Discovering hidden relationships between renal diseases and regulated genes through 3D network visualizations

Abstract Background In a recent study, two-dimensional (2D) network layouts were used to visualize and quantitatively analyze the relationship between chronic renal diseases and regulated genes. The results revealed complex relationships between disease type, gene specificity, and gene regulation type, which led to important insights about the underlying biological pathways. Here we describe an attempt to extend our understanding of these complex relationships by reanalyzing the data using three-dimensional (3D) network layouts, displayed through 2D and 3D viewing methods. Findings The 3D network layout (displayed through the 3D viewing method) revealed that genes implicated in many diseases (non-specific genes) tended to be predominantly down-regulated, whereas genes regulated in a few diseases (disease-specific genes) tended to be up-regulated. This new global relationship was quantitatively validated through comparison to 1000 random permutations of networks of the same size and distribution. Our new finding appeared to be the result of using specific features of the 3D viewing method to analyze the 3D renal network. Conclusions The global relationship between gene regulation and gene specificity is the first clue from human studies that there exist common mechanisms across several renal diseases, which suggest hypotheses for the underlying mechanisms. Furthermore, the study suggests hypotheses for why the 3D visualization helped to make salient a new regularity that was difficult to detect in 2D. Future research that tests these hypotheses should enable a more systematic understanding of when and how to use 3D network visualizations to reveal complex regularities in biological networks.http://deepblue.lib.umich.edu/bitstream/2027.42/112972/1/13104_2010_Article_700.pd

Virtual Reality and 3D Imaging to Support Collaborative Decision Making for Adaptation of Long-Life Assets

European companies of today are involved in many stages of the product life cycle. There is a trend towards the view of their business as a complex industrial product-service system (IPSS). This trend shifts the business focus from a traditional product oriented one to a function oriented one. With the function in focus, the seller shares the responsibility of for example maintenance of the product with the buyer. As such IPSS has been praised for supporting sustainable practices. This shift in focus also promotes longevity of products and promotes life extending work on the products such as adaptation and upgrades. Staying competitive requires continuous improvement of manufacturing and services to make them more flexible and adaptive to external changes. The adaptation itself needs to be performed efficiently without disrupting ongoing operations and needs to result in an acceptable after state. Virtual planning models are a key technology to enable planning and design of the future operations in parallel with ongoing operations. This chapter presents an approach to combine digitalization and virtual reality (VR) technologies to create the next generation of virtual planning environments. Through incorporating digitalization techniques such as 3D imaging, the models will reach a new level of fidelity and realism which in turn makes them accessible to a broader group of users and stakeholders. Increased accessibility facilitates a collaborative decision making process that invites and includes cross functional teams. Through such involvement, a broader range of experts, their skills, operational and tacit knowledge can be leveraged towards better planning of the upgrade process. This promises to shorte

Visual software analytics for the build optimization of large-scale software systems

Software visualization, Visual analytics, Static analysis,