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Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
Recommender systems play a crucial role in alleviating information overload by providing personalized recommendations tailored to users' preferences and interests. Recently, Graph Neural Networks (GNNs) have emerged as a promising approach…
Animal vision is thought to optimize various objectives from metabolic efficiency to discrimination performance, yet its ultimate objective is to facilitate the survival of the animal within its ecological niche. However, modeling animal…
Networks provide a meaningful way to represent and analyze complex biological information, but the methodological details of network-based tools are often described for a technical audience. Graphery is a hands-on tutorial webserver…
The tool mpbn offers a Python programming interface for an easy interactive editing of Boolean networks and the efficient computation of elementary properties of their dynamics, including fixed points, trap spaces, and reachability…
Summary: GeneFEAST, implemented in Python, is a gene-centric functional enrichment analysis summarisation and visualisation tool that can be applied to large functional enrichment analysis (FEA) results arising from upstream FEA pipelines.…
The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases in both the interactors (the nodes of the network) and interactions (the…
Increasing interest in the acquisition of biotic and abiotic resources from within the deep sea (e.g. fisheries, oil-gas extraction, and mining) urgently imposes the development of novel monitoring technologies, beyond the traditional…
Many ecological questions center on complex phenomena, such as species interactions, behaviors, phenology, and responses to disturbance, that are inherently difficult to observe and sparsely documented. Community science platforms such as…
We present APFEL Web, a web-based application designed to provide a flexible user-friendly tool for the graphical visualization of parton distribution functions (PDFs). In this note we describe the technical design of the APFEL Web…
Automated analysis of imaged phenotypes enables fast and reproducible quantification of biologically relevant features. Despite recent developments, recordings of complex, networked structures, such as: leaf venation patterns, cytoskeletal…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
Conan is a C++ library created for the accurate and efficient modelling, inference and analysis of complex networks. It implements the generation and modification of graphs according to several published models, as well as the unexpensive…
Biotic stress consists of damage to plants through other living organisms. Efficient control of biotic agents such as pests and pathogens (viruses, fungi, bacteria, etc.) is closely related to the concept of agricultural sustainability.…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
Variational inference is an increasingly popular method in statistics and machine learning for approximating probability distributions. We developed LINFA (Library for Inference with Normalizing Flow and Annealing), a Python library for…
Recent advances in deep neuroevolution have demonstrated that evolutionary algorithms, such as evolution strategies (ES) and genetic algorithms (GA), can scale to train deep neural networks to solve difficult reinforcement learning (RL)…
We present CAFA-evaluator, a powerful Python program designed to evaluate the performance of prediction methods on targets with hierarchical concept dependencies. It generalizes multi-label evaluation to modern ontologies where the…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene…
The Virtual Research Environment is an analysis platform developed at CERN serving the needs of scientific communities involved in European Projects. Its scope is to facilitate the development of end-to-end physics workflows, providing…