Related papers: MolSSI and BioExcel Workflow Workshop 2018 Report
A key hurdle is demonstrating compute resource capability with limited benchmarks. We propose workflow templates as a solution, offering adaptable designs for specific scientific applications. Our paper identifies common usage patterns for…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
We present a workflow for clinical data analysis that relies on Bayesian Structure Learning (BSL), an unsupervised learning approach, robust to noise and biases, that allows to incorporate prior medical knowledge into the learning process…
The formation of biomolecular materials via dynamical interfacial processes such as self-assembly and fusion, for diverse compositions and external conditions, can be efficiently probed using ensemble Molecular Dynamics. However, this…
In this thesis first we propose an intermediate data management scheme for a SWfMS. In our second attempt, we explored the possibilities and introduced an automatic recommendation technique for a SWfMS from real-world workflow data (i.e…
Life is a nonequilibrium phenomenon: metabolism provides a continuous supply of energy that drives nearly all cellular processes. However, very little is known about how much energy different cellular processes use, i.e. their energetic…
Scientific workflow management systems (SWMSs) and resource managers together ensure that tasks are scheduled on provisioned resources so that all dependencies are obeyed, and some optimization goal, such as makespan minimization, is…
Climate science is critical for understanding both the causes and consequences of changes in global temperatures and has become imperative for decisive policy-making. However, climate science studies commonly require addressing complex…
One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and…
Background: Security tools play a vital role in enabling developers to build secure software. However, it can be quite challenging to introduce and fully leverage security tools without affecting the speed or frequency of deployments in the…
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…
Fueled by breakthrough technology developments, the biological, biomedical, and behavioral sciences are now collecting more data than ever before. There is a critical need for time- and cost-efficient strategies to analyze and interpret…
Collaborative scientific authoring is increasingly being supported by software tools. Traditionally, desktop-based authoring tools had the most advanced editing features, allowed for more formatting options, and included more import/export…
Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount…
Sound data analysis is essential to retrieve meaningful biological information from single-cell proteomics experiments. This analysis is carried out by computational methods that are assembled into workflows, and their implementations…
Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and best practices available within the…
Scientific Workflow Systems such as Galaxy and Nextflow are essential for scalable, reproducible, and automated bioinformatics analyses. However, developing and understanding scientific workflows remains challenging for many domain…
While mechanobiology has demonstrated that precise control over mechanical properties at the whole-cell level is crucial for many biological functions, comparatively little attention has been paid to the intracellular mechanical properties.…
Experimental science is enabled by the combination of synthesis, imaging, and functional characterization. Synthesis of a new material is typically followed by a set of characterization methods aiming to provide feedback for optimization or…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…