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The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…
The "IMP Science Gateway Portal" (http://scigate.imp.kiev.ua) for complex workflow management and integration of distributed computing resources (like clusters, service grids, desktop grids, clouds) is presented. It is created on the basis…
Distributed infrastructures for computation and analytics are now evolving towards an interconnected ecosystem allowing complex scientific workflows to be executed across hybrid systems spanning from IoT Edge devices to Clouds, and…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…
Molecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of "HAL's MD…
Parallel dataflow systems are a central part of most analytic pipelines for big data. The iterative nature of many analysis and machine learning algorithms, however, is still a challenge for current systems. While certain types of bulk…
The increasing need for causal analysis in large-scale industrial datasets necessitates the development of efficient and scalable causal algorithms for real-world applications. This paper addresses the challenge of scaling causal algorithms…
Scientific communities naturally tend to organize around data ecosystems created by the combination of their observational devices, their data repositories, and the workflows essential to carry their research from observation to discovery.…
As data-driven methods are becoming pervasive in a wide variety of disciplines, there is an urgent need to develop scalable and sustainable tools to simplify the process of data science, to make it easier to keep track of the analyses being…
Motivation: With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to…
HiCCL (Hierarchical Collective Communication Library) addresses the growing complexity and diversity in high-performance network architectures. As GPU systems have envolved into networks of GPUs with different multilevel communication…
We suggest there is a need for a fresh perspective on the design and development of workflow systems and argue for a building blocks approach. We outline a description of this approach and define the properties of software building blocks.…
Apart from forming the backbone of compiler optimization, static dataflow analysis has been widely applied in a vast variety of applications, such as bug detection, privacy analysis, program comprehension, etc. Despite its importance,…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
The solutions of a system of polynomials in several variables are often needed, e.g.: in the design of mechanical systems, and in phase-space analyses of nonlinear biological dynamics. Reliable, accurate, and comprehensive numerical…
Large systems biology projects can encompass several workgroups often located in different countries. An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data…
The ability to repeat the experiments from a research study and obtain similar results is a corner stone in experiment-based scientific discovery. This essential feature has been often ignored by the distributed computing and networking…
The growing complexity and scale of scientific workflows in high performance computing (HPC) environments have led to significant challenges in managing energy consumption without compromising computational performance. Traditional…
An astonishingly diverse biomolecular circuitry orchestrates the functioning machinery underlying every living cell. These biomolecules and their circuits have been engineered not only for various industrial applications but also to perform…
Previous work has suggested that the structural restrictions of graphs from classes of bounded expansion--locally dense pockets in a globally sparse graph--naturally coincide with common properties of real-world networks such as clustering…