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MI-MatrixExplorer

A matrix visualization tool for exploring mutual information. It allows to take different views on the mutual information matrix by filtering, sorting, weighting, and zooming functionality. Thereby, the user can interactively navigate a huge matrix in real-time and search for e.g., patterns and unusual high or low values. A computation of the mutual information matrix for a sequence alignment in FASTA-format is possible. The respective stand-alone program computes in addition proper normalizations for a null model of neutral evolution and maps the mutual information to Z scores with respect to the null model.

The software can also be used for visual analytics of other matrix-like data, such as information obtained by DNA microarray experiments.

The package is platform-independently implemented in Java and free for academicusage under a GPL license.

This software is developed by the Computational Biology and Interactive-Graphics Systems groups at Technische Universität Darmstadt. It is provided for free use under the GNU License for Academic Use.
Download micatoMatrixVis.zip

 

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Institution: TU Darmstadt

ViPhy

ViPhy supports comparison of multiple phylogenetic trees. It relies on a set of interactive views comparing phylogenetic trees on various detail levels. The views incorporate information on similarity scores and allow highlighting of similar structures in multiple trees. They thereby reveal global and local tree similarities.

 

Video: http://www.gris.tu-darmstadt.de/research/vissearch/projects/ViPhy/Intera...
Program Files: ViPhy.zip || Version 1.3.1 (16.02.2014)

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Institution: TU Darmstadt

MulteeSum

Cells in an organism share the same genetic information in their DNA, but have very different forms and behavior because of the selective expression of subsets of their genes. The widely used approach of measuring gene expression over time from a tissue sample using techniques such as microarrays or sequencing do not provide information about the spatial position within the tissue where these genes are expressed. In contrast, we are working with biologists who use techniques that measure gene expression in every individual cell of entire fruitfly embryos over an hour of their development, and do so for multiple closely-related subspecies of Drosophila. These scientists are faced with the challenge of integrating temporal gene expression data with the spatial location of cells and, moreover, comparing this data across multiple related species. We have worked with these biologists over the past two years to develop MulteeSum, a visualization system that supports inspection and curation of data sets showing gene expression over time, in conjunction with the spatial location of the cells where the genes are expressed — it is the first tool to support comparisons across multiple such data sets. MulteeSum is part of a general and flexible framework we developed with our collaborators that is built around multiple summaries for each cell, allowing the biologists to explore the results of computations that mix spatial information, gene expression measurements over time, and data from multiple related species or organisms.  

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Pathline

Biologists pioneering the new field of comparative functional genomics attempt to infer the mechanisms of gene regulation by looking for similarities and differences of gene activity over time across multiple species. They use three kinds of data: functional data such as gene activity measurements, pathway data that represent a series of reactions within a cellular process, and phylogenetic relationship data that describe the relatedness of species. No existing visualization tool can visually encode the biologically interesting relationships between multiple pathways, multiple genes, and multiple species. We tackle the challenge of visualizing all aspects of this comparative functional genomics dataset with a new interactive tool called Pathline. In addition to the overall characterization of the problem and design of Pathline, our contributions include two new visual encoding techniques. One is a new method for linearizing metabolic pathways that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is the curvemap view, a depiction of time series data for comparison of gene activity and metabolite levels across multiple species. Pathline was developed in close collaboration with a team of genomic scientists.  

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SequenceJuxtaposer

SequenceJuxtaposer is a flexible sequence visualization tool used to explore a set of sequences. It provides an immediate view of a set of sequences that a user can navigate through with a few clicks of a mouse.

SequenceJuxtaposer is a tool for the exploration and comparison of biomolecular sequences. We use an information visualization technique called "accordion drawing'' that guarantees three key properties: context, visibility, and frame rate. We provide context through the navigation metaphor of a rubber sheet that can be smoothly stretched to show more details in the areas of focus, while the surrounding regions of context are correspondingly shrunk. Landmarks, such as user specified motifs or differences between aligned base pairs across multiple sequences, are guaranteed to be visible even if located in the shrunken areas of context. Our graphics infrastructure for progressive rendering provides immediate responsiveness to user interaction by guaranteeing that we redraw the scene at a target frame rate. Our preprocessing algorithms are subquadratic: O(nk) for k sequences of n base pairs each. All runtime rendering algorithms are sublinear in nk: they are O(v) where v is the number of items visible onscreen at once, and v \ll nk. SequenceJuxtaposer supports interaction at 20 frames per second when browsing collections of several hundred sequences that comprise over 1.7 million total base pairs. 

Any FASTA file (DNA or RNA) can be loaded into SequenceJuxtaposer.

 

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Institution: University of British Columbia

TaxonTree

TaxonTree combines dynamic query interfaces and zoomable graphics to visually accommodate highly interconnected data such as the Linnaean hierarchy for Kingdom Animalia . Because the structure of the data is visualized, the interface should be suitable both for biologists and for the general public. Names of organisms are essential to any biological database, including genomic databases, so a tool that allows effective searching and browsing of these names has wide application. 

TaxonTree allows full-text searching and browsing of a large, widely used multimedia database, University of Michigan's Animal Diversity Web via a classification of almost 200,000 animal names. At higher levels, binary branching illustrates relationships, and synapomorphies supporting those relationships are also available.  Scientific names have been compiled fromITIS, the UMMZ Bird Division, the EMBL Reptile DatabaseMammal Species of the World, and material from University of Maryland's BSCI 224 course taught by Jeff Jensen.

DoubleTree is an an application for comparing two trees using coupled interaction. DoubleTree is built on TaxonTree.

TaxonTree is built on SpaceTree, one of the HCIL Products.

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Institution: Cornell University

TreeJuxtaposer

TreeJuxtaposer is a new methodology for detailed structural comparison between two trees and provide a new nearly-linear algorithm for computing the best corresponding node from one tree to another. In addition, this utilises a new rectilinear Focus+Context technique for navigation that is well suited to the dynamic linking of side-by-side views while guaranteeing landmark visibility and constant frame rates. These three contributions result in a system delivering a fluid exploration experience that scales both in the size of the dataset and the number of pixels in the display. The design decisions for our system is based on the needs of a target audience of biologists who must understand the structural details of many phylogenetic, or evolutionary, trees. This tool is also useful in many other application domains where tree comparison is needed, ranging from network management to call graph optimization to genealogy.

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Institution: Cornell University, University of British Columbia

VIPER

VIPER (Visual Pedigree Explorer) is a tool for exploring large complex animal pedigrees and their associated genotype data. The tool combines a novel, space-efficient visualisation of the pedigree structure with an inheritance-checking algorithm. This allows users to explore the apparent errors within the genotype data in the full context of the family and pedigree structure. Ultimately, the aim is to develop an interactive software application that will allow users to identify, confirm and then remove errors from the pedigree structure and scored genotypes. 

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Institution: The Roslin Institute University of Edinburgh, School of Computing Edinburgh Napier University

TIALA

The time series alignment analysis tool Tiala allows one to align multiple time series experiments and to visually explore the aligned expression profiles. A two- and three-dimensional visualization strategy was implemented that is especially designed to enhance the display of multiple aligned time series expression profiles.

Tiala is available as a part of the microarray data analysis software Mayday. Mayday itself is open source software distributed under the terms of the GNU General Public License. It is available from http://it.inf.uni-tuebingen.de/?page_id=248.

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Institution: Center for Bioinformatics, Tubingen University of Tubingen

Part of this work has been funded by the DFG Priority Program 1335 “Scalable Visual Analytics”.

CGAP

The Contact Geometry Analysis Plugin (CGAP) (for CMView) allows incorporation of geometric orientation propensities into the process of interactive protein modeling and can be used for the generation of improved energy functions. It further supports the analysis of model quality, as it directly illustrates model consistency with known spatial propensities which, in turn, enables users to detect possible structural errors.

CGAP was developed as Plugin for CMView.

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Institution: University of Stuttgart, University of Magdeburg, Max Planck Institute for Molecular Genetics, Berlin

Future applications of the introduced visualizations include flexible docking and structure-based drug design as well as the development into an interactive modeling environment.

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