Related papers: Process Bigraphs and the Architecture of Compositi…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these…
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…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
In this paper, we present BIMS (Biomedical Information Management System). BIMS is a software architecture designed to provide a flexible computational framework to manage the information needs of a wide range of biomedical research…
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…
Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript…
We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
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:…
Researchers in biomedical research, public health, and the life sciences often spend weeks or months discovering, accessing, curating, and integrating data from disparate sources, significantly delaying the onset of actual analysis and…
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
Bigraphs are an emerging modeling formalism for structures in ubiquitous computing. Besides an algebraic notation, which can be adopted to provide an algebraic syntax for bigraphs, the bigraphical theory introduces a visual concrete syntax…
Advances in cellular imaging technologies, especially those based on fluorescence in situ hybridization (FISH) now allow detailed visualization of the spatial organization of human or bacterial cells. Quantifying this spatial organization…
Combinatorial algorithms such as those that arise in graph analysis, modeling of discrete systems, bioinformatics, and chemistry, are often hard to parallelize. The Combinatorial BLAS library implements key computational primitives for…
This article presents updates to lifex [Africa, SoftwareX (2022)], a C++ library for high-performance finite element simulations of multiphysics, multiscale and multidomain problems. In this release, we introduce an additional intergrid…
Recent diffusion and flow matching models have demonstrated strong capabilities in image generation and editing by progressively removing noise through iterative sampling. While this enables flexible inversion for semantic-preserving edits,…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
Large systems biology projects can encompass several workgroups often located in different countries. An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data…