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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

ALVIS

Alvis is an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles).

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Institution: Goldman Group, EMBL-EBI; Science Practice

Reactome

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases. These include NCBI GeneEnsembl and UniProt databases, the UCSC Genome Browser, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology.

The rationale behind Reactome is to convey the rich information in the visual representations of biological pathways familiar from textbooks and articles in a detailed, computationally accessible format. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer theraputics and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include classical intermediary metabolism, signaling, innate and acquired immune function, transcriptional regulation, apoptosis and disease.

Reactome provides an intuitive website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. Visualisation of Reactome data is facilitated by the Pathway Browser, a Systems Biology Graphical Notation (SBGN)-based interface, that supports zooming, scrolling and event highlighting. It exploits the PSIQUIC web services to overlay molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntActChEMBLBioGRID and iRefIndex.

Pathway Analysis tools analyze user-supplied datasets permitting ID mapping, pathway assignment and over-representation or enrichment analysis. The curated human pathway data are used to infer orthologous events in 17 non-human species including mouse, rat, chicken, worm, fly, yeast and plant. Species Comparison tool allows users to compare predicted pathways with those of human to find reactions and pathways common to a selected species and human. Additional pathway databases based upon the Reactome data model have been created by collaborating groups for the fruit fly, the chicken, and the plant Arabidopsis.

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Institution: Ontario Institute for Cancer Research; European Bioinformatics Institute; New York University Medical Center

xiNET

xiNET is a visualization tool for exploring cross-linking/mass spectrometry results. The interactive maps of the cross-link network that it generates are a type of node-link diagram. In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures.

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Institution: Rappsilber Laboratory, The University of Edinburgh

OneZoom

OneZoom is an interactive map of the evolutionary relationships between the species on our planet. Trees with millions of tips, richly embellished with additional data, can now be easily explored within the web browser of any modern hardware with a zooming user interface similar to that used in Google Maps.

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Institution: OneZoom CIO & Imperial College London

Version 1 developed at Imperial College London. Version 2 and 3 developed at OneZoom CIO.

VisRseq

VisRseq is a framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise. Features include R apps, which offer a semi-auto generated and unified graphical user interface for computational packages in R and repositories such as Bioconductor. To address the interactivity limitation inherent in R libraries, the framework includes several native apps that provide exploration and brushing operations as well as an integrated genome browser. The apps can be chained together to create more powerful analysis workflows.

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Institution: GrUVi Lab, Simon Fraser University, Canada

panX

panX is a powerful interactive platform for pan-genome exploration. It provides multiple different views on annotated genomes and allows rapid search by gene name, diversity, duplications, etc. Strain-specific meta data is integrated into the phylogenetic tree viewer such that associations between gene presence and phenotypes can be spotted.

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Institution: Max Planck Institute for Developmental Biology, Tuebingen, Germany

iobio

iobio uses immediate visual feedback to make understanding complex genomic datasets more intuitive, and analysis more interactive.  Applications include:

  • gene.iobio.io: a web app for investigating potential disease-causing variants
  • taxonomer.iobio.io: an ultra fast metagenomics classification and analysis app
  • bam.iobio.io: an alignment data inspector tool that quickly samples bam files and visualizes a series of metrics
  • vcf.iobio.io: a variant data inspector tool that quickly samples vcf files and visualizes a series of metrics
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Institution: Marth lab, USTAR Center for Genetic Discovery, University of Utah

Phandango

Phandango is a fully interactive tool to allow visualization of population scale bacterial genomic data connected by a phylogeny. Population-scale genomic studies have been incredibly useful at understanding the evolution of bacteria and provided insights into clinically relevant information such as the spread of drug resistance and transmission patterns of infections diseases. The datasets produced by these projects often comprise hundreds of genomes and generate data such as predicted recombination regions, pan-genome contents, various metadata and, recently, genotype-phenotype association data. Currently these data are often explored using static visualizations generated by scripts. Phandango is a tool which allows real-time interactive visualization of these datasets simply by dragging and dropping files onto the browser. It has been found to be extremely useful to quickly interpret and compare the results generated from a number of published bioinformatics software such as GUBBINS, BRAT NextGen, ROARY, LS-BSR, TRADIS, PLINK and Seer, as well as user generated metadata.

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Institution: Wellcome Trust Sanger Institute, Cambridge, UK

Hi-C Explorer

Sequencing techniques that probe the 3D organization of the genome generate large amounts of data whose processing, analysis and visualization is challenging. Hi-C Explorer is a set of tools for the analysis and visualization of chromosome conformation data. Hi-C explorer facilitates the creation of contact matrices, correction of contacts, TAD detection, merging, reordering or chromosomes, conversion from different formats and detection of long-range contacts. Moreover, it allows the visualization of multiple contact matrices along with other types of data like genes, compartments, ChIP-seq coverage tracks (and in general any type of genomic scores) and long range contacts.

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Institution: Max Planck Institute of Immunobiology and Epigenetics, Germany

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