Related papers: SBMLDiagrams: A python package to process and visu…
Functional groups and moieties are chemical descriptors of biomolecules that can be used to interpret their properties and functions, leading to the understanding of chemical or biological mechanisms. These chemical building blocks, or…
Summary: Shu is a visualization tool that integrates diverse data types into a metabolic map, with a focus on supporting multiple conditions and visualizing distributions. The goal is to provide a unified platform for handling the growing…
Motivation: Novel machine learning and statistical modeling studies rely on standardized comparisons to existing methods using well-studied benchmark datasets. Few tools exist that provide rapid access to many of these datasets through a…
Over the past decade, deep learning (DL) research in computer vision has been growing rapidly, with many advances in DL-based image analysis methods for biomedical problems. In this work, we introduce MMV_Im2Im, a new open-source python…
The brms package allows R users to easily specify a wide range of Bayesian single-level and multilevel models, which are fitted with the probabilistic programming language Stan behind the scenes. Several response distributions are…
Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
Current-generation Large Language Models (LLMs) have stirred enormous interest in recent months, yielding great potential for accessibility and automation, while simultaneously posing significant challenges and risk of misuse. To facilitate…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
This article provides a brief overview of the UML SP (UML Scientific Profile). It is an Object-Oriented Simulation Language and may find usage in OOS and ABS. UML SP allows for the application of Unified Process methodology for the…
This paper contributes to speeding up the design and deployment of engineering dynamical systems by proposing a strategy for exploiting domain and expert knowledge for the automated generation of a dynamical system computational model…
Software documentation frequently becomes outdated or fails to exist entirely, yet developers need focused views of their codebase to understand complex systems. While automated reverse engineering tools can generate UML diagrams from code,…
System models, a critical artifact in software development, provide a formal abstraction of both the structural and behavioral aspects of software systems, which can facilitate the early requirements analysis and architecture design.…
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…
Business process modelling languages typically enable the representation of business process models by employing (graphical) symbols. These symbols can vary depending upon the verbosity of the language, the modelling paradigm, the focus of…
This paper presents a generic web-based database interface implemented in Prolog. We discuss the advantages of the implementation platform and demonstrate the system's applicability in providing access to integrated biochemical data. Our…
Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein…
We introduce BSMArt, a python program for the exploration of parameter spaces of theories Beyond the Standard Model. Especially designed for use with the SARAH family of tools, it is also sufficiently flexible to be used with a wide variety…
Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their…
This paper describes a novel Python package, named causalgraph, for modeling and saving causal graphs embedded in knowledge graphs. The package has been designed to provide an interface between causal disciplines such as causal discovery…