Michael Walker edited Problems.tex  almost 9 years ago

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\section{These %\section{These  problems were tackled at HealthHack 2013} \subsection{A good visualisation tool for literature research!} 

\subsection{Visualising regions of interest in large graphs}  Large graphs arise commonly in bioinformatic analysis, for instance as the result of analysis. Examples include  inferring gene regulatory networks, or building graphs of and  DNA sequences for genome assembly. These graphs are generally too large to lay out and visualize interactively, having tens of thousands to potentially billions of nodes. Therefore, one team developed a visualization to interactively visualize a restricted neighbourhood of such a graph.  \subsubsection{Option 1:} 

\subsubsection{Option 2:}  Gene regulatory networks, particularly those containing indirect interactions, are complex to visualise both because of their size, and because they generally do not have a planar embedding.However it is possible to avoid both of these problem by concentrating on a subset of graph edges in a restricted neighbourhood of such a graph.  A web-based component for interactive viewing of a node and its would  be of considerable utility. For node positioning purposes, only a subset of edges that have a planar embedding would be considered, allowing simple interactive force-directed layout to be effective. Each node and edge will have its own set of properties (for example: gene information, expression level in a variety of samples, pairwise correlation of expression between genes) and ideally this information would be integrated into the visualisation of the graph neighbourhood. Similarly, clever navigation of the graph (to change the focal point, interactively updating the neighbourhood and layout) would be a desirable feature.