Related papers: PlayMolecule Viewer: a toolkit for the visualizati…
Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various…
At present each neutron scattering facility has its own set of data treatment software, normally based on a proprietary data format. The travelling scientist is either forced to continually learn new software or to write conversion routines…
GeneVis is a web-based tool to visualize complementary data sets of different disciplines within the field of genetics. It overlays gene-cluster information, gene-interaction data and gene-disease association data by means of web-based…
Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often…
Computational notebooks, such as Jupyter Notebook, have become data scientists' de facto programming environments. Many visualization researchers and practitioners have developed interactive visualization tools that support notebooks, yet…
The analysis of structured complex data, such as clustered graph based datasets, usually applies a variety of visual representation techniques and formats. The majority of currently available tools and approaches to exploratory…
Debugging is an essential part of software maintenance and evolution since it allows software developers to analyze program execution step by step. Understanding a program is required to fix potential flaws, alleviate bottlenecks, and…
Summary: Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks.…
We present here a browser-based application for visualizing patterns of connectivity in 3D stacked data matrices with large numbers of pairwise relations. Visualizing a connectivity matrix, looking for trends and patterns, and dynamically…
We introduce MultiMedEval, an open-source toolkit for fair and reproducible evaluation of large, medical vision-language models (VLM). MultiMedEval comprehensively assesses the models' performance on a broad array of six multi-modal tasks,…
Exploration and analysis of high-dimensional data are important tasks in many fields that produce large and complex data, like the financial sector, systems biology, or cultural heritage. Tailor-made visual analytics software is developed…
Understanding complex scientific and mathematical concepts, particularly those presented in dense research papers, poses a significant challenge for learners. Dynamic visualizations can greatly enhance comprehension, but creating them…
Chemists now routinely use software as part of their work. For example, virtual chemistry allows chemical reactions to be simulated. In particular, a selection of software is available for the visualisation of complex 3-dimensional…
Online user studies of visualizations, visual encodings, and interaction techniques are ubiquitous in visualization research. Yet, designing, conducting, and analyzing studies effectively is still a major burden. Although various packages…
pyscreener is a Python library that seeks to alleviate the challenges of large-scale structure-based design using computational docking. It provides a simple and uniform interface that is agnostic to the backend docking engine with which to…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
As machine learning (ML) systems become increasingly widespread, it is necessary to audit these systems for biases prior to their deployment. Recent research has developed algorithms for effectively identifying intersectional bias in the…
With the prospect of automating a number of chemical tasks with high fidelity, chemical language processing models are emerging at a rapid speed. Here, we present a cloud-based real-time platform that allows users to virtually screen…
Filtergraph is a web application being developed and maintained by the Vanderbilt Initiative in Data-intensive Astrophysics (VIDA) to flexibly and rapidly visualize a large variety of astronomy datasets of various formats and sizes. The…
This article presents a newly developed Web portal called VisIVOWeb that aims to provide the astrophysical community with powerful visualization tools for large-scale data sets in the context of Web 2.0. VisIVOWeb can effectively handle…