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Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
PHOTONAI is a high-level Python API designed to simplify and accelerate machine learning model development. It functions as a unifying framework allowing the user to easily access and combine algorithms from different toolboxes into custom…
Humans can finely perceive material textures, yet articulating such somatic impressions in words is a cognitive bottleneck in design ideation. We present OnomaCompass, a web-based exploration system that links sound-symbolic onomatopoeia…
Reference Publication Year Spectroscopy (RPYS) and Multi-RPYS provide algorithmic approaches to reconstructing the intellectual histories of scientific fields. With this brief communication, we describe a technical advancement for…
Analyzing data subgroups is a common data science task to build intuition about a dataset and identify areas to improve model performance. However, subgroup analysis is prohibitively difficult in datasets with many features, and existing…
This paper presents Coralai, a framework for exploring diverse ecosystems of Neural Cellular Automata (NCA). Organisms in Coralai utilize modular, GPU-accelerated Taichi kernels to interact, enact environmental changes, and evolve through…
Quantum simulation of chemistry and materials is predicted to be an important application for both near-term and fault-tolerant quantum devices. However, at present, developing and studying algorithms for these problems can be difficult due…
The stochastic simulation of large-scale biochemical reaction networks is of great importance for systems biology since it enables the study of inherently stochastic biological mechanisms at the whole cell scale. Stochastic Simulation…
We present AMADA, an interactive web application to analyse multidimensional datasets. The user uploads a simple ASCII file and AMADA performs a number of exploratory analysis together with contemporary visualizations diagnostics. The…
Internet users are vulnerable to privacy attacks despite the use of encryption. Webpage fingerprinting, an attack that analyzes encrypted traffic, can identify the webpages visited by a user in a given website. Recent research works have…
The analysis of spatial observations on a sphere is important in areas such as geosciences, physics and embryo research, just to name a few. The purpose of the package rcosmo is to conduct efficient information processing, visualisation,…
Using realistic laser profiles for simulations of laser-plasma interaction is critical to reproduce experimental measurements, but the interface between experiments and simulations can be challenging. Similarly, start-to-end simulations…
Cyber-Physical Systems (CPS) allow us to manipulate objects in the physical world by providing a communication bridge between computation and actuation elements. In the current scheme of things, this sought-after control is marred by…
Research software plays a crucial role in advancing scientific knowledge, but ensuring its sustainability, maintainability, and long-term viability is an ongoing challenge. The Sustainable Research Software Institute (SRSI) Model has been…
Simulations are valuable tools for empirically evaluating the properties of statistical methods and are primarily employed in methodological research to draw general conclusions about methods. In addition, they can often be useful to…
Purpose: As interest in CEST-MRI grows, particularly in the preclinical setting, the necessity for standardized and easy-to-use acquisition and data analysis pipelines has become apparent. While vendors have increasingly introduced support…
Scientific open-source software (OSS) has greatly benefited research communities through its transparent and collaborative nature. Given its critical role in scientific research, ensuring the sustainability of such software has become…
Research collaborations are continuously emerging catalyzed by online platforms, where people can share their codes, calculations, data and results. These virtual research platforms are innovative, community oriented, flexible and secure as…
Knowledge graphs are an increasingly common data structure for representing biomedical information. These knowledge graphs can easily represent heterogeneous types of information, and many algorithms and tools exist for querying and…
A Materials Project based open-source Python tool, MPInterfaces, has been developed to automate the high-throughput computational screening and study of interfacial systems. The framework encompasses creation and manipulation of interface…