profiling were verified with values of the MS2 fragmented and sequenced masses that resulted in protein identifications with a significant score.

Findings

Peptrix finds about the same number of peptide features as the other packages, but peptide masses are in some cases approximately 5 to 10 times less redundant present in the peptide profile matrix. The Peptrix profile matrix displays the largest overlap when comparing the number of masses in a pair between two software applications. The overlap of peptide masses between software packages of low intensity peaks in the spectra is remarkably low with about 50% of the detected masses in the individual packages. Peptrix does not differ from the other packages in detecting 96% of the masses that relate to highly abundant sequenced proteins. MS1 peak intensities vary between the applications in a non linear way as they are not processed using the same method.

Conclusions

Peptrix is capable of peptide profiling using Orbitrap? files and finding differential expressed peptides in body fluid and tissue samples. The number of peptide masses detected in Orbitrap? files can be increased by using more MS1 peptide profiling applications, including Peptrix, since it appears from the comparison of Peptrix with the other applications that all software packages have likely a high false negative rate of low intensity peptide peaks (missing peptides).     

REBASE-restriction enzymes and methylases.

REBASE is a comprehensive database of information about restriction enzymes and their associated methylases, including their recognition and cleavage sites and their commercial availability. Information from REBASE is available via monthly electronic mailings as well as via anonymous ftp, WAIS/gopher and through the World Wide Web (http://www.neb.com/rebase ). Specialized files are available that can be used directly by many software packages.