Search results for "computer.software_genre"
showing 10 items of 3858 documents
SKINK: a web server for string kernel based kink prediction in α-helices
2014
Abstract Motivation: The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. Here, we present a new web server, called SKINK, for string kernel based kink prediction. Extending our previous study, we also annotate the most probable kink position in a given α-helix sequence. Availability and implementation: The SKINK web server is freely accessible at http://biows-inf.zdv.uni-mainz.de/skink. Moreover, SKINK is a module of the BALL software, also freely available at www.ballview.org. Contact: benny.kneissl@roche.com
ArtiFuse—computational validation of fusion gene detection tools without relying on simulated reads
2019
Abstract Motivation Gene fusions are an important class of transcriptional variants that can influence cancer development and can be predicted from RNA sequencing (RNA-seq) data by multiple existing tools. However, the real-world performance of these tools is unclear due to the lack of known positive and negative events, especially with regard to fusion genes in individual samples. Often simulated reads are used, but these cannot account for all technical biases in RNA-seq data generated from real samples. Results Here, we present ArtiFuse, a novel approach that simulates fusion genes by sequence modification to the genomic reference, and therefore, can be applied to any RNA-seq dataset wit…
Fully Bayesian Approach to Image Restoration with an Application in Biogeography
1994
SUMMARY A common method of studying biogeographical ranges is an atlas survey, in which the research area is divided into a square grid and the data consist of the squares where observations occur. Often the observations form only an incomplete map of the true range, and a method is required to decide whether the blank squares indicate true absence or merely a lack of study there. This is essentially an image restoration problem, but it has properties that make the common empirical Bayesian procedures inadequate. Most notably, the observed image is heavily degraded, causing difficulties in the estimation of spatial interaction, and the assessment of reliability of the restoration is emphasi…
Testing for local structure in spatiotemporal point pattern data
2017
The detection of clustering structure in a point pattern is one of the main focuses of attention in spatiotemporal data mining. Indeed, statistical tools for clustering detection and identification of individual events belonging to clusters are welcome in epidemiology and seismology. Local second-order characteristics provide information on how an event relates to nearby events. In this work, we extend local indicators of spatial association (known as LISA functions) to the spatiotemporal context (which will be then called LISTA functions). These functions are then used to build local tests of clustering to analyse differences in local spatiotemporal structures. We present a simulation stud…
LipiDisease: associate lipids to diseases using literature mining
2021
Abstract Summary Lipids exhibit an essential role in cellular assembly and signaling. Dysregulation of these functions has been linked with many complications including obesity, diabetes, metabolic disorders, cancer and more. Investigating lipid profiles in such conditions can provide insights into cellular functions and possible interventions. Hence the field of lipidomics is expanding in recent years. Even though the role of individual lipids in diseases has been investigated, there is no resource to perform disease enrichment analysis considering the cumulative association of a lipid set. To address this, we have implemented the LipiDisease web server. The tool analyzes millions of recor…
RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing
2012
Abstract Motivation: Next-generation sequencing technology enables an entirely new perspective for clinical research and will speed up personalized medicine. In contrast to microarray-based approaches, RNA-Seq analysis provides a much more comprehensive and unbiased view of gene expression. Although the perspective is clear and the long-term success of this new technology obvious, bioinformatics resources making these data easily available especially to the biomedical research community are still evolving. Results: We have generated RNA-Seq Atlas, a web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression pr…
Test and power considerations for multiple endpoint analyses using sequentially rejective graphical procedures
2009
A variety of powerful test procedures are available for the analysis of clinical trials addressing multiple objectives, such as comparing several treatments with a control, assessing the benefit of a new drug for more than one endpoint, etc. However, some of these procedures have reached a level of complexity that makes it difficult to communicate the underlying test strategies to clinical teams. Graphical approaches have been proposed instead that facilitate the derivation and communication of Bonferroni-based closed test procedures. In this paper we give a coherent description of the methodology and illustrate it with a real clinical trial example. We further discuss suitable power measur…
ARC A computerized system for urban garbage collection
1993
In this paper we present ARC a computerized system developed for urban garbage collection. The package is intended to help the planners in the design of efficient collection routes and to facilitate the study and evaluation of alternatives concerning issues such as the type and number of vehicles, frequency of collection and type and location of refuse containers. The final product is a “user friendly” system designed to be used by the planners without outside assistance.
Is there a cost at encoding words with joined letters during visual word recognition?
2018
Abstract For simplicity, models of visual-word recognition have focused on printed words composed of separated letters, thus overlooking the processing of cursive words. Manso de Zuniga, Humphreys, and Evett (1991) claimed that there is an early “cursive normalization” encoding stage when processing written words with joined letters. To test this claim, we conducted a lexical decision experiment in which words were presented either with separated or joined letters. To examine if the cost of letter segmentation occurs early in processing, we also manipulated a factor (i.e., word-frequency) that is posited to affect subsequent lexical processing. Results showed faster response times for the w…
IndElec: A Software for Analyzing Party Systems and Electoral Systems
2011
IndElec is a software addressed to compute a wide range of indices from electoral data, which are intended to analyze both party systems and electoral systems in political studies. Further, IndElec can calculate such indices from electoral data at several levels of aggregation, even when the acronyms of some political parties change across districts. As the amount of information provided by IndElec may be considerable, this software also aids the user in the analysis of electoral data through three capabilities. First, IndElec automatically elaborates preliminary descriptive statistical reports of computed indices. Second, IndElec saves the computed information into text files in data matri…