Open source

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

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.

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.

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.

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.

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.

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.

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

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

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.