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Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites within molecules, but obtaining an integrated global view…

Quantitative Methods · Quantitative Biology 2015-09-04 John A. P. Sekar , Jose-Juan Tapia , James R. Faeder

Integrating textual content, such as titles, annotations, and captions, with visualizations facilitates comprehension and takeaways during data exploration. Yet current tools often lack mechanisms for integrating meaningful long-form prose…

Human-Computer Interaction · Computer Science 2024-08-07 Dennis Bromley , Vidya Setlur

The science of Human-Computer Interaction (HCI) is populated by isolated empirical findings, often tied to specific technologies, designs, and tasks. This situation probably lies in observing the wrong object of study, that is to say,…

Human-Computer Interaction · Computer Science 2025-10-08 Guillaume Rivière

Phylogenetic trees are the primary framework for conveying evolutionary relationships. While many tools exist for visualizing phylogenetic trees, most are limited to static graphics, require coding expertise, or are developed for a specific…

Populations and Evolution · Quantitative Biology 2026-05-15 Zachary S. L. Foster , Jeff H. Chang , Niklaus J. Grunwald

This article introduces WebXAII, an open-source web framework designed to facilitate research on human interaction with eXplainable Artificial Intelligence (XAI) systems. The field of XAI is rapidly expanding, driven by the growing societal…

Human-Computer Interaction · Computer Science 2025-06-23 Jules Leguy , Pierre-Antoine Jean , Felipe Torres Figueroa , Sébastien Harispe

The desktop GUI catalogue analysis tool TOPCAT, and its command-line counterpart STILTS, offer among other capabilities visual exploration of locally stored tables containing millions of rows or more. They offer many variations on the theme…

Distributed, Parallel, and Cluster Computing · Computer Science 2020-12-22 Mark Taylor

Modern display environments offer great potential for involving multiple users in presentations, discussions, and data analysis sessions. By showing multiple views on multiple displays, information exchange can be improved, several…

Graphics · Computer Science 2019-12-19 Christian Eichner , Heidrun Schumann , Christian Tominski

Astrochemical modeling is needed for understanding the formation and evolution of interstellar molecules, and for extracting physical information from spectroscopic observations of interstellar clouds. The modeling usually involves handling…

Solar and Stellar Astrophysics · Physics 2021-05-05 Fujun Du

This work introduces a novel, modular, layered web based platform for managing machine learning experiments on grid-based High Performance Computing infrastructures. The coupling of the communication services offered by the grid, with an…

Distributed, Parallel, and Cluster Computing · Computer Science 2016-10-12 Chairi Kiourt , Dimitris Kalles

Web applications need better user interface to be interactive and attractive. A new approach/concept of dimensional enhancement - 2.5D "a 2D display of a virtual 3D environment", which can be implemented in social networking sites and…

Human-Computer Interaction · Computer Science 2012-10-03 Saurabh Sarkar

Quick interaction between a human teacher and a learning machine presents numerous benefits and challenges when working with web-scale data. The human teacher guides the machine towards accomplishing the task of interest. The learning…

Let's HPC (www.letshpc.org) is an open-access online platform to supplement conventional classroom oriented High Performance Computing (HPC) and Parallel & Distributed Computing (PDC) education. The web based platform provides online…

Computers and Society · Computer Science 2017-01-24 Akshar Varma , Yashwant Keswani , Yashodhan Bhatnagar , Bhaskar Chaudhury

Analyzing large complex image collections in domains like forensics, accident investigation, or social media analysis involves interpreting intricate, overlapping relationships among images. Traditional clustering and classification methods…

Graphics · Computer Science 2025-10-24 Floris Gisolf , Zeno J. M. H. Geradts , Marcel Worring

Network Repository (NR) is the first interactive data repository with a web-based platform for visual interactive analytics. Unlike other data repositories (e.g., UCI ML Data Repository, and SNAP), the network data repository…

Digital Libraries · Computer Science 2015-05-29 Ryan A. Rossi , Nesreen K. Ahmed

Analyzing data subgroups is a common data science task to build intuition about a dataset and identify areas to improve model performance. However, subgroup analysis is prohibitively difficult in datasets with many features, and existing…

Human-Computer Interaction · Computer Science 2025-02-18 Venkatesh Sivaraman , Zexuan Li , Adam Perer

Summary: Shu is a visualization tool that integrates diverse data types into a metabolic map, with a focus on supporting multiple conditions and visualizing distributions. The goal is to provide a unified platform for handling the growing…

Molecular Networks · Quantitative Biology 2024-03-08 Jorge Carrasco Muriel , Nicholas Cowie , Marjan Mansouvar , Teddy Groves , Lars Keld Nielsen

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…

Neurons and Cognition · Quantitative Biology 2018-01-04 David J. Caldwell , Jing Wu , Kaitlyn Casimo , Jeffrey G. Ojemann , Rajesh P. N. Rao

This paper presents an interactive technique to explain visual patterns in network visualizations to analysts who do not understand these visualizations and who are learning to read them. Learning a visualization requires mastering its…

Human-Computer Interaction · Computer Science 2024-08-05 Xinhuan Shu , Alexis Pister , Junxiu Tang , Fanny Chevalier , Benjamin Bach

Traceroute is the main tools to explore Internet path. It provides limited information about each node along the path. However, Traceroute cannot go further in statistics analysis, or \emph{Man-Machine Interface (MMI)}. Indeed, there are no…

Networking and Internet Architecture · Computer Science 2017-03-20 Xavier Nicolay , Réhan Noordally , Yassine Gangat

We propose a novel structure, the data-sharing graph, for characterizing sharing patterns in large-scale data distribution systems. We analyze this structure in two such systems and uncover small-world patterns for data-sharing…

Networking and Internet Architecture · Computer Science 2007-05-23 Adriana Iamnitchi , Matei Ripeanu , Ian Foster