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We created a custom pipeline (histo-fetch) to efficiently extract random patches and labels from pathology whole slide images (WSIs) for input to a neural network on-the-fly. We prefetch these patches as needed during network training,…

Over the last half century, the main application of Brain Computer Interfaces, BCIs has been controlling wheelchairs and neural prostheses or generating text or commands for people with restricted mobility. There has been very limited…

As computers become more ubiquitous, traditional two-dimensional interfaces must be replaced with interfaces based on a three-dimensional metaphor. However, these interfaces must still be as simple and functional as their two-dimensional…

Recently, we see a new type of interfaces for programmers based on web technology. For example, JSFiddle, IPython Notebook and R-studio. Web technology enables cloud-based solutions, embedding in tutorial web pages, atractive rendering of…

While coarse-grained reconfigurable arrays (CGRAs) have emerged as promising programmable accelerator architectures, pipelining applications running on CGRAs is required to ensure high maximum clock frequencies. Current CGRA compilers…

In the past decade, the modeling community has produced many feature-rich modeling editors and tool prototypes not only for modeling standards but particularly also for many domain-specific languages. More recently, however, web-based…

Virtual e-Science infrastructures supporting Web-based scientific workflows are an example for knowledge-intensive collaborative and weakly-structured processes where the interaction with the human scientists during process execution plays…

Scientific computing can in some sense be distilled to the execution of an application - or rather sets of applications which are combined into complex workflows. Due to the complexity and number both of scientific packages as well as…

The interactive command line, also known as the shell, is a prominent mechanism used extensively by a wide range of software professionals (engineers, system administrators, data scientists, etc.). Shell customizations can therefore provide…

Currently, most people use PubMed to search the MEDLINE database, an important bibliographical information source for life science and biomedical information. However, PubMed has some drawbacks that make it difficult to find relevant…

Logic-based paradigms are nowadays widely used in many different fields, also thank to the availability of robust tools and systems that allow the development of real-world and industrial applications. In this work we present LoIDE, an…

This paper proposes a visual analytics framework that addresses the complex user interactions required through a command-line interface to run analyses in distributed data analysis systems. The visual analytics framework facilitates 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…

In this paper we present a framework for creating natural language interfaces to action-based applications. Our framework uses a number of reusable application-independent components, in order to reduce the effort of creating a natural…

In the ever-evolving landscape of scientific computing, properly supporting the modularity and complexity of modern scientific applications requires new approaches to workflow execution, like seamless interoperability between different…

With recent advances in the fields of quantum information theory [J. Pablo. Nature 12, 2172 (2021)] and the approach of the Noisy Intermediate-Scale Quantum (NISQ) [J. Preskill. Quantum 2, 79 (2018)] computing era, it is necessary to…

RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like…

Modern rendering libraries provide unprecedented realism, producing real-time photorealistic 3D graphics on commodity hardware. Visual fidelity, however, comes at the cost of increased complexity and difficulty of usage, with many rendering…

Constructing lineages of malware is an important cyber-defense task. Performing this task is difficult, however, due to the amount of malware data and obfuscation techniques by the authors. In this work, we formulate the lineage task as a…

Open source bioinformatics tools running under MS Windows are rare to find, and those running under Windows HPC cluster are almost non-existing. This is despite the fact that the Windows is the most popular operating system used among life…