20 papers · ranked by Valyu relevance
William JR Longabaugh
Background The analysis of large, complex networks is an important aspect of ongoing biological research. Yet there is a need for entirely new, scalable approaches for network visualization that can provide more insight into the structure and function of these complex networks. Results To address this need, we have…
Velitchko Filipov, Alessio Arleo, Silvia Miksch
Networks are abstract and ubiquitous data structures, defined as a set of data points and relationships between them. Network visualization provides meaningful representations of these data, supporting researchers in understanding the connections, gathering insights, and detecting and identifying unexpected patterns.…
Thibault Rolland, Fabrizio De Vico Fallani, Praveen Kumar Donta
In many fields of science and technology we are confronted with complex networks. Making sense of these networks often require the ability to visualize and explore their intermingled structure consisting of nodes and links. To facilitate the identification of significant connectivity patterns, many methods have been…
Vaja Liluashvili, Selim Kalayci, Eugene Flouder, Manda Wilson + 2 more
Visualizations of biomolecular networks assist in systems-level data exploration in myriad cellular processes in health and disease. While these networks are increasingly informed by data generated from high-throughout (HT) experiments, current tools do not adequately scale with concomitant increase in their size and…
Alan Demétrius Baria Valejo, Renato Fabbri, Alneu de Andrade Lopes, Liang Zhao + 1 more
Bipartite networks are pervasive in modeling real-world phenomena and play a fundamental role in graph theory. Interactive exploratory visualization of such networks is an important problem, and particularly challenging when handling large networks. In this paper we present results from an investigation on using a…
Henry Heberle, Marcelo Falsarella Carazzolle, Guilherme P. Telles, Gabriela Vaz Meirelles + 1 more
The advent of “omics” science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract…
Sergio Pablo-García, Raúl Pérez-Soto, Albert Sabadell-Rendón, Diego Garay-Ruiz + 2 more
In the study of chemical reactions, visualizing reaction networks is pivotal for identifying crucial compounds and reactions. Traditional methods, such as network schematics and reaction path linear plots, often struggle to effectively represent complex reaction networks due to their size and intricate connectivity.…
J. Garcia-Algarra, J. M. Pastor, M. L. Mouronte, J. Galeano
Interactions between two different guilds of entities are pervasive in biology. They may happen at molecular level, like in a diseasome, or amongst individuals linked by biotic relationships, such as mutualism or parasitism. These sets of interactions are complex bipartite networks. Visualization is a powerful tool to…
Thibault Rolland, Fabrizio De Vico Fallani
To facilitate the identification of significant connectivity patterns, many methods have been developed based on the rearrangement of the nodes so as to avoid link criss-cross. However, real networks are often embedded in a geometrical space and the nodes code for an intrinsic physical feature of the system that one…
Tommaso Venturini, Mathieu Jacomy, Pablo Jensen
It is an increasingly common practice in several natural and social sciences to rely on network visualisations both as heuristic tools to get a first overview of relational datasets and as a way to offer an illustration of network analysis findings. Such practice has been around long enough to prove that scholars find…
James Scott-Brown, Benjamin Bach
—This paper introduces NetPanorama, a domain-specific language and declarative grammar for interactive network visualizations. Exploring complex networks with multivariate, geographical, or temporal information often require bespoke visualization designs, such as adjacency matrices, arc-diagrams, small multiples…
Jayamohan Pillai C. S., Ayan Chatterjee, M. Geetha, Amitava Mukherjee
'Amitava Mukherjee'] Abstract—The process of visually presenting networks is an effective way to understand entity relationships within the networks since it reveals the overall structure and topology of the network. Real networks are extremely difficult to visualize due to their immense complexity, which includes vast…
Giuseppe Agapito, Pietro Hiram Guzzi, Mario Cannataro
Background Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in…
James Mathews, Saad Nadeem, Maryam Pouryahya, Zehor Belkhatir + 2 more
We present a framework based on optimal mass transport to construct, for a given network, a reduction hierarchy which can be used for interactive data exploration and community detection. Given a network and a set of numerical data samples for each node, we calculate a new computationally-efficient comparison metric…
Benjamin Ries, Richard J Gowers, James RB Eastwood, Irfan Alibay + 4 more
Alchemical free energy campaigns can be planned using graph theory by building up networks that contain nodes representing molecules that are connected by possible transformations as edges. We introduce Konnektor, an open-source Python package, for systematically planning, modifying, and analyzing free energy…
Kevin Mildau, Christoph Büschl, Jürgen Zanghellini, Justin J.J. van der Hooft
Computational metabolomics workflows have revolutionized the untargeted metabolomics field. However, the organization and prioritization of metabolite features remains a laborious process. Organizing metabolomics data is often done through mass fragmentation-based spectral similarity grouping, resulting in feature sets…
Carolina Nobre, Marc Streit, Alexander Lex
Graph visualization is a challenging problem, especially when the size of the graph exceeds a few hundred nodes. This lack of scalability is exacerbated when rich attributes for the nodes and/or the links need to be considered when analyzing a graph. Such multivariate graphs are common across domains: biologists, for…
Urszula Czerwinska, Laurence Calzone, Emmanuel Barillot, Andrei Zinovyev
Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistical insights into biological functions. Currently, high-throughput data are usually visualized on top of predefined network layouts which are not always adapted to a given data analysis task. We…
Stefan Paul Feyer, Bruno Pinaud, Karsten Klein, Etienne Lein + 1 more
'Falk Schreiber'] Title: Abstract Animal behaviour is often modelled as networks, where, for example, the nodes are individuals of a group and the edges represent behaviour within this group. Different types of behaviours or behavioural categories are then modelled as different yet connected networks which form a…
Authors not listed
Effective visualization of complex synthesis routes is critical for computeraided synthesis planning (CASP), yet current solutions are limited in scope, integration flexibility, and chemical intuition. We introduce RouteWise, a versatile, containerized web application designed to address these unmet needs. Its modular…