57,967 research outputs found
Dynamic Influence Networks for Rule-based Models
We introduce the Dynamic Influence Network (DIN), a novel visual analytics
technique for representing and analyzing rule-based models of protein-protein
interaction networks. Rule-based modeling has proved instrumental in developing
biological models that are concise, comprehensible, easily extensible, and that
mitigate the combinatorial complexity of multi-state and multi-component
biological molecules. Our technique visualizes the dynamics of these rules as
they evolve over time. Using the data produced by KaSim, an open source
stochastic simulator of rule-based models written in the Kappa language, DINs
provide a node-link diagram that represents the influence that each rule has on
the other rules. That is, rather than representing individual biological
components or types, we instead represent the rules about them (as nodes) and
the current influence of these rules (as links). Using our interactive DIN-Viz
software tool, researchers are able to query this dynamic network to find
meaningful patterns about biological processes, and to identify salient aspects
of complex rule-based models. To evaluate the effectiveness of our approach, we
investigate a simulation of a circadian clock model that illustrates the
oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres
CancerLinker: Explorations of Cancer Study Network
Interactive visualization tools are highly desirable to biologist and cancer
researchers to explore the complex structures, detect patterns and find out the
relationships among bio-molecules responsible for a cancer type. A pathway
contains various bio-molecules in different layers of the cell which is
responsible for specific cancer type. Researchers are highly interested in
understanding the relationships among the proteins of different pathways and
furthermore want to know how those proteins are interacting in different
pathways for various cancer types. Biologists find it useful to merge the data
of different cancer studies in a single network and see the relationships among
the different proteins which can help them detect the common proteins in cancer
studies and hence reveal the pattern of interactions of those proteins. We
introduce the CancerLinker, a visual analytic tool that helps researchers
explore cancer study interaction network. Twenty-six cancer studies are merged
to explore pathway data and bio-molecules relationships that can provide the
answers to some significant questions which are helpful in cancer research. The
CancerLinker also helps biologists explore the critical mutated proteins in
multiple cancer studies. A bubble graph is constructed to visualize common
protein based on its frequency and biological assemblies. Parallel coordinates
highlight patterns of patient profiles (obtained from cBioportal by WebAPI
services) on different attributes for a specified cancer studyComment: 7 pages, 9 figure
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps
Molecular biology knowledge can be systematically represented in a
computer-readable form as a comprehensive map of molecular interactions. There
exist a number of maps of molecular interactions containing detailed
description of various cell mechanisms. It is difficult to explore these large
maps, to comment their content and to maintain them. Though there exist several
tools addressing these problems individually, the scientific community still
lacks an environment that combines these three capabilities together. NaviCell
is a web-based environment for exploiting large maps of molecular interactions,
created in CellDesigner, allowing their easy exploration, curation and
maintenance. NaviCell combines three features: (1) efficient map browsing based
on Google Maps engine; (2) semantic zooming for viewing different levels of
details or of abstraction of the map and (3) integrated web-based blog for
collecting the community feedback. NaviCell can be easily used by experts in
the field of molecular biology for studying molecular entities of their
interest in the context of signaling pathways and cross-talks between pathways
within a global signaling network. NaviCell allows both exploration of detailed
molecular mechanisms represented on the map and a more abstract view of the map
up to a top-level modular representation. NaviCell facilitates curation,
maintenance and updating the comprehensive maps of molecular interactions in an
interactive fashion due to an imbedded blogging system. NaviCell provides an
easy way to explore large-scale maps of molecular interactions, thanks to the
Google Maps and WordPress interfaces, already familiar to many users. Semantic
zooming used for navigating geographical maps is adopted for molecular maps in
NaviCell, making any level of visualization meaningful to the user. In
addition, NaviCell provides a framework for community-based map curation.Comment: 20 pages, 5 figures, submitte
Connecting Seed Lists of Mammalian Proteins Using Steiner Trees
Multivariate experiments and genomics studies applied to mammalian cells often produce lists of genes or proteins altered under treatment/disease vs. control/normal conditions. Such lists can be identified in known protein-protein interaction networks to produce subnetworks that “connect” the genes or proteins from the lists. Such subnetworks are valuable for biologists since they can suggest regulatory mechanisms that are altered under different conditions. Often such subnetworks are overloaded with links and nodes resulting in connectivity diagrams that are illegible due to edge overlap. In this study, we attempt to address this problem by implementing an approximation to the Steiner Tree problem to connect seed lists of mammalian proteins/genes using literature-based protein-protein interaction networks. To avoid over-representation of hubs in the resultant Steiner Trees we assign a cost to Steiner Vertices based on their connectivity degree. We applied the algorithm to lists of genes commonly mutated in colorectal cancer to demonstrate the usefulness of this approach
Information visualization for DNA microarray data analysis: A critical review
Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work
Visualization of Publication Impact
Measuring scholarly impact has been a topic of much interest in recent years.
While many use the citation count as a primary indicator of a publications
impact, the quality and impact of those citations will vary. Additionally, it
is often difficult to see where a paper sits among other papers in the same
research area. Questions we wished to answer through this visualization were:
is a publication cited less than publications in the field?; is a publication
cited by high or low impact publications?; and can we visually compare the
impact of publications across a result set? In this work we address the above
questions through a new visualization of publication impact. Our technique has
been applied to the visualization of citation information in INSPIREHEP
(http://www.inspirehep.net), the largest high energy physics publication
repository
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A Single Visualization Technique for Displaying Multiple Metabolite-Phenotype Associations.
To assist with management and interpretation of human metabolomics data, which are rapidly increasing in quantity and complexity, we need better visualization tools. Using a dataset of several hundred metabolite measures profiled in a cohort of ~1500 individuals sampled from a population-based community study, we performed association analyses with eight demographic and clinical traits and outcomes. We compared frequently used existing graphical approaches with a novel 'rain plot' approach to display the results of these analyses. The 'rain plot' combines features of a raindrop plot and a conventional heatmap to convey results of multiple association analyses. A rain plot can simultaneously indicate effect size, directionality, and statistical significance of associations between metabolites and several traits. This approach enables visual comparison features of all metabolites examined with a given trait. The rain plot extends prior approaches and offers complementary information for data interpretation. Additional work is needed in data visualizations for metabolomics to assist investigators in the process of understanding and convey large-scale analysis results effectively, feasibly, and practically
Complexity and biourbanism: thermodynamical architectural and urban models integrated in modern geographic mapping
The paper was presented on 5th April 2012 by Eleni Tracada in Theoretical Currents II conference in the University of Lincoln.Abstract Vital elements in urban fabric have been often suppressed for reasons of ‘style’. Recent theories, such as Biourbanism, suggest that cities risk becoming unstable and deprived of healthy social interactions. Our paper aims at exploring the reasons for which, fractal cities, which have being conceived as symmetries and patterns, can have scientifically proven and beneficial impact on human fitness of body and mind. During the last few decades, modern urban fabric lost some very important elements, only because urban design and planning turned out to be stylistic aerial views or new landscapes of iconic technological landmarks. Biourbanism attempts to re-establish lost values and balance, not only in urban fabric, but also in reinforcing human-oriented design principles in either micro or macro scale. Human life in cities and beyond emerges during ‘connectivity’ via geometrical continuity of grids and fractals, via path connectivity among highly active nodes, via exchange/movement of people and, finally via exchange of information (networks). All these elements form a hypercomplex system of several interconnected layers of a dynamic structure, all influencing each other in a non-linear manner. Sometimes networks of communication at all levels may suffer from sudden collapse of dynamic patterns, which have been proved to be vital for a long time either to landscapes and cityscapes. We are now talking about negotiating boundaries between human activities, changes in geographic mapping and, mainly about sustainable systems to support continuous growth of communities. We are not only talking about simple lives (‘Bios’) as Urban Syntax (bio and socio-geometrical synthesis), but also about affinities between developing topographies created by roadways and trajectories and the built environment. We shall also have the opportunity to show recent applications of these theories in our postgraduate students’ work, such as a 3D model as a new method of cartography of the Island of Mauritius, with intend to highlight developments in topography and architecture through a series of historical important events and mutating socio-political and economical geographies. This model may be able to predict failures in proposed and/or activated models of expansion, which do not follow strictly morphogenetic and physiological design processes. The same kind of modelling is capable to enable recognition of ‘optimal forms’ at different feedback scales, which, through morphogenetic processes, guarantee an optimal systemic efficiency, and therefore quality of life.ADT funds, university of Derby
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