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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…
Simulation ensembles are a common tool in physics for understanding how a model outcome depends on input parameters. We analyze an active particle system, where each particle can use energy from its surroundings to propel itself. A…
BrainPainter is a software for the 3D visualization of human brain structures; it generates colored brain images using user-defined biomarker data for each brain region. However, BrainPainter is only able to generate human brain images. In…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
In this article we introduce PINGSoft, a set of IDL routines designed to visualise and manipulate, in an interactive and friendly way, Integral Field Spectroscopic data. The package is optimised for large databases and a fast visualisation…
Web agents--autonomous systems that navigate and execute tasks on the web on behalf of users--have the potential to transform how people interact with the digital world. However, the most capable web agents today rely on proprietary models…
While clustering is one of the most popular methods for data mining, analysts lack adequate tools for quick, iterative clustering analysis, which is essential for hypothesis generation and data reasoning. We introduce Clustrophile, an…
Although many tools have been presented in the research literature of software visualization, there is little evidence of their adoption. To choose a suitable visualization tool, practitioners need to analyze various characteristics of…
Embeddings are ubiquitous in machine learning, appearing in recommender systems, NLP, and many other applications. Researchers and developers often need to explore the properties of a specific embedding, and one way to analyze embeddings is…
DORAEMON is an open-source PyTorch library that unifies visual object modeling and representation learning across diverse scales. A single YAML-driven workflow covers classification, retrieval and metric learning; more than 1000 pretrained…
Multilayer networks are widely used across biology to represent systems in which complex networks vary across space, time, or interaction types. However, interactive visualization tools remain limited. We present MiRA (Multilayer…
We present a middleware for visualization and exploration of complex datasets in a VO framework, that performs interaction between data archives and existing VO client applications using PLASTIC. It comprises: (1) PLASTIC-enabled Java…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
Virtual reality is expected to play a significant role in the transformation of education and psychological studies. The possibilities for its application as a visual research method can be enhanced as established frameworks and toolkits…
Visualizations have become an indispensable part of the scientific process. A vibrant ecosystem of visualization tools exists, catering to a wide variety of different needs. Real-time visualizations of numerical simulations offer scientists…
Summary: Integration of multi-omics data on chemical exposure of cells or organisms promises a more complete representation of the responding pathways than single omics data. Data of different omics layers, like transcriptome or proteome is…
Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets…
Efficient explorative data analysis systems must take into account both what a user knows and wants to know. This paper proposes a principled framework for interactive visual exploration of relations in data, through views most informative…
The Collective Variables Dashboard is a software tool for real-time, seamless exploration of molecular structures and trajectories in a customizable space of collective variables. The Dashboard arises from the integration of the Collective…
Biomedical research increasingly relies on heterogeneous, high-dimensional datasets, yet effective visualization remains hindered by fragmented code resources, steep programming barriers, and limited domain-specific guidance. Bizard is an…