Table 1: List of tools used for temporal biological data visualization. The Comments column highlights distinctive features of the respective software.
Name
Platform
Description
Comments
URL
Win, Linux
Simulation and visualization of processes in the area of
Can handle large macromolecule systems. Provides
http://accelrys.com/products/dis
molecular dynamics, molecular and quantum mechanics;
stereo graphics and hardware acceleration support.
covery-studio/
pharmacophore
Includes a variety of charts, histograms, heat maps
Molecular level
Discovery Studio
ICM-Pro
Jmol
MacroModel
Win, Linux, Mac
Web-based
Win, Linux, Mac
modelling;
structure-based
design;
docking. Provided by Accelrys Software Inc.
etc.
Part of the molsoft software suite, visualizes folding
Enables structural database search. Includes a
http://www.molsoft.com/icm_pro
conformations and molecular dynamics simulation results.
variety of chemistry tools.
.html
Visualizes
Can visualize any structures or trajectories in the web
http://jmol.sourceforge.net/
chemical
structures,
including
molecular
dynamics trajectories in 3D
browser.
Force field-based molecular modeller and visualizer.
The
Developed by Schrödinger, LLC.
exploration of a wide range of conformations.
force
field-based
calculations
enable
the
http://www.schrodinger.com/pro
ductpage/14/11/
Different force fields can be selected.
PyMOL
Sirius
Win, Linux, Mac
Win, Linux, Mac
Visualizes molecular dynamics and other protein structure
Supports scripting and module plug-in, which confers
features
a lot of flexibility in the analysis.
Visualization of molecular dynamics trajectories, with
Supports
multi-file
simulations
and
real-time
http://www.pymol.org/
http://www.ngbw.org/sirius/
UCSF Chimera
Win, Linux, Mac
possibility to export trajectories as video
secondary structure and RMSD calculations.
Visualization and analysis of molecular structures and
Highly extensible platform; besides protein structures
http://www.cgl.ucsf.edu/chimera
related data, including trajectories and conformational
it also integrates EM density maps and SAXS profiles.
/
Visualization of macromolecular structures, including
The most popular tool for visualizing trajectories. Can
http://tinyurl.com/VMD-viewer/
dynamic simulations
act as graphical front end for external molecular
ensembles
VMD
Win, Linux, Mac
dynamics programs.
Yasara
Win, Linux, Mac
Molecular graphics application that provides, among other
Provides fast molecular dynamics algorithms and
things, fast molecular dynamics simulations, including
specialized membrane protein dynamics simulations.
http://www.yasara.org/
membrane protein simulations and visualization.
Gene level
BiGGEsTS
Win, Linux, Mac
Biclustering visualization of gene expression time series
Extracts subsets of genes that exhibit coherent
http://tinyurl.com/BIGGEsTS/
expression profiles. Supports filtering, sorting and
gene ontology annotation.
GATE
Win, Linux, Mac
Visualization of time series gene expression
Visualizes clusters of gene expression in a hexagonal
http://tinyurl.com/GATEsoft/
pattern and expression changes with time. Networks
can be overlaid on the grid.
STEM
Win, Linux, Mac
Short time series gene expression visualization
Produces plots corresponding to clusters of time
expression profiles for genes.
http://gene.ml.cmu.edu/stem/
TimeSearcher
Win
Time series analysis, applicable to biology and other
Facilitates interactive query and exploration of time
fields
series data through simultaneous display of different
http://tinyurl.com/timesearcher/
types of plots. Supports long time series (>10000
points).
Network level
Arena3D
Win, Linux, Mac
Time course visualization on different biological layers
Enables linking of different levels of biological
http://arena3d.org/
information (gene, protein, disease etc.) through the
use of a multi-layered layout.
BioTapestry
Win, Linux, Mac,
Time series visualization for gene regulatory networks
web-based
CellDesigner
Win, Linux, Mac Gene regulatory and biochemical networks editor and
Win, Linux, Mac
http://www.biotapestry.org/
regulatory networks.
simulator
Copasi
Allows interactive building and simulation of gene
Flexible framework for pathway design, import and
http://www.celldesigner.org/
simulation.
Simulation and analysis of biochemical network dynamics
Specialized simulator of biochemical reaction systems
(using
ODEs
and stochastic
simulations),
http://www.copasi.org/
with
extensive support for parameter estimation and
optimization.
Dizzy
GENeVis
Win, Linux, Mac
Win, Linux, Mac
Chemical kinetics simulation software
Visualization
of
genome
expression
Supports
and
dynamics in regulatory and metabolic networks
network
different
stochastic
algorithms.
Uses
http://magnet.systemsbiology.n
Cytoscape for model visualization.
et/software/Dizzy/
Enables parallel visualization of changes in gene
http://tinyurl.com/GENeVis/
regulatory and metabolic networks.
iPath
web-based
Interactive visualization of metabolic pathways
Can map dynamics and other properties customized
http://pathways.embl.de/
by the user onto metabolic and regulatory pathways in
a full network context.
JigCell
Win, Linux, Mac
Pathway model builder and simulator
Enables model comparison through quantitative
http://jigcell.cs.vt.edu/
analysis of multiple datasets.
MODAM
MultiColored Nodes
SpotXplore
Win, Linux, Mac
Win, Linux, Mac
Win, Linux, Mac
Cytoscape
plugin,
visualizes
fluxes
in
multi-omics
Integrates data from different omics experiments. Can
https://sites.google.com/site/mo
integrated networks
visualize metabolic fluxes through the network.
damplugin/
Cytoscape plugin, can visualize time-course data in pie
Maps time course profiles to network nodes as
http://sourceforge.net/projects/
chart slices
differently colored slices of a pie chart.
multicolor/
Cytoscape plugin, embeds bar charts of time course
Maps time series profiles of genes in a bar chart
http://www.win.tue.nl/~mwesten
expression within the node corresponding to the gene
representation within nodes that also captures
b/spotxplore/
up/downregulation.
TVNViewer
VANTED
Web-based
Win,
Linux,
Mac,
web-
Visualization of spatiotemporal changes in network
Captures connectivity dynamics in a network by
http://tinyurl.com/tvnview/
connectivity
rewiring its links correspondingly at every time point.
Visualization of multimodal experimental data in a
Enables pathway editing and time series analysis in
http://vanted.ipk-
temporal and pathway context
the context of different genotypes and phenotypes.
gatersleben.de/
Cytoscape plug-in, visualizes changes in gene expression
Visualizes expression changes through updates in
http://tinyurl.com/VistaClara/
by animating color changes in the network
network node colors, in parallel with a heat map.
based
VistaClara
Win, Linux, Mac
WilmaScope
Win, Linux, Mac
Metabolic time course visualization (and not only)
Specializes in metabolic flux visualization through
http://wilma.sourceforge.net/
unfolding of pathway evolution in 3D.
Cell level
E-Cell
Mac
Whole-cell simulation environment
Incorporates different numerical methods for the
http://ecell3d.iab.keio.ac.jp/
modelling, simulation and analysis of biological
processes in the cell. Uses advanced 3D graphics to
visualize dynamic behavior.
STSE
Win, Linux, Mac
Spatiotemporal simulation environment from microscopy
Digitizes,
models
and
analyzes
spatiotemporal
imaging data
distribution of molecules, as derived from acquired
http://www.stse-software.org/
microscopy images.
VCell
Win, Mac, web-
Physical modelling and analysis of cellular processes
Models the topology, molecular characteristics and
based
interaction
parameters
of
a
biological
http://www.nrcam.uchc.edu/
system.
Generates differential equations automatically for
simulation and analysis.
Illoura
Win, Linux, Mac
In silico visualization of 3D cellular organization
Uses
ontologies
and semantic
relationships to
http://www.imb.uq.edu.au/tools
represent cellular objects.
Evolutionary level
Circos
Win, Linux, Mac
Genome
visualizer
for
genome evolution tracing
comparative
genomics
and
Uses a circular display with associations between
genomic regions depicted as links. A wide variety of
http://circos.ca/
bar charts, histograms and other plots can be added
to convey statistics and evolutionary relationships.
ClustalX
Win, Linux, Mac
Multiple alignment visualizer
Versatile and flexible alignment visualizer that allows
http://www.clustal.org/clustal2/
changing the alignment order, highlighting conserved
features, analyzing the quality of the alignment,
displaying phylogenetic trees etc.
Dendroscope
Win, Linux, Mac
Visualizes phylogenetic trees and rooted networks
Allows browsing of phylogenetic trees with hundreds
http://ab.inf.uni-
of thousands of taxa, offering different views and
tuebingen.de/software/dendros
manipulation options (rerooting, rotating, annotation
cope/
etc.).
iTOL
web-based
Phylogeny tree constructor and annotator
Visualizes
phylogeny
dendograms
in
classical,
http://itol.embl.de/
circular and unrooted modes, along with static or
dynamic plots: bar, pie charts, circles, heat maps,
time series data etc.
Jalview
Win,
Linux,
Mac,
web-
Multiple alignment editor
Alignment visualizer with several added features:
http://www.jalview.org/
alignment editing, phylogenetic tree analysis, principle
based
component analysis plots and molecular structure
visualization, among others.
MEGA
Win, Mac
Molecular evolutionary genetics analysis tool
Integrates sequence alignment, phylogenetic tree
inference, database mining and statistical assessment
http://www.megasoftware.net/
of evolutionary parameters. Used to reconstruct
evolutionary histories of species.
Mizbee
Win, Linux, Mac
Genome browser that visualizes synteny for comparative
Uses a circular representation of the genome to
http://www.cs.utah.edu/~miriah/
genomics studies
explore conservation relationships at different scales.
mizbee
Layering and edge bundling strategies enhance
visualization.
SPREAD
Win, Linux, Mac
Phylogeographical tracking of disease evolution and
Reconstructs phylogeographic trees using Bayesian
http://www.kuleuven.ac.be/aidsl
expansion
methods and visualizes the spatiotemporal diffusion
ab/phylogeography/SPREAD.ht
of diseases or other variables within geographic
ml
maps.
Strap
Win,
Linux,
Mac,
web-
Structure-based sequence aligner and visualizer
based
Aligns proteins by sequence and 3D structure.
http://www.bioinformatics.org/str
Supports simultaneous analysis of hundreds of
ap/
proteins.
Also
integrates
genomic
and
mRNA
information.
TreeView
Win, Linux, Mac
Phylogenetic tree drawing tool
Visualizes trees in a variety of graphical styles.
http://taxonomy.zoology.gla.ac.
Supports tree manipulation (collapse, expand, reroot)
uk/rod/treeview.html
and accepts a wide range of file formats.
Vista
Web-based
Genome browser for comparative genomics
Can
perform
genome-wide
alignments
for
comparative sequence analysis and conservation
http://pipeline.lbl.gov/
inference.