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ApiNATOMY

ApiNATOMY is a multi-centre effort that brings together expertise in computer science, image processing, bioengineering and medicine to manage knowledge in physiology and pathology.

ApiNATOMY is an effort to provide an interface between the physiology expert’s knowledge and all ranges of data relevant to physiology. It does this through an intuitive graphical interface for managing semantic metadata and ontologies relevant to physiology.

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Institution: UCL

HiPiler

HiPiler an interactive visualization interface for the exploration and visualization of regions-of-interest in large genome interaction matrices. Genome interaction matrices approximate the physical distance of pairs of genomic regions to each other and can contain up to 3 million rows and columns with many sparse regions. Traditional matrix aggregation or pan-and-zoom interfaces largely fail in supporting search, inspection, and comparison of local regions-of-interest (ROIs). ROIs can be defined, e.g., by sets of adjacent rows and columns, or by specific visual patterns in the matrix. ROIs are first-class objects in HiPiler, which represents them as thumbnail-like “snippets”. Snippets can be laid out automatically based on their data and meta attributes. They are linked back to the matrix and can be explored interactively. The design of HiPiler is based on a series of semi-structured interviews with 10 domain experts involved in the analysis and interpretation of genome interaction matrices. In the paper we describe six exploration tasks that are crucial for analysis of interaction matrices and demonstrate how HiPiler supports these tasks. We report on a user study with a series of data exploration sessions with domain experts to assess the usability of HiPiler as well as to demonstrate respective findings in the data.

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Institution: Harvard University

HiPiler is implemented as a web application consisting of a frontend interface for the visualizations and a server-side component that provides the data. The frontend is entirely written in JavaScript utilizing Aurelia as its application framework and Redux for fine-grained, history-aware state management. The matrix snippets are visualized with WebGL using Three.js as a middleware. Finally, HiGlass is integrated as a library for displaying the interaction matrix and genomic tracks. The server-side backend serves data to HiGlass and provides the matrix snippets. The backend is implemented in Python and uses Django as its application framework. The contact matrices are accessed through Cooler, a Python-based service library for storing and querying of Hi-C data. The front and backend are two separate applications that can be decoupled to load different data types. HiPiler is open source and available on GitHub.

SeqMonk

SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions. It's main features are:

  • Import of mapped data from mapped data (BAM/SAM/bowtie etc)
  • Creation of data groups for visualisation and analysis
  • Visualisation of mapped regions against an annotated genome.
  • Flexible quantitation of the mapped data to allow comparisons between data sets
  • Statistical analysis of data to find regions of interest
  • Creation of reports containing data and genome annotation
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Institution: Babraham Institute

HaptiMOL

The HaptiMOL suite enables interaction with protein structures using force feedback, through the use of a haptic feedback device:

  • HaptiMOL ISAS enables users to interact with the solvent accessible surface of biomolecules, by probing the surface with a sphere. 
  • HaptiMOL ENM enables users to apply forces to atoms in an elastic network model and to observe the resulting deformation. (A mouse version is also available).
  • HaptiMOL RD (coming soon) will be designed for rigid molecular docking. 
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Institution: University of East Anglia

cellVIEW

cellVIEW is a tool that provides interactive real-time visualization of large biological macromolecular scenes, for instance, depicting bacteria and viruses at atomic resolution. CellVIEW is unique and has been specifically designed to match the ambitions of structural biologist to model and interactively visualize structures comprised of several billions atoms, which corresponds to sizes of small bacterial organisms.

The main purpose of cellVIEW is currently the visualization of the static structures of these microorganisms. We are continuously working on extending cellVIEW's capabilities, for instance in order to allow the depiction of the dynamic machineries of life within these organisms, as well as including modeling capabilities for these nano scale structures.

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Institution: TU Wien

MegaMol

MegaMol™ is a visualization middleware used to visualize point-based molecular datasets.

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Institution: ​Visualization Research Center (VISUS) of the University of Stuttgart, Germany

MegaMol™ is a visualization middleware used to visualize point-based molecular datasets. This software is developed within the Collaborative Research Center 716, subproject D.3 at the Visualization Research Center (VISUS) of the University of Stuttgart and at the Computer Graphics and Visualization Group of the TU Dresden.

CooccurViewer

The project seeks to expose correlation of observations made between any pair of events in a data sequence. In this project, we present two methods for identifying interesting co-occurrences (see the manuscript for a detailed discussion).

A demo is availble of these two approaches through the project website.

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Institution: Department of Computer Sciences at the University of Wisconsin—Madison

Sequence Bundles

Sequence Bundles is a new tool for visualising and exploring sequence motifs in multiple sequence alignment (MSA) data.

It enables the discovery of data features that would otherwise remain hidden.

In Sequence Bundles, MSA sequences are visualised as continuous strings of data, which helps in preserving and exposing important residue correlations.

Use Sequence Bundles web tool to easily look at your own MSA data in a completely new way.

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Institution: Science Practice

Sequence Bundles were designed by Science Practice in collaboration with Goldman group at the EMBL-EBI. For more details visit Sequence Bundles project homepage and read our article: BMC Proceedings 2014, 8(Suppl 2):S8

Vaa3D

Vaa3D(in Chinese ‘挖三维’) is an Open Source visualization and analysis software suite created mainly by Hanchuan Peng and his team at Janelia Research Campus, HHMI and Allen Institute for Brain Science. The software performs 3D, 4D and 5D rendering and analysis of very large image data sets, especially those generated using various modern microscopy methods, and associated 3D surface objects. This software has been used in several large neuroscience initiatives and a number of applications in other domains. It has been viewed as one of the leading Open Source software suites in the related research fields. It has also been used in several other award-winning work, e.g. mapping of dragonfly neurons and large-scale visualization of cellular data.

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Institution: Janelia Research Campus, HHMI; Allen Institute for Brain Science

GeneProf

GeneProf is a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; "Next-Generation Sequencing" or NGS): Next-gen analysis for next-gen data!GeneProf makes extensive use of visualisation to explore ChIP-seq and RNA-seq data in the context of the genome as well as for data quality control, visualisation of results from individual experiments and for meta-analysis across experiments. Some of GeneProf's highlights include:                                
  • Easy-to-use web-based interface:Access your data at any time from any reasonably modern computer with a working internet connection
  • Analysis wizards make your life easy:Pre-defined, step-by-step workflows make it possible for anybody to analyse their short read data in a minimum of hands-on time).
  • Versatile modules:Advanced users and data analysis experts benefit from GeneProf's broad range of analysis modules, which can be combined freely a minimum of hands-on time
  • Integrated Analysis:Analysis of ChIP-seq and RNA-seq data in one place, plus support for the integration of other external data (e.g. from microarrays).
  • Comprehensive Resource:GeneProf provides a comprehensive resource of analyzed next-generation sequencing data. Experimental results can be easily accessed and compared and the analysis procedures employed to produce the data are fully transparent and can be accessed readily
  • Extensibility:Algorithm developers and computer programmers can develop their own modules and extend the functionality of GeneProf. Existing software can be easily wrapped and integrated in the GeneProf framework  and data from GeneProf may be used externally
                  
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Institution: Centre for Regenerative Medicine, University of Edinburgh

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