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In research labs, there is often a need to customise software at every step in a given bioinformatics workflow, but traditionally it has been difficult to obtain both a high degree of customisability and good performance.…
Bioinformatics tools are essential for complex computational biology tasks, yet their integration with emerging AI-agent frameworks is hindered by incompatible interfaces, heterogeneous input-output formats, and inconsistent parameter…
Difficulty replicating baselines, high computational costs, and required domain expertise create persistent barriers to clinical AI research. To address these challenges, we introduce PyHealth 2.0, an enhanced clinical deep learning toolkit…
HEP Cluster is designed and implemented in Scientific Linux Cern 5.5 to grant High Energy Physics researchers one place where they can go to undertake a particular task or to provide a parallel processing architecture in which CPU resources…
Biologists who want to analyse their single-cell transcriptomics dataset must install and use specialist software via the command line. This is often impractical for non-bioinformaticians. Whilst the popular CELLxGENE software provides an…
Motivation: Bioinformatics software often lacks graphical user interfaces (GUIs), which can limit its adoption by non-technical members of the scientific community. Web interfaces are a common alternative for building cross-platform GUIs,…
In this paper I describe some results on the use of virtual processors technology for parallelize some SPMD computational programs in a cluster environment. The tested technology is the INTEL Hyper Threading on real processors, and the…
Large-scale ad hoc analytics of genomic data is popular using the R-programming language supported by 671 software packages provided by Bioconductor. More recently, analytical jobs are benefitting from on-demand computing and storage, their…
Statistical methods for genomewide association studies (GWAS) continue to improve. However, the increasing volume and variety of genetic and genomic data make computational speed and ease of data manipulation mandatory in future software.…
Distributed systems are becoming more common place, as computers typically contain multiple computation processors. The SpiNNaker architecture is such a distributed architecture, containing millions of cores connected with a unique…
The open-source PyNX toolkit [Favre-Nicolin et al (2011) arXiv:1010.2641, Mandula et al (2016)] has been extended to provide tools for coherent X-ray imaging data analysis and simulation. All calculations can be executed on graphical…
High-performance computing (HPC) is reshaping computational drug discovery by enabling large-scale, time-efficient molecular simulations. In this work, we explore HPC-driven pipelines for Alzheimer's disease drug discovery, focusing on…
High-throughput computing projects require the solution of large numbers of problems. In many cases, these problems can be solved on desktop PCs, or can be broken down into independent "PC-solvable" sub-problems. In such cases, the projects…
In this paper, we present a nonlinear analysis software toolkit, which can help in biomechanical gait data analysis by implementing various nonlinear statistical analysis algorithms. The toolkit is proposed to tackle the need for an…
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…
Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable…
We introduce SciWING, an open-source software toolkit which provides access to pre-trained models for scientific document processing tasks, inclusive of citation string parsing and logical structure recovery. SciWING enables researchers to…
The advent of affordable parallel computers such as Beowulf PC clusters and, more recently, of multi-core PCs has been highly beneficial for a large number of scientists and smaller institutions that might not otherwise have access to…
Methods: We have developed a software suite (DataSet Tracker) for real-time analysis designed to run on computers, smartphones, and smart glasses hardware and suitable for resource-constrained, on-the-fly computing in microscopes without…
In the rapidly evolving domain of next generation sequencing and bioinformatics analysis, data generation is one aspect that is increasing at a concomitant rate. The burden associated with processing large amounts of sequencing data has…