PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers

BACKGROUND: Long thought "relics" of evolution, not until recently have pseudogenes been of medical interest regarding regulation in cancer. Often, these regulatory roles are a direct by-product of their close sequence homology to protein-coding genes. Novel pseudogene-gene (PGG) functional associations can be identified through the integration of biomedical data, such as sequence homology, functional pathways, gene expression, pseudogene expression, and microRNA expression. However, not all of the information has been integrated, and almost all previous pseudogene studies relied on 1:1 pseudogene-parent gene relationships without leveraging other homologous genes/pseudogenes. RESULTS: We produce PGG families that expand beyond the current 1:1 paradigm. First, we construct expansive PGG databases by (i) CUDAlign graphics processing unit (GPU) accelerated local alignment of all pseudogenes to gene families (totaling 1.6 billion individual local alignments and >40,000 GPU hours) and (ii) BLAST-based assignment of pseudogenes to gene families. Second, we create an open-source web application (PseudoFuN [Pseudogene Functional Networks]) to search for integrative functional relationships of sequence homology, microRNA expression, gene expression, pseudogene expression, and gene ontology. We produce four "flavors" of CUDAlign-based databases (>462,000,000 PGG pairwise alignments and 133,770 PGG families) that can be queried and downloaded using PseudoFuN. These databases are consistent with previous 1:1 PGG annotation and also are much more powerful including millions of de novo PGG associations. For example, we find multiple known (e.g., miR-20a-PTEN-PTENP1) and novel (e.g., miR-375-SOX15-PPP4R1L) microRNA-gene-pseudogene associations in prostate cancer. PseudoFuN provides a "one stop shop" for identifying and visualizing thousands of potential regulatory relationships related to pseudogenes in The Cancer Genome Atlas cancers. CONCLUSIONS: Thousands of new PGG associations can be explored in the context of microRNA-gene-pseudogene co-expression and differential expression with a simple-to-use online tool by bioinformaticians and oncologists alike

MolSieve: A Progressive Visual Analytics System for Molecular Dynamics Simulations

Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's evolution is key to selecting the best candidates for new drugs, materials for manufacturing, and countless other practical applications. With today's technology, these simulations can encompass millions of unit transitions between discrete molecular structures, spanning up to several milliseconds of real time. Attempting to perform a brute-force analysis with data-sets of this size is not only computationally impractical, but would not shed light on the physically-relevant features of the data. Moreover, there is a need to analyze simulation ensembles in order to compare similar processes in differing environments. These problems call for an approach that is analytically transparent, computationally efficient, and flexible enough to handle the variety found in materials based research. In order to address these problems, we introduce MolSieve, a progressive visual analytics system that enables the comparison of multiple long-duration simulations. Using MolSieve, analysts are able to quickly identify and compare regions of interest within immense simulations through its combination of control charts, data-reduction techniques, and highly informative visual components. A simple programming interface is provided which allows experts to fit MolSieve to their needs. To demonstrate the efficacy of our approach, we present two case studies of MolSieve and report on findings from domain collaborators.Comment: Updated references to GPCC

Visualisering av geografiske data som varierer over tid

This task creates a web application that visualizes data that varies geograph- ically and over time on a digital map. The development used the PERN as a technology stack and was implemented accordingly. The application uses Mapbox as a digital map, which also has great navigation options in terms of usability. The visualization dealt with data from Statistics Norway and MET which gave real values that were visualized over Norway. Several principles from both User-Centered Design and Visualization Pipeline were practiced.This task creates a web application that visualizes data that varies geograph- ically and over time on a digital map. The development used the PERN as a technology stack and was implemented accordingly. The application uses Mapbox as a digital map, which also has great navigation options in terms of usability. The visualization dealt with data from Statistics Norway and MET which gave real values that were visualized over Norway. Several principles from both User-Centered Design and Visualization Pipeline were practiced

Visualisering av geografiske data som varierer over tid

This task creates a web application that visualizes data that varies geograph- ically and over time on a digital map. The development used the PERN as a technology stack and was implemented accordingly. The application uses Mapbox as a digital map, which also has great navigation options in terms of usability. The visualization dealt with data from Statistics Norway and MET which gave real values that were visualized over Norway. Several principles from both User-Centered Design and Visualization Pipeline were practiced.This task creates a web application that visualizes data that varies geograph- ically and over time on a digital map. The development used the PERN as a technology stack and was implemented accordingly. The application uses Mapbox as a digital map, which also has great navigation options in terms of usability. The visualization dealt with data from Statistics Norway and MET which gave real values that were visualized over Norway. Several principles from both User-Centered Design and Visualization Pipeline were practiced

Visualisering av geografiske data som varierer over tid

This task creates a web application that visualizes data that varies geograph- ically and over time on a digital map. The development used the PERN as a technology stack and was implemented accordingly. The application uses Mapbox as a digital map, which also has great navigation options in terms of usability. The visualization dealt with data from Statistics Norway and MET which gave real values that were visualized over Norway. Several principles from both User-Centered Design and Visualization Pipeline were practiced.This task creates a web application that visualizes data that varies geograph- ically and over time on a digital map. The development used the PERN as a technology stack and was implemented accordingly. The application uses Mapbox as a digital map, which also has great navigation options in terms of usability. The visualization dealt with data from Statistics Norway and MET which gave real values that were visualized over Norway. Several principles from both User-Centered Design and Visualization Pipeline were practiced

ArcBASINS: a GIS model for the BASINS database

Center for Research in Water Resource

Preserving Command Line Workflow for a Package Management System Using ASCII DAG Visualization

Package managers provide ease of access to applications by removing the time-consuming and sometimes completely prohibitive barrier of successfully building, installing, and maintaining the software for a system. A package dependency contains dependencies between all packages required to build and run the target software. Package management system developers, package maintainers, and users may consult the dependency graph when a simple listing is insufficient for their analyses. However, users working in a remote command line environment must disrupt their workflow to visualize dependency graphs in graphical programs, possibly needing to move files between devices or incur forwarding lag. Such is the case for users of Spack, an open source package management system originally developed to ease the complex builds required by supercomputing environments. To preserve the command line workflow of Spack, we develop an interactive ASCII visualization for its dependency graphs. Through interviews with Spack maintainers, we identify user goals and corresponding visual tasks for dependency graphs. We evaluate the use of our visualization through a command line-centered study, comparing it to the system's two existing approaches. We observe that despite the limitations of the ASCII representation, our visualization is preferred by participants when approached from a command line interface workflow.U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344, LLNL-JRNL-746358]This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

The matrix revisited: A critical assessment of virtual reality technologies for modeling, simulation, and training

A convergence of affordable hardware, current events, and decades of research have advanced virtual reality (VR) from the research lab into the commercial marketplace. Since its inception in the 1960s, and over the next three decades, the technology was portrayed as a rarely used, high-end novelty for special applications. Despite the high cost, applications have expanded into defense, education, manufacturing, and medicine. The promise of VR for entertainment arose in the early 1990\u27s and by 2016 several consumer VR platforms were released. With VR now accessible in the home and the isolationist lifestyle adopted due to the COVID-19 global pandemic, VR is now viewed as a potential tool to enhance remote education. Drawing upon over 17 years of experience across numerous VR applications, this dissertation examines the optimal use of VR technologies in the areas of visualization, simulation, training, education, art, and entertainment. It will be demonstrated that VR is well suited for education and training applications, with modest advantages in simulation. Using this context, the case is made that VR can play a pivotal role in the future of education and training in a globally connected world

Visualization of graphs and trees for software analysis

A software architecture is an abstraction of a software system, which is indispensable for many software engineering tasks. Unfortunately, in many cases information pertaining to the software architecture is not available, outdated, or inappropriate for the task at hand. The RECONSTRUCTOR project focuses on software architecture reconstruction, i.e., obtaining architectural information from an existing system. Our research, which is part of RECONSTRUCTOR, focuses on interactive visualization and tries to answer the following question: How can users be enabled to understand the large amounts of information relevant for program understanding using visual representations? To answer this question, we have iteratively developed a number of techniques for visualizing software systems. A large number of these cases consists of hierarchically organized data, combined with adjacency relations. Examples are function calls within a hierarchically organized software system and correspondence relations between two different versions of a hierarchically organized software system. Hierarchical Edge Bundles (HEBs) are used to visualize adjacency relations in hierarchically organized data, such as the aforementioned function calls within a software system. HEBs significantly reduce visual clutter by visually bundling relations together. Massive Sequence Views (MSVs) are used in conjunction with HEBs to enable analysis of sequences of relations, such as function-call traces. HEBs are furthermore used to visually compare hierarchically organized data, e.g., two different versions of a software system. HEBs visually emphasize splits, joins, and relocations of subhierarchies and provide for interactive selection of sets of relations. Since HEBs require a hierarchy to perform the bundling, we present Force-Directed Edge Bundles (FDEBs) as an alternative to visually bundle relations together in the absence of a hierarchical component. FDEBs use a self-organizing approach to bundling in which edges are modeled as flexible springs that can attract each other. As a result, visual clutter is reduced and high-level edge patterns are better visible. Finally, in all these methods, a clear depiction of the direction of edges is important. We have therefore performed a separate study in which we evaluated ten representations (including the standard arrow) for depicting directed edges in a controlled user study