Biology data visualization is a branch of bioinformatics concerned with the application of

computer graphics Computer graphics deals with generating images with the aid of computers. Today, computer graphics is a core technology in digital photography, film, video games, cell phone and computer displays, and many specialized applications. A great de ...

scientific visualization Scientific visualization ( also spelled scientific visualisation) is an interdisciplinary branch of science concerned with the visualization of scientific phenomena. Michael Friendly (2008)"Milestones in the history of thematic cartography, s ...

, and

information visualization Information is an abstract concept that refers to that which has the power to inform. At the most fundamental level information pertains to the interpretation of that which may be sensed. Any natural process that is not completely random, a ...

to different areas of the life sciences. This includes visualization of

sequences In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is called t ...

genomes In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...

, alignments,

phylogenies A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging data. Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems.

State-of-the-art and perspectives

Today we are experiencing a rapid growth in volume and diversity of

biological data Biological data refers to a compound or information derived from living organisms and their products. A medicinal compound made from living organisms, such as a serum or a vaccine, could be characterized as biological data. Biological data is highly ...

, presenting an increasing challenge for biologists. A key step in understanding and learning from these data is visualization. Thus, there has been a corresponding increase in the number and diversity of systems for visualizing biological data. An emerging trend is the blurring of boundaries between the visualization of 3D structures at atomic resolution, visualization of larger complexes by

cryo-electron microscopy Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample s ...

, and visualization of the location of proteins and complexes within whole cells and tissues. A second emerging trend is an increase in the availability and importance of time-resolved data from systems biology, electron microscopy and cell and tissue imaging. In contrast, visualization of trajectories has long been a prominent part of

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of t ...

. Finally, as datasets are increasing in size, complexity, and interconnectedness, biological visualization systems are improving in usability,

data integration Data integration involves combining data residing in different sources and providing users with a unified view of them. This process becomes significant in a variety of situations, which include both commercial (such as when two similar companies ...

and standardization.

List of visualization software

Many software systems are available for visualization biological data. The list below links some popularly used software, and systems grouped by application areas. * Medusa - A simple tool for interaction graph analysis. It is a Java based application and available as an applet. * Cytoscape - An open source software for integrating bio-molecular interaction networks with high-throughput expression data and other molecular states. * Proviz - ProViz is a standalone open source application under the GPL license. * PATIKA - It is a tool with integrated visual environment for collaborative construction and analysis of cellular pathways. File:Genome_viewer_screenshot_small.png, Genomic and assembly data File:Tree_of_life_SVG.svg, Alignments,

phylogeny A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spe ...

and evolution File:Signal transduction v1.png, Systems biology File:CaMKII.png,

Molecular graphics Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekul� ...

File:Kinetochore.jpg, Microscopy File:DTI-sagittal-fibers.jpg, Magnetic resonance imaging

References

External links

Related conferences

BioVis: Symposium on Biological Data Visualization

Applications of Information Visualization in Bioinformatics

CIBDV: Computational Intelligence for Biological Data Visualization

* ttp://www.faculty.jacobs-university.de/llinsen/vmls/2009 VMLS: Visualization in Medicine & Life Sciences
VIZBI: Workshop on Visualizing Biological Data
{{DEFAULTSORT:Biological Data Visualization Bioinformatics Visualization (graphics)