Actively maintained

You are here

Tool is being activelty miantained. This tool is considered complete. Bugs will be fixed, but no new features will be added 

I-PV

Today’s genome browsers and protein databanks supply vast amounts of information about proteins. The challenge is to concisely bring together this information in an interactive, easy to generate and an aesthetic format. Moreover, our goal is to make this data accessible to not only biologists/geneticists, but also medical doctors, patients and young students by using custom and intuitive interfaces that are effective. We have developed an interactive CIRCOS module called i-PV to visualize user supplied protein sequence, conservation, variation and related metadata in a live presentable layout that unites the figure generation, live presentation, customization and analysis in a single-page html application.

Release Date:
Status:
Availability:
Data type:
Techniques:
Software:
Technology:
Platform:
Requirements:

Project development

Institution: VUB, Brussels, Belgium; KUL, Leuven, Belgium; UZ Brussel, Brussels, Belgium

Mango

Current genomics visualization tools are intended for a single node environment and lack computational resources to provide interactive speeds. Data from the 1000 Genomes Project provides 1.6 terabytes of variant data and over 14 terabytes of alignment data. However, typical genomic visualizations materialize less than 10 kbp, approximately 3.3e-7% of the genome. Mango is a visualization browser that selectively materializes and organizes genomic data to provide fast in memory queries. Mango materializes data from persistent storage as the user requests different regions of the genome. This data is efficiently partitioned and organized in memory using interval trees, which enables quick range queries over genomic data.

Release Date:
Status:
Availability:
Data type:
Techniques:
Software:
Technology:
Platform:
Requirements:

Project development

Institution: UC Berkeley, CA

ClearVolume

ClearVolume is a real-time live 3D visualization library designed for high-end volumetric microscopes such as SPIM and DLSM microscopes. With ClearVolume you can see live on your screen the stacks acquired by your microscope instead of waiting for offline post-processing to give you an intuitive and comprehensive view on your data. The biologists can immediately decide whether a sample is worth imaging.ClearVolume can easily be integrated into existing Java, C/C++, Python, or LabVIEW based microscope software. It has a dedicated interface to MicroManager/OpenSpim/OpenSpin control software. ClearVolume supports multi-channels, live 3D data streaming from remote microscopes, and uses a multi-pass Fibonacci rendering algorithm that can handle large volumes. Moreover, ClearVolume is integrated into the Fiji/ImageJ2/KNIME ecosystem. You can now open your stacks with ClearVolume from within these popular frameworks for offline viewing.

Release Date:
Status:
Availability:
Data type:
Techniques:
Software:
Technology:
Platform:
Requirements:

Project development

Institution: Center for Systems Biology & Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany; Technische Universität Dresden, Dresden, Germany

EpiTools

EpiTools provides user-friendly graphical user interfaces for accurately segmenting and tracking the contours of cell membrane signals obtained from 4D confocal imaging. It is designed for a broad audience, especially biologists with no computer-science background. Quantitative data extraction is integrated into a larger bioimaging platform, Icy, to increase the visibility and usability of thetools.

Release Date:
Status:
Availability:
Data type:
Techniques:
Software:
Technology:
Platform:
Requirements:

Project development

Institution: UZH, Zurich, Switzerland; ZHAW, Zurich, Switzerland; SIB, Lausanne, Switzerland; UCL, London, United Kingdom; Kingston University, Kingston, United Kingdom; Cancer Research UK, London, United Kingdom

SynTView

SynTView is a recently published interactive multi-view genome browser for next-generation comparative microorganism genomics. The software is characterised by the presentation of syntenic organisations of microbial genomes and the visualisation of polymorphism data obtained from next generation sequencing. SynTView is built as a generic genome browser including sub-maps that hold information about genomic objects. After selecting genomes of interest, the users can explore them visually by genomic location, or directly go to specific genes by name. Several genomic maps can be stacked on top of each other. The creation of a SynTView website is very helpful in the analysis of a large number of strains, bringing together phylogeny, polymorphisms, larger variants such as indels, coverage, as well as functional annotations and strains meta-data. SynTView is designed to visualise information about polymorphism across a large number of bacterial strains. The SNP maps allow the user to navigate through polymorphism data sets. SynTView has been integrated to the Listeriomics web site, a platform for visualizing and analysing every heterogeneous Listeria "omics" dataset published to date.

Release Date:
Status:
Availability:
Data type:
Techniques:
Software:
Technology:
Platform:
Requirements:

Project development

Institution: Institut Pasteur, Paris, France

PlantGenIE

The Plant Genome Integrative Explorer is a collection of interoperable web resources for searching, visualizing and analyzing genomics and transcriptomics data for different plant species. Currently it includes dedicated web portals for enabling in-depth exploration of poplar, Norway spruce, and Arabidopsis. The PlantGenIE platform uses Chado databases and is based on the GenIE CMS (Content Management System). Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. PlantGenIE includes RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated.

Release Date:
Status:
Availability:
Data type:
Techniques:
Software:
Technology:
Platform:
Requirements:

Project development

Institution: Umeå University

Pan-Tetris

Pan-Tetris is our interactive software tool that enables the visual inspection of gene occurrences in a pan-genome table. It allows the user to modify the composition of such pan gene groups with an aggregation technique that is inspired by the famous Tetris game.

Release Date:
Status:
Availability:
Data type:
Techniques:
Software:
Technology:
Platform:
Requirements:

Project development

Institution: Universität Tübingen

BioJS

BioJS is a library of over hundred JavaScript components enabling you to visualize and process data using current web technologies.

Release Date:
Status:
Availability:
Data type:
Techniques:
Software:
Technology:
Platform:
Requirements:

Project development

Institution: BioJS

Molecular Maya

Molecular Maya (mMaya) is a free plugin for Autodesk Maya that lets users import, model and animate molecular structures. We leverage the power and flexibility of Maya while offering innovative, intuitive tools specialized for the challenges of molecular modeling and animation. mMaya is further enhanced by a series of 'kits' that expand its functionality and greatly streamline molecular modeling, animation, and simulation.

Release Date:
Status:
Availability:
Data type:
Techniques:
Software:
Technology:
Platform:
Requirements:

Project development

Institution: Digizyme Inc.

eHistology Atlas

The eHistology Atlas is a Javascript-based zoom viewer of large 2D histology images with anatomy annotations provided via point locations that can be selected to show additional imformation. The tiled images are provided by an Image Internet Protocol (IIP) server and the anatomy annotations from a mySQL database. All software is available from the matech GitHub repository https://github.com/ma-tech. The browser code is Javascript and tested on Firefox, Chrome and Safari. The eMouseAtlas resource provide access to the eHistology Atlas.

Release Date:
Status:
Availability:
Data type:
Techniques:
Software:
Technology:
Platform:
Requirements:

Project development

Institution: MRC Human Genetics Unit, University of Edinburgh

Pages