MotivationWe present an overview of the Kappa platform, an integrated suite of analysis and visualization techniques for building and interactively exploring rule-based models. The main components of the platform are the Kappa Simulator, the Kappa Static Analyzer and the Kappa Story Extractor. In addition to these components, we describe the Kappa User Interface, which includes a range of interactive visualization tools for rule-based models needed to make sense of the complexity of biological systems. We argue that, in this approach, modeling is akin to programming and can likewise benefit from an integrated development environment. Our platform is a step in this direction.ResultsWe discuss details about the computation and rendering of static, dynamic, and causal views of a model, which include the contact map (CM), snaphots at different resolutions, the dynamic influence network (DIN) and causal compression. We provide use cases illustrating how these concepts generate insight. Specifically, we show how the CM and snapshots provide information about systems capable of polymerization, such as Wnt signaling. A well-understood model of the KaiABC oscillator, translated into Kappa from the literature, is deployed to demonstrate the DIN and its use in understanding systems dynamics. Finally, we discuss how pathways might be discovered or recovered from a rule-based model by means of causal compression, as exemplified for early events in EGF signaling.Availability and implementationThe Kappa platform is available via the project website at kappalanguage.org. All components of the platform are open source and freely available through the authors’ code repositories.

Modern cosmology predicts that matter in our Universe has assembled today into a vast network of filamentary structures colloquially termed the Cosmic Web. Because this matter is either electromagnetically invisible (i.e., dark) or too diffuse to image in emission, tests of this cosmic web paradigm are limited. Wide-field surveys do reveal web-like structures in the galaxy distribution, but these luminous galaxies represent less than 10% of baryonic matter. Statistics of absorption by the intergalactic medium (IGM) via spectroscopy of distant quasars support the model yet have not conclusively tied the diffuse IGM to the web. Here, we report on a new method inspired by the Physarum polycephalum slime mold that is able to infer the density field of the Cosmic Web from galaxy surveys. Applying our technique to galaxy and absorption-line surveys of the local Universe, we demonstrate that the bulk of the IGM indeed resides in the Cosmic Web. From the outskirts of Cosmic Web filaments, at approximately the cosmic mean matter density (ρ m ) and ∼ 5 virial radii from nearby galaxies, we detect an increasing H i absorption signature towards higher densities and the circumgalactic medium, to ∼ 200ρ m . However, the absorption is suppressed within the densest environments, suggesting shock-heating and ionization deep within filaments and/or feedback processes within galaxies.

Fig. 1. The stereoscopic highlighting technique illustrated with separate images for the left and right eye. The highlighted yellow node and all of its immediate neighbors are rendered at a depth closer to the viewer. The two images above represent a stereo pair. By crossing eyes, the reader can perceive the 3rd dimension of the stereoscopic highlighting.Abstract-In this paper we present a new technique and prototype graph visualization system, stereoscopic highlighting, to help answer accessibility and adjacency queries when interacting with a node-link diagram. Our technique utilizes stereoscopic depth to highlight regions of interest in a 2D graph by projecting these parts onto a plane closer to the viewpoint of the user. This technique aims to isolate and magnify specific portions of the graph that need to be explored in detail without resorting to other highlighting techniques like color or motion, which can then be reserved to encode other data attributes. This mechanism of stereoscopic highlighting also enables focus+context views by juxtaposing a detailed image of a region of interest with the overall graph, which is visualized at a further depth with correspondingly less detail. In order to validate our technique, we ran a controlled experiment with 16 subjects comparing static visual highlighting to stereoscopic highlighting on 2D and 3D graph layouts for a range of tasks. Our results show that while for most tasks the difference in performance between stereoscopic highlighting alone and static visual highlighting is not statistically significant, users performed better when both highlighting methods were used concurrently. In more complicated tasks, 3D layout with static visual highlighting outperformed 2D layouts with a single highlighting method. However, it did not outperform the 2D layout utilizing both highlighting techniques simultaneously. Based on these results, we conclude that stereoscopic highlighting is a promising technique that can significantly enhance graph visualizations for certain use cases.

Fast radio burst (FRB) 190608 was detected by the Australian Square Kilometre Array Pathfinder (ASKAP) and localized to a spiral galaxy at in the Sloan Digital Sky Survey (SDSS) footprint. The burst has a large dispersion measure ( ) compared to the expected cosmic average at its redshift. It also has a large rotation measure ( ) and scattering timescale (τ = 3.3 ms at 1.28 GHz). Chittidi et al. perform a detailed analysis of the ultraviolet and optical emission of the host galaxy and estimate the host DM contribution to be . This work complements theirs and reports the analysis of the optical data of galaxies in the foreground of FRB 190608 in order to explore their contributions to the FRB signal. Together, the two studies delineate an observationally driven, end-to-end study of matter distribution along an FRB sightline, the first study of its kind. Combining our Keck Cosmic Web Imager (KCWI) observations and public SDSS data, we estimate the expected cosmic dispersion measure along the sightline to FRB 190608. We first estimate the contribution of hot, ionized gas in intervening virialized halos ( ). Then, using the Monte Carlo Physarum Machine methodology, we produce a 3D map of ionized gas in cosmic web filaments and compute the DM contribution from matter outside halos ( ). This implies that a greater fraction of ionized gas along this sightline is extant outside virialized halos. We also investigate whether the intervening halos can account for the large FRB rotation measure and pulse width and conclude that it is implausible. Both the pulse broadening and the large Faraday rotation likely arise from the progenitor environment or the host galaxy.

BackgroundMolecular and systems biologists are tasked with the comprehension and analysis of incredibly complex networks of biochemical interactions, called pathways, that occur within a cell. Through interviews with domain experts, we identified four common tasks that require an understanding of the causality within pathways, that is, the downstream and upstream relationships between proteins and biochemical reactions, including: visualizing downstream consequences of perturbing a protein; finding the shortest path between two proteins; detecting feedback loops within the pathway; and identifying common downstream elements from two or more proteins.ResultsWe introduce ReactionFlow, a visual analytics application for pathway analysis that emphasizes the structural and causal relationships amongst proteins, complexes, and biochemical reactions within a given pathway. To support the identified causality analysis tasks, user interactions allow an analyst to filter, cluster, and select pathway components across linked views. Animation is used to highlight the flow of activity through a pathway.ConclusionsWe evaluated ReactionFlow by providing our application to two domain experts who have significant experience with biomolecular pathways, after which we conducted a series of in-depth interviews focused on each of the four causality analysis tasks. Their feedback leads us to believe that our techniques could be useful to researchers who must be able to understand and analyze the complex nature of biological pathways. ReactionFlow is available at https://github.com/CreativeCodingLab/ReactionFlow.