Related papers: Kliko - The Scientific Compute Container Format
We consider the problem of coded distributed computing where a large linear computational job, such as a matrix multiplication, is divided into $k$ smaller tasks, encoded using an $(n,k)$ linear code, and performed over $n$ distributed…
Background: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main…
The Statistical Toolkit is an open source system specialized in the statistical comparison of distributions. It addresses requirements common to different experimental domains, such as simulation validation (e.g. comparison of experimental…
In high-energy particle physics, workflow management systems are primarily used as tailored solutions in dedicated areas such as Monte Carlo production. However, physicists performing data analyses are usually required to steer their…
DisCoPy (Distributional Compositional Python) is an open source toolbox for computing with string diagrams and functors. In particular, the diagram data structure allows to encode various kinds of quantum processes, with functors for…
Topological quantum computing is a way of allowing precise quantum computations to run on noisy and imperfect hardware. One implementation uses surface codes created by forming defects in a highly-entangled cluster state. Such a method of…
We present a consistent system for referring crosscutting functionality, relating crosscutting concerns to specific implementation idioms, and formalizing their underlying relations through queries. The system is based on generic…
The computer programs most users interact with daily are driven by a graphical user interface (GUI). However, many scientific applications are used with a command line interface (CLI) for the ease of development and increased flexibility…
Containers, enabling lightweight environment and performance isolation, fast and flexible deployment, and fine-grained resource sharing, have gained popularity in better application management and deployment in addition to hardware…
In the recent years, scientific workflows gained more and more popularity. In scientific workflows, tasks are typically treated as black boxes. Dealing with their complex interrelations to identify optimization potentials and bottlenecks is…
Software design patterns present general code solutions to common software design problems. Modern software systems rely heavily on containers for running their constituent service components. Yet, despite the prevalence of ready-to-use…
The integration of command-line tools into the Galaxy platform is crucial for making complex computational methods accessible to a broader audience and ensuring reproducible research. However, the manual development of tool wrappers is a…
Scientific workflows facilitate computational, data manipulation, and sometimes visualization steps for scientific data analysis. They are vital for reproducing and validating experiments, usually involving computational steps in scientific…
Due to densification of wireless networks, there exist abundance of idling computation resources at edge devices. These resources can be scavenged by offloading heavy computation tasks from small IoT devices in proximity, thereby overcoming…
With quantum computers promising advantages even in the near-term NISQ era, there is a lively community that develops software and toolkits for the design of corresponding quantum circuits. Although the underlying problems are different,…
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…
We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to i) spend less time on data management and processing, ii)…
Context: Software has become an innovative solution nowadays for many applications and methods in science and engineering. Ensuring the quality and correctness of software is challenging because each program has different configurations and…
Measuring software complexity plays an important role to meet the demands of complex software. The cyclomatic complexity is one of most used and renowned metric among the other three proposed and researched metrics that are namely: Line of…
The cloud computing landscape is rapidly expanding and growing in complexity. It has witnessed the emergence of Cloud Computing as a widely adopted model for efficiently processing large volumes of data by harnessing clusters of commodity…