Active additional development

BioViz Studio from Dark Star Systems is a web-based tool to help scientists create beautiful short videos of proteins and other molecules. It's simple and quick; new users can create a video from scratch in twenty minutes. It includes professionally designed backgrounds and cinematic camera moves. Final renders are done automatically in the cloud with Blender and no graphics experience is needed.

It is aimed at structural biologists and biochemists with PDB or similar structures. We at Dark Star Systems care deeply about science, truth, and the idea that scientists have important stories to tell. We want to help them do that in a way that brings art and beauty to them, to make them more compelling to all kinds of audiences.

HiGlass is a web-based tool for visually exploring and comparing 2D genomic contact matrices, 1D genomic tracks, or other datasets too large to view at once. It features synchronized navigation of multiple views as well as continuous zooming and panning for navigation across genomic loci and resolutions. It supports visual comparison of genomic (e.g., Hi-C, ChIP-seq, or bed annotations) and other data (e.g., geographic maps, gigapixel images, or abstract 1D and 2D sequential data) from different experimental conditions and can be used to efficiently identify salient outcomes of experimental perturbations, generate new hypotheses, and share the results with the community.

Project website: higlass.io

Source code: github.com/higlass/higlass

Publication: Kerpedjiev et al. (2018) HiGlass: Web-based visual comparison and exploration of genome interaction maps. Genome Biology, 19:125.

PhenoPlot is a glyph-based visualization method of multidimensional image-based phenotypic data. It facilitates data interpretation and analysis by providing a pictorial quantitative representation of the data. It can be used to represent cell image data including shape measurements of the cell or nuclei, texture, intensity, and protrusions. It can also represent tumor data such as tumor size, grade and cellularity. Currently, PhenoPlot offers 21 elements that the user can assign to their measurements of choice.

PhenoPlot is a free and open source Matlab toolbox that comes with a graphical user interface (GUI).

karyoploteR is an R/Bioconductor package to plot genomic data along the genome. It implements a genomic coordinates version of most R graphical primitives facilitating the creation of rich and powerful genome visualizations. Since karyoploteR does not try to "understand" the data it is plotting, it can plot almost anything, any data type,  as long as it is positioned on the genome. In addition, while the package includes data for some of the most used genomes, it can automatically download genome information from external sources and accepts custom genomes directly from the user, thus making it possible to "plot anything on any genome". karyoploteR covers the whole zoom range, going from single base to whole genome changing a single parameter in a function call.  There are additional higher level functions to plot specific types of data, for example one to compute and plot the density of features along the genome, another to plot the coverage level directly from a BAM file or a third one to plot links between genomic regions. 

To know more about the functionality of karyoploteR you can check the package vignette or head to the karyoploteR tutorial page, were you will find a step-by-step tutorial on how to use the package as well as some more involved examples with detailed explanations including how to use karyoploteR to plot different standard data types: RNA-seq differential expression results, SNP-array data, somatic mutation distance using rainfall plots.

Bioconductor landing page: http://bioconductor.org/packages/karyoploteR/

Tuorial and Examples: https://bernatgel.github.io/karyoploter_tutorial/

Source code at github: https://github.com/bernatgel/karyoploteR

Goldsmiths and Imperial announce the launch of BioBlox2D and BioBlox3D molecular docking games.
 
BioBlox2D is free to download from the App store and Google Play.
 
BioBlox2D turns the science of how proteins fit together with smaller molecules, such as medicines and vitamins, into a Tetris-style puzzle game and quiz.

BioBlox3D is a free and fully accessible web game and is playable on the website aimed at the specialist user enabling them to dock 3D proteins.

Best Regards,
Mike, Frederic and William.

Project Leads
Prof Mike Sternberg. Imperial College.
Prof Frederic Leymarie. Goldsmiths.
Prof William Latham. Goldsmiths.
Email: info@bioblox.org

ApiNATOMY is a multi-centre effort that brings together expertise in computer science, image processing, bioengineering and medicine to manage knowledge in physiology and pathology.

ApiNATOMY is an effort to provide an interface between the physiology expert’s knowledge and all ranges of data relevant to physiology. It does this through an intuitive graphical interface for managing semantic metadata and ontologies relevant to physiology.

HiPiler an interactive visualization interface for the exploration and visualization of regions-of-interest in large genome interaction matrices. Genome interaction matrices approximate the physical distance of pairs of genomic regions to each other and can contain up to 3 million rows and columns with many sparse regions. Traditional matrix aggregation or pan-and-zoom interfaces largely fail in supporting search, inspection, and comparison of local regions-of-interest (ROIs). ROIs can be defined, e.g., by sets of adjacent rows and columns, or by specific visual patterns in the matrix. ROIs are first-class objects in HiPiler, which represents them as thumbnail-like “snippets”. Snippets can be laid out automatically based on their data and meta attributes. They are linked back to the matrix and can be explored interactively. The design of HiPiler is based on a series of semi-structured interviews with 10 domain experts involved in the analysis and interpretation of genome interaction matrices. In the paper we describe six exploration tasks that are crucial for analysis of interaction matrices and demonstrate how HiPiler supports these tasks. We report on a user study with a series of data exploration sessions with domain experts to assess the usability of HiPiler as well as to demonstrate respective findings in the data.

SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions. It's main features are:

• Import of mapped data from mapped data (BAM/SAM/bowtie etc)
• Creation of data groups for visualisation and analysis
• Visualisation of mapped regions against an annotated genome.
• Flexible quantitation of the mapped data to allow comparisons between data sets
• Statistical analysis of data to find regions of interest
• Creation of reports containing data and genome annotation

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. 

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.