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Biological neural networks are often modeled as systems of coupled, nonlinear, ordinary or partial differential equations. The number of differential equations used to model a network increases with the size of the network and the level of…
Laboratory research is a complex, collaborative process that involves several stages, including hypothesis formulation, experimental design, data generation and analysis, and manuscript writing. Although reproducibility and data sharing are…
Many existing scientific workflows require High Performance Computing environments to produce results in a timely manner. These workflows have several software library components and use different environments, making the deployment and…
In a new effort to make our research transparent and reproducible by others, we developed a workflow to run and share computational studies on the public cloud Microsoft Azure. It uses Docker containers to create an image of the application…
Complex workflows play a critical role in accelerating scientific discovery. In many scientific domains, efficient workflow management can lead to faster scientific output and broader user groups. Workflows that can leverage resources…
The convergence of IoT, Edge, Cloud, and HPC technologies creates a compute continuum that merges cloud scalability and flexibility with HPC's computational power and specialized optimizations. However, integrating cloud and HPC resources…
Quantum-chemical subsystem and embedding methods require complex workflows that may involve multiple quantum-chemical program packages. Moreover, such workflows require the exchange of voluminous data that goes beyond simple quantities such…
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…
The Agent Based Model community has a rich and diverse ecosystem of libraries, platforms, and applications to help modelers develop rigorous simulations. Despite this robust and diverse ecosystem, the complexity of life from microbial…
We introduce the Balsam service to manage high-throughput task scheduling and execution on supercomputing systems. Balsam allows users to populate a task database with a variety of tasks ranging from simple independent tasks to dynamic…
Notebooks provide an author-friendly environment for iterative development, modular execution, and easy sharing. Distributed workflows are increasingly being authored and executed in notebooks, yet sharing and reproducing them remains…
Developing software to undertake complex, compute-intensive scientific processes requires a challenging combination of both specialist domain knowledge and software development skills to convert this knowledge into efficient code. As…
This paper describes a building blocks approach to the design of scientific workflow systems. We discuss RADICAL-Cybertools as one implementation of the building blocks concept, showing how they are designed and developed in accordance with…
Scientific workflows are a cornerstone of modern scientific computing. They are used to describe complex computational applications that require efficient and robust management of large volumes of data, which are typically stored/processed…
Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Scientific discovery increasingly requires executing heterogeneous scientific workflows on high-performance computing (HPC) platforms. Heterogeneous workflows contain different types of tasks (e.g., simulation, analysis, and learning) that…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Simulations based on particle methods, such as Smoothed Particle Hydrodynamics (SPH), are known to be computationally demanding. While such methods have for long been executed in parallel on multi-core CPUs, in recent years the increasing…