Figure 1: A screenshot of the RuleVis interface, depicting a user in the process of building a rule, consisting of two patterns that describe the 'before' and 'after' states of the system (separated by an arrow). The editor panel (left) enables users to add and delete agents, sites, and links in the visualization in the display panel (right). The text and visualization are mirrored, and changes made to one representation are immediately reflected in the other. ABSTRACTWe introduce RuleVis, a web-based application for defining and editing "correct-by-construction" executable rules that model biochemical functionality, which can be used to simulate the behavior of protein-protein interaction networks and other complex systems. Rule-based models involve emergent effects based on the interactions between rules, which can vary considerably with regard to the scale of a model, requiring the user to inspect and edit individual rules. RuleVis bridges the graph rewriting and systems biology research communities by providing an external visual representation of salient patterns that experts can use to determine the appropriate level of detail for a particular modeling context. We describe the visualization and interaction features available in RuleVis and provide a detailed example demonstrating how RuleVis can be used to reason about intracellular interactions.

We introduce IGM‐Vis, a novel astrophysics visualization and data analysis application for investigating galaxies and the gas that surrounds them in context with their larger scale environment, the Cosmic Web. Environment is an important factor in the evolution of galaxies from actively forming stars to quiescent states with little, if any, discernible star formation activity. The gaseous halos of galaxies (the circumgalactic medium, or CGM) play a critical role in their evolution, because the gas necessary to fuel star formation and any gas expelled from widely observed galactic winds must encounter this interface region between galaxies and the intergalactic medium (IGM). We present a taxonomy of tasks typically employed in IGM/CGM studies informed by a survey of astrophysicists at various career levels, and demonstrate how these tasks are facilitated via the use of our visualization software. Finally, we evaluate the effectiveness of IGM‐Vis through two in‐depth use cases that depict real‐world analysis sessions that use IGM/CGM data.

We introduce CosmoVis, an open source web-based visualization tool for the interactive analysis of massive hydrodynamic cosmological simulation data. CosmoVis was designed in close collaboration with astrophysicists to enable researchers and citizen scientists to share and explore these datasets, and to use them to investigate a range of scientific questions. CosmoVis visualizes many key gas, dark matter, and stellar attributes extracted from the source simulations, which typically consist of complex data structures multiple terabytes in size, often requiring extensive data wrangling. CosmoVis introduces a range of features to facilitate real-time analysis of these simulations, including the use of "virtual skewers," simulated analogues of absorption line spectroscopy that act as spectral probes piercing the volume of gaseous cosmic medium. We explain how such synthetic spectra can be used to gain insight into the source datasets and to make functional comparisons with observational data. Furthermore, we identify the main analysis tasks that CosmoVis enables and present implementation details of the software interface and the client-server architecture. We conclude by providing details of three contemporary scientific use cases that were conducted by domain experts using the software and by documenting expert feedback from astrophysicists at different career levels.

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