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This paper describes HyperStream, a large-scale, flexible and robust software package, written in the Python language, for processing streaming data with workflow creation capabilities. HyperStream overcomes the limitations of other…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
With the increased availability of rich tactile sensors, there is an equally proportional need for open-source and integrated software capable of efficiently and effectively processing raw touch measurements into high-level signals that can…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
Tensors are higher-order extensions of matrices. While matrix methods form the cornerstone of machine learning and data analysis, tensor methods have been gaining increasing traction. However, software support for tensor operations is not…
In the modern semiconductor industry, automatic generation of parameterized and recurring layout structures plays an important role and should be present as a feature in Electronic Design Automation (EDA)-tools. Currently these layout…
We present PyMoosh, a Python-based simulation library designed to provide a comprehensive set of numerical tools allowing to compute essentially all optical characteristics of multilayered structures, ranging from reflectance and…
ePSproc provides codes for post-processing results from ePolyScat (ePS), a suite of codes for the calculation of quantum scattering problems, developed and released by Luchesse \& co-workers (Gianturco et al. 1994)(Natalense and Lucchese…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
PyLlama is a handy Python toolkit to compute the electromagnetic reflection and transmission properties of arbitrary multilayered linear media, including the case of anisotropy. Relying on a $4 \times 4$-matrix formalism, PyLlama implements…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…
Data visualizations can reveal trends and patterns that are not otherwise obvious from the raw data or summary statistics. While visualizing low-dimensional data is relatively straightforward (for example, plotting the change in a variable…
Motivation: The ability to perform operations on encrypted data has a growing number of applications in bioinformatics, with implications for data privacy in health care and biosecurity. The SEAL library is a popular implementation of fully…
pyssam is a Python library for creating statistical shape and appearance models (SSAMs) for biological (and other) shapes such as bones, lungs or other organs. A point cloud best describing the anatomical 'landmarks' of the organ are…
Process mining extends far beyond process discovery and conformance checking, and also provides techniques for bottleneck analysis and organizational mining. However, these techniques are mostly backward-looking. PMSD is a web application…
Since Lorenz's seminal work on a simplified weather model, the numerical analysis of nonlinear dynamical systems has become one of the main subjects of research in physics. Despite of that, there remains a need for accessible, efficient,…
The Active Matter Evaluation Package (AMEP) is a Python library for analyzing simulation data of particle-based and continuum simulations. It provides a powerful and simple interface for handling large data sets and for calculating and…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
Machine learning is a general-purpose technology holding promises for many interdisciplinary research problems. However, significant barriers exist in crossing disciplinary boundaries when most machine learning tools are developed in…
Almost all applications stop scaling at some point; those that don't are seldom performant when considering time to solution on anything but aspirational/unicorn resources. Recognizing these tradeoffs as well as greater user functionality…