Free

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

Aquaria is a free and open-source web resource for biologists that simplifies the process of gaining insight from protein structures. For all SwissProt protein sequences, Aquaria provides a concise visual summary of all related 3D structures, and the facility to map features onto related structures (e.g., SNPs, PTMs, domains, etc.), including user-defined features.

The inherent conformation of polysaccharides possess major challenge to determine/predict their 3D structure; despite their importance in various biological processes in all the organisms. Capsular polysaccharides (K antigen) are long-chain polysaccharides that make up the capsules of encapsulated Gram-negative bacteria. They help bacteria to escape from host defense mechanisms. We have developed a manually curated 3D structures’ database for 72 K antigens from various serotypes of Escherichia coli and developed an organized repository namely EK3D, which can be accessed by www.iith.ac.in/EK3D/. Using the Cartesian coordinate’s translation method, multimers of all 72 K antigens of E. coli can be generated of any desired length and torsion angles. Subsequently, generated modelscan be downloaded and used in docking studies or as starting model for NMR structure refinement.

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.

NinjaViewer is an interactive web-based data analysis and visualisation platform designed to integrate multiple related biological datasets. The current prototype enables visual analysis and cross referencing of genomic, evolutionary and gene expression data from 21 species of mosquito and 7 species of the malaria parasite. The platform is being developed to be extensible and datatype agnostic. Several visualisation modes are already implemented including self-organising maps, hierarchical clustering and Voronoi maps, which enable analysis of tens of thousands of genes and orthologous gene groups at once. Several statistical analyses are also implemented including term enrichment and spatial correlation analyses in addition to violin and species matrix displays of cluster-specific properties. NinjaViewer is not just a viewer, it is a knowledge discovery tool that makes the most of the human-computer interaction: harnessing the user's intuitive visual processing power and the computer's ability to search data and perform statistical tests very rapidly.

Gene Expression Commons is an open platform for objective gene expression profiling of any cell type for any gene, rather than profiling of relative difference for limited number of genes between two samples. This was enabled by global-scale meta-analysis of thousands of microarray data in public repository to obtain dynamic-range and expression kinetics of every gene. Gene Expression Commons can tell what genes are actively expressed in what cell types. Now the platform has been expanded toward profiling of geneset activity. On Gene Expression Commons, users find interesting set of genes in many contexts by Gene Search or Pattern Search. By submitting such interesting set of genes as a Geneset, Gene Expression Commons automatically computes similarity to known genesets defined by Gene Ontology etc., and what cell types actively express the Geneset.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org) is an open access resource powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies. As a member of the worldwide Protein Data Bank, the RCSB PDB curates and annotates PDB data. The RCSB PDB enhances the value of the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond. PDB-101 is an educational portal (pdb101.rcsb.org) for teachers, students, and the general public that promotes exploration in the world of proteins and nucleic acids. Learning about the diverse shapes and functions of these biological macromolecules helps to understand many aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy.

GenomeCRISPR is the world’s first database for high-throughput screens using the CRISPR/Cas-9 system. Searching for a gene of interest, users are able to find data about relevant screening experiments. Moreover, GenomeCRISPR provides information about phenotypic effects that were observed after perturbation of the gene. Comprehensive visualisations displaying applied sgRNAs and their effects in genomic context complement this information. This enables users to gain an unbiased understanding of sgRNA efficiency, facilitating the selection of sgRNAs for future experiments. As GenomeCRISPR holds data from high-throughput experiments, traditional ways of representing data using data tables and static figures quickly reach their limits. To guarantee the clear and intuitive representation of large amounts of data, we rely on modern JavaScript based frameworks such as BioJavaScript or D3. Exploiting the power of these cutting edge technologies data is visualised interactively, enabling users to explore and make sense of large amounts of information.

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.

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.