Assessing 2D visual encoding of 3D spatial connectivity.

Introduction: When visualizing complex data, the layout method chosen can greatly affect the ability to identify outliers, spot incorrect modeling assumptions, or recognize unexpected patterns. Additionally, visual layout can play a crucial role in communicating results to peers. Methods: In this paper, we compared the effectiveness of three visual layouts-the adjacency matrix, a half-matrix layout, and a circular layout-for visualizing spatial connectivity data, e.g., contacts derived from chromatin conformation capture experiments. To assess these visual layouts, we conducted a study comprising 150 participants from Amazon's Mechanical Turk, as well as a second expert study comprising 30 biomedical research scientists. Results: The Mechanical Turk study found that the circular layout was the most accurate and intuitive, while the expert study found that the circular and half-matrix layouts were more accurate than the matrix layout. Discussion: We concluded that the circular layout may be a good default choice for visualizing smaller datasets with relatively few spatial contacts, while, for larger datasets, the half- matrix layout may be a better choice. Our results also demonstrated how crowdsourcing methods could be used to determine which visual layouts are best for addressing specific data challenges in bioinformatics.

Temporal ordering of omics and multiomic events inferred from time-series data.

Temporal changes in omics events can now be routinely measured; however, current analysis methods are often inadequate, especially for multiomics experiments. We report a novel analysis method that can infer event ordering at better temporal resolution than the experiment, and integrates omic events into two concise visualizations (event maps and sparklines). Testing our method gave results well-correlated with prior knowledge and indicated it streamlines analysis of time-series data.

SnapShot: S-Phase Entry and Exit.

S-phase entry and exit are regulated by hundreds of protein complexes that assemble "just in time," orchestrated by a multitude of distinct events. To help understand their interplay, we have created a tailored visualization based on the Minardo layout, highlighting over 80 essential events. This complements our earlier visualization of M-phase, and both can be displayed together, giving a comprehensive overview of the events regulating the cell division cycle. To view this SnapShot, open or download the PDF.

No single, stable 3D representation can explain pointing biases in a spatial updating task.

People are able to keep track of objects as they navigate through space, even when objects are out of sight. This requires some kind of representation of the scene and of the observer's location but the form this might take is debated. We tested the accuracy and reliability of observers' estimates of the visual direction of previously-viewed targets. Participants viewed four objects from one location, with binocular vision and small head movements then, without any further sight of the targets, they walked to another location and pointed towards them. All conditions were tested in an immersive virtual environment and some were also carried out in a real scene. Participants made large, consistent pointing errors that are poorly explained by any stable 3D representation. Any explanation based on a 3D representation would have to posit a different layout of the remembered scene depending on the orientation of the obscuring wall at the moment the participant points. Our data show that the mechanisms for updating visual direction of unseen targets are not based on a stable 3D model of the scene, even a distorted one.

A benchmark dataset for analyzing and visualizing the dynamic epiproteome.

In this paper, we present a benchmark dataset to evaluate the currently available analysis methods and visualizations for epiproteomic data. The benchmark dataset is a subset of a high-throughput time-series study of phosphoevents occurring upon insulin stimulation. Our dataset is provided in multiple formats for use with four currently available tools. We also provide a file containing the kinase assignments for the sites, as well as a simple kappa model on phosphorylation changes in insulin signalling. A detailed description of the tools, their analysis methods, and the visualizations generated using the input files described here, are discussed in detail in the accompanying review titled "Visualization and analysis of epiproteome dynamics" [1].

Visualization and Analysis of Epiproteome Dynamics.

The epiproteome describes the set of all post-translational modifications (PTMs) made to the proteins comprising a cell or organism. The extent of the epiproteome is still largely unknown; however, advances in experimental techniques are beginning to produce a deluge of data, tracking dynamic changes to the epiproteome in response to cellular stimuli. These data have potential to revolutionize our understanding of biology and disease. This review covers a range of recent visualization methods and tools developed specifically for dynamic epiproteome data sets. These methods have been designed primarily for data sets on phosphorylation, as this the most studied PTM; however, most of these methods are also applicable to other types of PTMs. Unfortunately, the currently available methods are often inadequate for existing data sets; thus, realizing the potential buried in epiproteome data sets will require new, tailored bioinformatics methods that will help researchers analyze, visualize, and interactively explore these complex data sets.

SnapShot: Phosphoregulation of Mitosis.

During mitosis, a cell divides its duplicated genome into two identical daughter cells. This process must occur without errors to prevent proliferative diseases (e.g., cancer). A key mechanism controlling mitosis is the precise timing of more than 32,000 phosphorylation and dephosphorylation events by a network of kinases and counterbalancing phosphatases. The identity, magnitude, and temporal regulation of these events have emerged recently, largely from advances in mass spectrometry. Here, we show phosphoevents currently believed to be key regulators of mitosis. For an animated version of this SnapShot, please see http://www.cell.com/cell/enhanced/odonoghue2.

Bone fibrillogenesis and mineralization: quantitative analysis and implications for tissue elasticity.

Data from bone drying, demineralization, and deorganification tests, collected over a time span of more than 80 years, evidence a myriad of different chemical compositions of different bone materials. However, careful analysis of the data, as to extract the chemical concentrations of hydroxyapatite, of water, and of organic material (mainly collagen) in the extracellular bone matrix, reveals an astonishing fact: it appears that there exists a unique bilinear relationship between organic concentration and mineral concentration, across different species, organs, and age groups, from early childhood to old age: During organ growth, the mineral concentration increases linearly with the organic concentration (which increases during fibrillogenesis), while from adulthood on, further increase of the mineral concentration is accompanied by a decrease in organic concentration. These relationships imply unique mass density-concentration laws for fibrillogenesis and mineralization, which - in combination with micromechanical models - deliver 'universal' mass density-elasticity relationships in extracellular bone matrix-valid across different species, organs, and ages. They turn out as quantitative reflections of the well-instrumented interplay of osteoblasts, osteoclasts, osteocytes, and their precursors, controlling, in a fine-tuned fashion, the chemical genesis and continuous transformation of the extracellular bone matrix. Consideration of the aforementioned rules may strongly affect the potential success of tissue engineering strategies, in particular when translating, via micromechanics, the aforementioned growth and mineralization characteristics into tissue-specific elastic properties.