Visualisation Tools

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This is a collection of many of the most notable visualisation tools produced by biologists and visualisation researchers. If you have a tool you would like to see here, please register and you will be able to add your visualisation tool to the site or contact us for more advice.

BioBlox
Molecular
Reactome
Pathway
XCluSim
Genome
Pan-Tetris
Genome
Biopython KGML module
Pathway
Comparison of 29 bacterial genomes, colouring CDS by sequence identity to a reference genome.
GenomeDiagram
Genome
MI MatrixExplorer GUI
MI-MatrixExplorer
Genome, Phylogenetics
GeneProf
Genome, Molecular
Paramorama: visual parameter optimisation for biomedical image processing
Cells and Organisms
Orchestral
Genome
Leeds Virtual Microscope
Leeds Virtual Microscope
Cell-o-pane: a cell lineage visualisation tool
Cells and Organisms, Molecular
FoldSynth
Molecular
Ensembl Genome Browser
Genome
A Tool for Comparative Functional Genomics
Pathline
Pathway
3D structure, contact map and distance map of Ribosomal Protein L30.
CMView
Molecular
PedVis
PedVis
Populations
Zomit
Zomit
Genome
TJ sunflower pictures. TreeJuxtaposer
TreeJuxtaposer
Phylogenetics
Flapjack
Flapjack
Genome
a multiscale synteny browser for comparative genomics data
MizBee
Genome
BioFabric
BioFabric
Pathway
PhyloDet
PhyloDet
Phylogenetics
BirdVis
BirdVis
Populations
GeneaQuilts
GeneaQuilts
Populations
Circos - Conservation
Circos
Genome
Stratome X
StratomeX
Genome
ePMV
ePMV
Molecular
molecular Screenshot with Autodesk Maya
Autodesk Maya
Cells and Organisms, Genome
TCA cycle showing new implmentation of the mEPN-3D notation
Miru (formerly known as BioLayout Express3D)
Cells and Organisms, Genome, Pathway
Assemble2
Assemble2
Molecular
Genome Browser
UCSC Genome Browser
Genome
Paver example
Paver
Genome, Pathway
 Example images of the application using the proposed visualization technique. The proposed rendering algorithm has been implemented in the framework Voreen. The top left illustration A is showing the 3D view with three axis-aligned slice views of our application. An enlarged version of the upper right slice view is shown in B. C shows the enlarged MIP rendering of the 3D view without the slice planes. A DVR rendering including a clipping plane is shown in D.
Voreen
Pathway
An visualization example of branching uncertainty and branching probability factor in the resulting structure. Branching uncertainty is accumulated using a Gaussian kernel centered at the probability threshold for branching and growing. It is visualized in the new branches as transition from white, no uncertainty, to red, high uncertainty. The blue color indicates how the branching probability for cases when no new branch was creat
Polymerization Illustration
Molecular
GenAMap is a visual analytics system for structured association mapping. It incorporates several different visualizations in a novel way to lead biologists to relevant SNPs and their associated traits. GenAMap enables biologists to explore the structure of the genome and trait data while exploring association strengths
GenAMap
Genome, Populations
GTB dynamic filters applied to a feature/annotation track: (1) filtered for higher scoring features and (2) filtered for featues with higher FPKM (an abundance measure).
Galaxy Track Browser
Genome
Relationship between structural microenvironments and primary sequence. (a) Neighborhood in 3D: The central Formula$C_{\alpha}$-atom is highlighted as an oversized red sphere, whereas the Formula$C_{\alpha}$-atoms for all contacting residues are plotted in dark blue. For clarity, only the sidechains of the central and one contacting residue is shown. The contact threshold radius (red transparent circle) was set to 8Å.All residue contacts defined by the cut-off are shown as thin lines.
CGAP
Molecular
An image of ligans and receptors bound together in a network
Apoptosis Graph
Cells and Organisms, Molecular
Implicit clipping plane. a) The implicit function evaluates the molecular surface (green). It takes into account only atoms that intersect the plane or lie in the half-space defined by the plane (arrows). b) Protein Pr3 is colored according to the distance to the plane, where within range Formula the final color is interpolated as it is sketched by the blue rectangles in (a).
Physioillustration: Interactive molecular illustration
Anatomy Physiology and Atlases, Molecular
The components of the enRoute visualization technique. An analyst can choose a path in the pathway view, which is then shown side-by-side with the associated experimental data.
enRoute
Pathway
(1): Insulin signaling model to illustrate the use of our visual analytics system. Edoes and vertices are colored based on the standard deviation at the steady state Formula of flux samples Formula and concentrations Formula, respectively. The time courses of fluxes and concentrations can be analyzed within lineplots (see (6) and (7)), where within (6) the lines for all fluxes that have been predicted reliably are hidden to reduce clutter. The table of mean values and standard deviations for the static para
iVUN
Pathway
Visualization of a dynamic molecular channel. The surface shows the accumulated components of one path component traced over time. The time is shown by pseudo-coloring the extension surface. Here, red represents an early time and blue a later time. The time is linearly mapped to the color map.
Dynamic Biomolecular Path Viz
Molecular
Another reconstructed Drosophila wing imaginal disc at 108 hours A
Epithelial Volume Viz
Anatomy Physiology and Atlases
A conserved operon examined using Gene-RiViT. Left(a): The RiViT view provides local context information about gene neighborhoods. Homologous genes are aligned in green. Genes shown in grey show that no homologs were found for an organism. Right(b): A zoomed view of the dot plot view shows a conserved operon for two query species. Five homologous genes are highlighted around a central selected gene. All other points are shaded grey to reduce visibility.
Gene-RiViT
Genome, Populations
Screenshot of two volumes, each using a different transfer function
Electron Microscopy Visualisation
Anatomy Physiology and Atlases
Comparison of culling efficacy between a skeleton octree with maximum depth 6 and the GPU based algorithm at 3 different distances. The scene consist of 100 neurons arranged in a vertical structure known as minicolumn. In every screenshot, the white inner square is the actual viewport; anything draw on the gray background is out of the view frustum.
Real-time Neuron Viz
Anatomy Physiology and Atlases
Table-based visualization of the MSA from the Abp2 family (PF09441) using the Clustal color-coding scheme. While the visualization of the first 10 sequences limited to the first 117 columns in the MSA provides both, focus and context (a), the visualization of the whole MSA makes the identification of features difficult Formula$(b)$
GVF Alignment Viz
Genome, Molecular
Fiber and actin visualization. (a) is the visualization of Figure 5(a). (b) is the visualization of Figure 5(b)
CAB Visualization
Anatomy Physiology and Atlases
COMBat applied to a dataset with 268 genes-annotated with in total 634 gene ontology (GO) identifiers [1]-on both the rows and the columns. Three property matrices are shown, in which each cell contains the set of GO identifiers that the corresponding genes have in common. Each cell is colored by the number of elements in the set as given by the colormap (see legend in the lower-left corner). The cell is gray if no data is associated with it. In the top-left corner, the initial, un-sorted property matrix is
COMBat
Genome
Construction of a Level 1 MoClo Module
MoClo Planner
Genome, Molecular
 Screenshot of our software after few analysis steps. Panel (A) contains the visualization widget and interaction tools, here four subnetworks are represented and our dedicated Bring & Go is used on an element. The neighborhood of that element is highlighted in all views. Panel (B) contains the exploration tree view. In that tree, the root node corresponds to the original data and each time an algorithm is applied on a node (i.e. a-sub-network), we create a son in the tree corresponding to the output of the
rNAV
Genome, Pathway
Matse
Genome, Pathway