Related papers: WinBioinfTools: Bioinformatics Tools for Windows H…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Backgr: Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology.…
One of the major challenges providing large databases like the WFCAM Science Archive (WSA) is to minimize ingest times for pixel/image metadata and catalogue data. In this article we describe how the pipeline processed data are ingested…
In recent years development in the area of Single Board Computing has been advancing rapidly. At Wolters Kluwer's Corporate Legal Services Division a prototyping effort was undertaken to establish the utility of such devices for practical…
In year 2006 Biolinux inter alia with the work of Tim Booth gives its rise and provide an operating system that was and is specialized in providing an environment for the needs of bioinformatics. Since than some years have been seen and the…
Large-scale plasma simulations are critical for designing and developing next-generation fusion energy devices and modeling industrial plasmas. BIT1 is a massively parallel Particle-in-Cell code designed for specifically studying plasma…
Shared high-performance computing (HPC) platforms, such as those provided by XSEDE and Compute Canada, enable researchers to carry out large-scale computational experiments at a fraction of the cost of the cloud. Most systems require the…
To uncover the genetic basis of complex disease, individuals are often measured at a large number of genetic variants (usually SNPs) across the genome. GemTools provides computationally efficient tools for modeling genetic ancestry based on…
The Statistical Toolkit is an open source system specialized in the statistical comparison of distributions. It addresses requirements common to different experimental domains, such as simulation validation (e.g. comparison of experimental…
The demand for high-performance computing (HPC) is ever-increasing for everyday statistical computing purposes. The downside is that we need to write specialized code for each HPC environment. CPU-level parallelization needs to be…
Knowledge graphs are an increasingly common data structure for representing biomedical information. These knowledge graphs can easily represent heterogeneous types of information, and many algorithms and tools exist for querying and…
With the upcoming generation of telescopes, cluster scale strong gravitational lenses will act as an increasingly relevant probe of cosmology and dark matter. The better resolved data produced by current and future facilities requires…
Currently, the most energy-efficient hardware platforms for floating point-intensive calculations (also known as High Performance Computing, or HPC) are graphical processing units (GPUs). However, porting existing scientific codes to GPUs…
The increase of existing computational capabilities has made simulation emerge as a third discipline of Science, lying midway between experimental and purely theoretical branches [1, 2]. Simulation enables the evaluation of quantities which…
Applications like Big Data, Machine Learning, Deep Learning and even other Engineering and Scientific research requires a lot of computing power; making High-Performance Computing (HPC) an important field. But access to Supercomputers is…
With advances in hardware and networking technologies and mass manufacturing, the cost of high end hardware had fall dramatically in recent years. However, software cost still remains high and is the dominant fraction of the overall…
The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive…
Research processes often rely on high-performance computing (HPC), but HPC is often seen as antithetical to "reproducibility": one would have to choose between software that achieves high performance, and software that can be deployed in a…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
Runtime scheduling and workflow systems are an increasingly popular algorithmic component in HPC because they allow full system utilization with relaxed synchronization requirements. There are so many special-purpose tools for task…