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SATORI

SATORI is an ontology-guided visual exploration system for data repositories, which combines powerful metadata search with a treemap and a node-link diagram that visualize the repository structure, provide context to retrieved data sets, and serve as an interface to drive semantic querying and exploration, and thereby support the information foraging loop. SATORI is  web-based, open-source, and integrated  in  the Refinery-Platform—an application for biomedical data management, analysis, and visualization.

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Institution: Harvard Medical School

Why?  Biomedical repositories are growing rapidly and provide scientists with tremendous opportunities to re-use data. In order to exploit published data sets efficiently, it is crucial to understand the content of repositories and to discover data relevant to a question of interest. These are challenging tasks, as most repositories currently only support finding data sets through  text-based search of metadata and in some cases also through metadata-based browsing. To address this, we conducted a task analysis through semi-structured interviews with 8 PhD-level domain experts and identified 3 distinct user roles.

What?  Biological data sets consists of experimental data and metadata describing the studies, properties of the analyzed biological samples, and attributes of individual data files. In this context, a data set is a collection of data files, along with the metadata. Additionally, metadata is partially annotated with ontology terms. An ontology describes a certain domain (e.g. human anatomy), defines controlled vocabularies for its concepts and relationships (e.g., kidney and is-part-of) and relates concepts with each other (e.g., nephron is-part-of kidney). By means of ontology terms, sets of annotated data sets can be classified hierarchically. SATORI extracts free-text and ontologically annotated metadata. The free-text metadata is indexed in a text-based search system. Additionally, data set-related ontology classes are parsed and visualized to provide  semantic context to data sets. Since SATORI's goal is to support exploration rather than to visualize ontologies themselves, only a relevant subtree of the ontologies is shown, i.e., effectively enforcing a strict containment hierarchy.

How?  SATORI is composed of two main interlinked views: the data set view and the exploration view. In the treemap an ontology term is illustrated by a rectangle. The area of the rectangle visualizes the size of the term relative to its sibling terms and the color indicates the distance to the farthest child term. The farther away this child term is, the darker is the color. The node-link diagram represents ontology terms as nodes and links shown parent and child terms. Additionally, the diagram visualizes the precision and recall for each term given the currently retrieved data sets. In this context, precision is useful to understand how frequently a term is used for annotation in the retrieved set of data sets and recall provides a notion of information scent by indicating if there are more data sets annotated with this term. Finally, the exploration view acts as a semantic query interface and lets users filter down collections of data sets via ontology term-based Boolean queries.

InterMine

InterMine is an open source data warehouse built specifically for the integration and analysis of complex biological data. Developed by the Micklem lab at the University of Cambridge, InterMine enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding your own data. InterMine includes an attractive, user-friendly web interface that works 'out of the box' and can be easily customised for your specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to your data.

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Institution: Micklem Lab, University of Cambridge

MARender

MARender is a JavaScript 3D rendering system based on three.js (http://threejs.org/).

The rendering system is centred around a JavaScript class MARenderer and aimed at simple web-based visualisation of 3D bio-medical datasets, with particular emphasis on anatomy and mapped spatial data (eg gene expression).

Typical uses combine surface, section and point cloud renderings. Surfaces and point clouds are most readily read from VTK format files using the modified VTK loader https://github.com/ma-tech/three.js/blob/master/examples/js/loaders/MAVTKLoader.js and sections either from static images or from an IIP3D server (https://github.com/ma-tech/WlzIIPSrv).

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Institution: MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh

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

Supramap

Supramap is a completely new method of generating and sharing knowledge about evolution and biogeography.  A supramap gives people a quick and easy way to integrate genotypic and phenotypic data in a geospatial context. When viewed in a virtual globe (e.g. Google Earth or NASA WorldWind), the user has an interactive map of the spread of various lineages of organisms (e.g. strains of pathogens) over the earth.

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Institution: UNC Charlotte

FigTree

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST.

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Institution: The University of Edinburgh

Epiviz

Visualization is an integral aspect of genomics data analysis. Algorithmic-statistical analysis and interactive visualization are most effective when used iteratively. Epiviz, a web-based genome browser, and the Epivizr Bioconductor package allow interactive, extensible and reproducible visualization within a state-of-the-art data-analysis platform.

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Institution: University of Maryland, USA

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

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