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
HaptiMOL
HaptiMOL
Molecular
xiNET
xiNET
Molecular
Aquaria
Aquaria
Molecular
RCSB PDB logo
RCSB Protein Data Bank
Molecular
cellVIEW
Molecular
MegaMol
Molecular
Summary image of applications
IBM UKSC history
Molecular
Molecular Maya molecular modeling simulation intuitive
Molecular Maya
Molecular
GraphiteLifeExplorer
GraphiteLifeExplorer
Molecular
GeneProf
Genome, Molecular
Cell-o-pane: a cell lineage visualisation tool
Cells and Organisms, Molecular
FoldSynth
Molecular
3D structure, contact map and distance map of Ribosomal Protein L30.
CMView
Molecular
Pseudoviewer
Pseudoviewer 3
Genome, Molecular
ePMV
ePMV
Molecular
Assemble2
Assemble2
Molecular
Semi-automatic Placement of 1O5W into a heterogeneous lipid bilayer
MembraneEditor
Cells and Organisms, Molecular
was used in Chimera to annotate the barrel structure of green fluorescent protein with its centroid, major axis (red arrow), and an enclosing cylinder (shown with green hoops). The BILD file green.bild was generated with the python program green.py using the coordinates in green.pdb. Gallery entry courtesy of Mike Ess, Yeast Resource Center, University of Washington.
UCSF Chimera
Molecular
Software for Interactive Analysis of Large Molecular Assemblies
MolViewer
Molecular
Example MIM drawn with MIMTool
MIMTool
Molecular
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
The MDMap system discovers the state transition graph for molecular dynamics (M D) simulations to produce visual layouts highlighting different aspects of the simulation.
MDMap
Molecular
A color mapped height field (left). Using the high contrast option for height field rendering (right), small peaks and background noise, which might otherwise be hidden, are easily seen
OmicsVis
Molecular
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
2D-schematic of the molecular surface definitions. The rolling probe traces out the SAS and the SES.
GPGPU-based Contour Surfaces
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
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
Overview of mzRepeat user interface
mzRepeat
Molecular
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
Construction of a Level 1 MoClo Module
MoClo Planner
Genome, Molecular