Related papers: MolSSI and BioExcel Workflow Workshop 2018 Report
This volume contains the accepted papers at the third Workshop on Membrane Computing and Biologically Inspired Process Calculi, held in Bologna on 5th September 2009. The papers are devoted to both membrane computing and biologically…
The prevalence of scientific workflows with high computational demands calls for their execution on various distributed computing platforms, including large-scale leadership-class high-performance computing (HPC) clusters. To handle the…
This volume contains the proceedings of the Second International Workshop Hybrid Systems and Biology (HSB 2013) held in Taormina (Italy), on September 2th, 2013. The workshop is affiliated to the 12th European Conference on Artificial Life…
Scientific workflows process extensive data sets over clusters of independent nodes, which requires a complex stack of infrastructure components, especially a resource manager (RM) for task-to-node assignment, a distributed file system…
Active learning (AL) plays a critical role in materials science, enabling applications such as the construction of machine-learning interatomic potentials for atomistic simulations and the operation of self-driving laboratories. Despite its…
Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description…
Over the last two decades, the field of computational science has seen a dramatic shift towards incorporating high-throughput computation and big-data analysis as fundamental pillars of the scientific discovery process. This has…
Programming is ubiquitous in applied biostatistics; adopting software engineering skills will help biostatisticians do a better job. To explain this, we start by highlighting key challenges for software development and application in…
Bacterial biofilms are among the oldest and most prevalent multicellular life forms on Earth and are increasingly relevant in research areas related to industrial fouling, medicine and biotechnology. The main hurdles to obtaining definitive…
Nowadays, many scientific workflows from different domains, such as Remote Sensing, Astronomy, and Bioinformatics, are executed on large computing infrastructures managed by resource managers. Scientific workflow management systems (SWMS)…
The work described in this paper is a contribution to the problems of managing in data-intensive scientific applications. First, we discuss scientific workflows and motivate there use in scientific applications. Then, we introduce the…
Experiments in research on memory, language, and in other areas of cognitive science are increasingly being analyzed using Bayesian methods. This has been facilitated by the development of probabilistic programming languages such as Stan,…
Molecular dynamics (MD) simulations are widely used to study large-scale molecular systems. HPC systems are ideal platforms to run these studies, however, reaching the necessary simulation timescale to detect rare processes is challenging,…
For teams using distributed version control systems, the right collaborative development workflows can help maintaining the long-term quality of project repositories and improving work efficiency. Despite the fact that the workflows are…
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…
Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as…
Scientific workflow management systems offer features for composing complex computational pipelines from modular building blocks, for executing the resulting automated workflows, and for recording the provenance of data products resulting…
With the advent of open source software, a veritable treasure trove of previously proprietary software development data was made available. This opened the field of empirical software engineering research to anyone in academia. Data that is…
As the amount of available data continues to grow in fields as diverse as bioinformatics, physics, and remote sensing, the importance of scientific workflows in the design and implementation of reproducible data analysis pipelines…
The rising popularity of computational workflows is driven by the need for repetitive and scalable data processing, sharing of processing know-how, and transparent methods. As both combined records of analysis and descriptions of processing…