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GitHub Copilot, an extension for the Visual Studio Code development environment powered by the large-scale language model Codex, makes automatic program synthesis available for software developers. This model has been extensively studied in…
High-Performance Computing (HPC) processors are nowadays integrated Cyber-Physical Systems demanding complex and high-bandwidth closed-loop power and thermal control strategies. To efficiently satisfy real-time multi-input multi-output…
Branch is a web application that provides users with no programming with the ability to interact directly with large biomedical datasets. The interaction is mediated through a collaborative graphical user interface for building and…
Linux container technologies such as Docker and Singularity offer encapsulated environments for easy execution of software. In high performance computing, this is especially important for evolving and complex software stacks with…
Multiple signal classification algorithm (MUSICAL) provides a super-resolution microscopy method. In the previous research, MUSICAL has enabled data-parallelism well on a desktop computer or a Linux-based server. However, the running time…
The ability to understand how a scientific application is executed on a large HPC system is of great importance in allocating resources within the HPC data center. In this paper, we describe how we used system performance data to identify:…
BioImageLoader (BIL) is a python library that handles bioimage datasets for machine learning applications, easing simple workflows and enabling complex ones. BIL attempts to wrap the numerous and varied bioimages datasets in unified…
Diversity represents a key concept in ecology, and there are various methods of assessing it. The multitude of diversity indices are quite puzzling and sometimes difficult to compute for a large volume of data. This paper promotes a…
Tomographic imaging has benefited from advances in X-ray sources, detectors and optics to enable novel observations in science, engineering and medicine. These advances have come with a dramatic increase of input data in the form of faster…
Modern HPC file systems can contain billions of files and hundreds of petabytes of data, making even simple questions increasingly intractable to answer. Traditional file system utilities such as find and du fail to scale to these sizes.…
For scientific software, especially those used for large-scale simulations, achieving good performance and efficiently using the available hardware resources is essential. It is important to regularly perform benchmarks to ensure the…
The emergence of large-scale AI models, like GPT-4, has significantly impacted academia and industry, driving the demand for high-performance computing (HPC) to accelerate workloads. To address this, we present HPCClusterScape, a…
In this chapter, we describe the Parallel Sparse Computation Toolkit (PSCToolkit), a suite of libraries for solving large-scale linear algebra problems in an HPC environment. In particular, we focus on the tools provided for the solution of…
Computer-based scientific experiments are becoming increasingly data-intensive, necessitating the use of High-Performance Computing (HPC) clusters to handle large scientific workflows. These workflows result in complex data and control…
Curated databases have become important sources of information across scientific disciplines, and due to the manual work of experts, often become important reference works. Features such as provenance tracking, archiving, and data citation…
There are many science applications that require scalable task-level parallelism and support for flexible execution and coupling of ensembles of simulations. Most high-performance system software and middleware, however, are designed to…
With the increasing amount of data and use of computation in science, software has become an important component in many different domains. Computing is now being used more often and in more aspects of scientific work including data…
Interactive high-performance computing is doubtlessly beneficial for many computational science and engineering applications whenever simulation results should be visually processed in real time, i.e. during the computation process.…
Bright-field microscopy, a cost-effective solution for live-cell culture, is often the only resource available, along with standard CPUs, for many low-budget labs. The inherent challenges of bright-field images -- their noisiness, low…
Bioinformatics web servers are critical resources in modern biomedical research, facilitating interactive exploration of datasets through custom-built interfaces with rich visualization capabilities. However, this human-centric design…