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Motivation: This paper presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language SBML). Results:…
We introduce a new flexible one-dimensional photochemical model named Photochemical and RadiatiOn Transport model for Extensive USe (PROTEUS), which consists of a Python graphical user interface (GUI) program and Fortran 90 modules. PROTEUS…
SpartyJet is a set of software tools for jet finding and analysis, built around the FastJet library of jet algorithms. SpartyJet provides four key extensions to FastJet: a simple Python interface to most FastJet features, a powerful…
We introduce CBXPy and ConsensusBasedX.jl, Python and Julia implementations of consensus-based interacting particle systems (CBX), which generalise consensus-based optimization methods (CBO) for global, derivative-free optimisation. The…
Recent studies have presented compelling evidence that large language models (LLMs) can equip embodied agents with the self-driven capability to interact with the world, which marks an initial step toward versatile robotics. However, these…
EasyVitessce is a Python package that turns existing static Scanpy and SpatialData plots into interactive visualizations by virtue of adding a single line of Python code. The package uses Vitessce internally to render interactive plots, and…
Studying facial expressions is a notoriously difficult endeavor. Recent advances in the field of affective computing have yielded impressive progress in automatically detecting facial expressions from pictures and videos. However, much of…
In this work, we present scikit-fingerprints, a Python package for computation of molecular fingerprints for applications in chemoinformatics. Our library offers an industry-standard scikit-learn interface, allowing intuitive usage and easy…
Designers often encounter friction when animating static SVG graphics, especially when the visual structure does not match the desired level of motion detail. Existing tools typically depend on predefined groupings or require technical…
WorkingWiki is a software extension for the popular MediaWiki platform that makes a wiki into a powerful environment for collaborating on publication-quality manuscripts and software projects. Developed in Jonathan Dushoff's theoretical…
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent…
Our open-source Python package BoFire combines Bayesian Optimization (BO) with other design of experiments (DoE) strategies focusing on developing and optimizing new chemistry. Previous BO implementations, for example as they exist in the…
Simulations of hadronic and nuclear interactions are essential in both collider and astroparticle physics. The Chromo package provides a unified Python interface to multiple widely used hadronic event generators, including EPOS, DPMJet,…
Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…
We present SRWToolkit, an open-source Wizard of Oz toolkit designed to facilitate the rapid prototyping of social robotic avatars powered by local large language models (LLMs). Our web-based toolkit enables multimodal interaction through…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
We present BSTModelKit.jl, an open-source Julia package for constructing, solving, and analyzing Biochemical Systems Theory (BST) models of biochemical networks. The package implements S-system representations, a canonical power-law…
The integration of robotics and automation into self-driving laboratories (SDLs) can introduce additional safety complexities, in addition to those that already apply to conventional research laboratories. Personal protective equipment…
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…
Bio-orthogonal click chemistry based on [3 + 2] dipolar cycloadditions has had a profound impact on the field of biochemistry and significant effort has been devoted to identify promising new candidate reactions for this purpose. To gauge…