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Simulation-driven development of intelligent machines benefits from artificial terrains with controllable, well-defined characteristics. However, most existing tools for terrain generation focus on artist-driven workflows and visual…
We present MXtalTools, a flexible Python package for the data-driven modelling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis,…
Advanced image segmentation and processing tools present an opportunity to study cell processes and their dynamics. However, image analysis is often routine and time-consuming. Nowadays, alternative data-driven approaches using deep…
Interest in applying Artificial Intelligence (AI) techniques to compiler optimizations is increasing rapidly, but compiler research has a high entry barrier. Unlike in other domains, compiler and AI researchers do not have access to the…
BondGraphTools is a Python library for scripted modelling of complex multi-physics systems. In contrast to existing modelling solutions, BondGraphTools is based upon the well established bond graph methodology, provides a programming…
Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and Nextflow enable users to automate the…
Motivation: Automatically testing changes to code is an essential feature of continuous integration. For open-source code, without licensed dependencies, a variety of continuous integration services exist. The COnstraint-Based…
The increasing necessity for fisheye cameras in fields such as robotics and autonomous driving has led to the proposal of various fisheye camera models. While the evolution of camera models has facilitated the development of diverse systems…
Profiling data by plotting distributions and analyzing summary statistics is a critical step throughout data analysis. Currently, this process is manual and tedious since analysts must write extra code to examine their data after every…
Systems biology is an inter-disciplinary field that studies systems of biological components at different scales, which may be molecules, cells or entire organism. In particular, systems biology methods are applied to understand functional…
Synthesizer is a fast, flexible, modular, and extensible Python package that empowers astronomers to turn theoretical galaxy models into realistic synthetic observations - including spectra, photometry, images, and spectral cubes - with a…
FPGAs have found their way into data centers as accelerator cards, making reconfigurable computing more accessible for high-performance applications. At the same time, new high-level synthesis compilers like Xilinx Vitis and runtime…
Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application…
High-throughput synthesis of solution-processable structurally variable small-molecule semiconductors is both an opportunity and a challenge. A large number of diverse molecules provide a possibility for quick material discovery and machine…
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)…
pyscreener is a Python library that seeks to alleviate the challenges of large-scale structure-based design using computational docking. It provides a simple and uniform interface that is agnostic to the backend docking engine with which to…
Systematically developing high--quality reusable software components is a difficult task and requires careful design to find a proper balance between potential reuse, functionalities and ease of implementation. Extendibility is an important…
This paper proposes a software repository model together with associated tooling and consists of several complex, open-source GUI driven applications ready to be used in empirical software research. We start by providing the rationale for…
Summary: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein assocation network modules appear as groups of densely interconnected…
Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…