Biology data visualization is a branch of

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combine ...

concerned with the application of computer graphics,

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, sta ...

, 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, ...

to different areas of the

life sciences This list of life sciences comprises the branches of science that involve the scientific study of life – such as microorganisms, plants, and animals including human beings. This science is one of the two major branches of natural science, th ...

. 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 calle ...

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 ...

, alignments, phylogenies, macromolecular structures,

systems biology Systems biology is the computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic ap ...

microscopy Microscopy is the technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye (objects that are not within the resolution range of the normal eye). There are three well-known branches of mic ...

, and

magnetic resonance imaging Magnetic resonance imaging (MRI) is a medical imaging technique used in radiology to form pictures of the anatomy and the physiological processes of the body. MRI scanners use strong magnetic fields, magnetic field gradients, and radio waves ...

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 sol ...

, 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

electron microscopy An electron microscope is a microscope that uses a beam of accelerated electrons as a source of illumination. As the wavelength of an electron can be up to 100,000 times shorter than that of visible light photons, electron microscopes have a hi ...

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 the s ...

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

usability Usability can be described as the capacity of a system to provide a condition for its users to perform the tasks safely, effectively, and efficiently while enjoying the experience. In software engineering, usability is the degree to which a soft ...

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 Standardization or standardisation is the process of implementing and developing technical standards based on the consensus of different parties that include firms, users, interest groups, standards organizations and governments. 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 spec ...

and evolution File:Signal transduction v1.png,

Systems biology Systems biology is the computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic ap ...

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 Keku ...

File:Kinetochore.jpg,

Microscopy Microscopy is the technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye (objects that are not within the resolution range of the normal eye). There are three well-known branches of mic ...

File:DTI-sagittal-fibers.jpg,

Magnetic resonance imaging Magnetic resonance imaging (MRI) is a medical imaging technique used in radiology to form pictures of the anatomy and the physiological processes of the body. MRI scanners use strong magnetic fields, magnetic field gradients, and radio waves ...

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)