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Software repository mining is the foundation for many empirical software engineering studies. The collection and analysis of detailed data can be challenging, especially if data shall be shared to enable replicable research and open science…
Delivering effective data analytics is of crucial importance to the interpretation of the multitude of biological datasets currently generated by an ever increasing number of high throughput techniques. Logic programming has much to offer…
Artificial intelligence has become pervasive across disciplines and fields, and biomedical image and signal processing is no exception. The growing and widespread interest on the topic has triggered a vast research activity that is…
BioStatFlow is a free web application, useful to facilitate the performance of statistical analyses of "omics", including metabolomics, data using R packages. It is a fast and easy on-line tool for biologists who are not experts in…
Exosphere provides researcher-friendly software for managing computing workloads on OpenStack cloud infrastructure. Exosphere is a user-friendly alternative to Horizon, the default OpenStack graphical interface. Exosphere can be used with…
Biosensors are essential tools which have been traditionally used to monitor environmental pollution, detect the presence of toxic elements and biohazardous bacteria or virus in organic matter and biomolecules for clinical diagnostics. In…
In this paper, we introduce OpenSocInt, an open-source software package providing a simulator for multi-modal social interactions and a modular architecture to train social agents. We described the software package and showcased its…
Brain-Computer Interface (BCI) is a powerful communication tool between users and systems, which enhances the capability of the human brain in communicating and interacting with the environment directly. Advances in neuroscience and…
OpenSesame is a program for generating tabular equations of state (EOS), with capabilities for multiphase EOS construction. In this tutorial, we provide an overview of how to run OpenSesame to construct a multiphase EOS. We discuss some…
The BeatBox simulation environment combines flexible script language user interface with the robust computational tools, in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level, so that cell…
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation…
We describe OHBA Software Library for the analysis of electrophysiological data (osl-ephys). This toolbox builds on top of the widely used MNE-Python package and provides unique analysis tools for magneto-/electro-encephalography (M/EEG)…
In recent years, deep learning revolutionized machine learning and its applications, producing results comparable to human experts in several domains, including neuroscience. Each year, hundreds of scientific publications present…
This paper presents OpenGridGym, an open-source Python-based package that allows for seamless integration of distribution market simulation with state-of-the-art artificial intelligence (AI) decision-making algorithms. We present the…
Matlab has been considered as a leader computational platform for many engineering fields. Well documented and reliable, Matlab presents as a great advantage its ability to increase the user productivity. However, Python and Octave are…
BayesSim is a statistical technique for domain randomization in reinforcement learning based on likelihood-free inference of simulation parameters. This paper outlines BayesSimIG: a library that provides an implementation of BayesSim…
Open source is the connective tissue for much of the information economy. You would be hard-pressed to find a scenario where your data does not pass through at least one open source component. Many of the services and technology we all rely…
In this paper, we discuss the need for an integrated software stack that unites artificial intelligence (AI) and modeling and simulation (ModSim) tools to advance scientific discovery. The authors advocate for a unified AI/ModSim software…
Software is everywhere. The increasing requirement of supporting a wide variety of domains has rapidly increased the complexity of software systems, making them hard to maintain and the training process harder for end-users, which in turn…
The Open Science Grid (OSG) includes work to enable new science, new scientists, and new modalities in support of computationally based research. There are frequently significant sociological and organizational changes required in…