Related papers: BioSimulators: a central registry of simulation en…
Summary: More sophisticated models are needed to address problems in bioscience, synthetic biology, and precision medicine. To help facilitate the collaboration needed for such models, the community developed the Simulation Experiment…
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…
This survey aims at providing a comprehensive overview of the recent trends in the field of modeling and simulation (M&S) of interactions between users and recommender systems and applications of the M&S to the performance improvement of…
With high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational…
Although simulation represents a major advance in the understanding of problems in complex systems, the field currently does not has standards in place that would guide the reporting of the data underlying each model, the process for model…
This paper presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models \ expressed using Systems Biology Markup Language (SBML). SBML is the most widely…
Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…
Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators do not always take full advantage of modern hardware and often have a field-specific software design. Results:…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
Programming is ubiquitous in applied biostatistics; adopting software engineering skills will help biostatisticians do a better job. To explain this, we start by highlighting key challenges for software development and application in…
Simulators are a critical component of modern robotics research. Strategies for both perception and decision making can be studied in simulation first before deployed to real world systems, saving on time and costs. Despite significant…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
Despite the success of large language models (LLMs) on general-purpose tasks, their performance in highly specialized domains such as biomedicine remains unsatisfactory. A key limitation is the inability of LLMs to effectively leverage…
Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area…
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving…
Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been…
CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that…
Assessing the validity of user simulators when used for the evaluation of information retrieval systems remains an open question, constraining their effective use and the reliability of simulation-based results. To address this issue, we…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…