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Biological data visualization is a branch of
bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...
concerned with the application of
computer graphics Computer graphics deals with generating images and art with the aid of computers. Computer graphics is a core technology in digital photography, film, video games, digital art, cell phone and computer displays, and many specialized applications. ...
,
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, st ...
, and
information visualization Data and information visualization (data viz/vis or info viz/vis) is the practice of designing and creating Graphics, graphic or visual Representation (arts), representations of a large amount of complex quantitative and qualitative data and i ...
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, ...
. 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 call ...
,
genomes 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 genes, other functional regions of the genome such as ...
, alignments, phylogenies, macromolecular structures,
systems biology Systems biology is the computational modeling, 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 system ...
,
microscopy Microscopy is the technical field of using microscopes to view subjects too small to 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 microscopy: optical mic ...
, and
magnetic resonance imaging Magnetic resonance imaging (MRI) is a medical imaging technique used in radiology to generate pictures of the anatomy and the physiological processes inside the body. MRI scanners use strong magnetic fields, magnetic field gradients, and ...
data. Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems. An emerging trend is the blurring of boundaries between the visualization of 3D structures at atomic resolution, the visualization of larger complexes by
cryo-electron microscopy Cryogenic electron microscopy (cryo-EM) is a transmission electron microscopy technique applied to samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An ...
, and the visualization of the location of proteins and complexes within whole cells and tissues. There has also been an increase in the availability and importance of time-resolved data from
systems biology Systems biology is the computational modeling, 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 system ...
,
electron microscopy An electron microscope is a microscope that uses a beam of electrons as a source of illumination. It uses electron optics that are analogous to the glass lenses of an optical light microscope to control the electron beam, for instance focusing i ...
, and cell and tissue imaging.


Sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between ...

Sequence alignment visualization plays a crucial role in
bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...
and
genomics Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, ...
by enabling researchers to interpret and analyze complex genetic data effectively. Visualizing sequence alignments allows for the identification of similarities, differences, conserved regions, and evolutionary patterns within
DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
or
protein sequences Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthes ...
, aiding in understanding genetic relationships, functional elements, and evolutionary processes. Sequence alignment visualization is essential for several reasons: Identifying
conserved sequence In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids ( DNA and RNA) or proteins across species ( orthologous sequences), or within a genome ( paralogous sequences), or between donor and receptor taxa ...
: Visualization helps researchers identify conserved regions across sequences, which are indicative of functional importance or evolutionary relationships. Detecting mutations and variations: Visualization tools enable the detection of
mutations In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mitosi ...
, insertions, deletions, and other variations within sequences, providing insights into
genetic diversity Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species. It ranges widely, from the number of species to differences within species, and can be correlated to the span of survival for a species. It is d ...
and disease-causing mutations. Understanding evolutionary relationships: By visualizing sequence alignments, researchers can infer evolutionary relationships, construct phylogenetic trees, and study the evolutionary history of species or genes. Predicting functional elements: Visualization aids in predicting functional elements such as protein domains, motifs, and regulatory regions within sequences, facilitating functional genomics studies. Comparing genomes:
comparative genomics Comparative genomics is a branch of biological research that examines genome sequences across a spectrum of species, spanning from humans and mice to a diverse array of organisms from bacteria to chimpanzees. This large-scale holistic approach c ...
rely on
sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between ...
visualization to compare
genomes 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 genes, other functional regions of the genome such as ...
, identify orthologous and paralogous genes, and study genome evolution across species. To visualize sequence alignments and their features, researchers often rely on popular bioinformatics software tools such a
Clustal OmegaMUSCLET-Coffee
an
MAFFT
These tools provide interactive platforms for aligning sequences, highlighting conserved regions, displaying sequence variations, and identifying sequence motifs. Additionally, visualization software lik
JalviewBioEdit
an
Geneious
offer advanced features for visualizing and analyzing sequence alignments, making it easier for researchers to interpret and extract meaningful information from genetic data. Techniques Besides software tools, such a
Clustal OmegaMUSCLET-Coffee
an
MAFFT
several popular techniques exist for genomic sequence alignment visualization, which plays a crutial role in helping researchers understand generic relationship, functional elements, and evolutionary processes. Among popular tools, common techniques in sequence alignment visualization include: Sequence logo: Sequence logos are graphical representations of sequence alignments that display the conservation of residues at each position as well as the relative frequency of each
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...
or
nucleotide Nucleotides are Organic compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both o ...
. Sequence logos provide a compact and informative visualization of
conserved sequence In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids ( DNA and RNA) or proteins across species ( orthologous sequences), or within a genome ( paralogous sequences), or between donor and receptor taxa ...
and variability. Multiple sequence alignment: Multiple sequence alignment viewers, such a
Jalview
an
MEGA
provide interactive platforms for visualizing and analyzing multiple sequence alignment. These tools offer features for highlighting
conserved sequence In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids ( DNA and RNA) or proteins across species ( orthologous sequences), or within a genome ( paralogous sequences), or between donor and receptor taxa ...
regions, identifying motifs, and exploring evolutionary relationships within sequences. Protein structure alignment tools: tools lik
PyMOL
an
UCSF Chimera
enable the visualization of sequence alignments in the context of protein structures. By superimposing aligned sequences onto protein structures, researchers can analyze the spatial arrangement of conserved residues and functional domains. Phylogenetic tree visualization: Phylogenetic tree visualization tools, such a
FigTree
an
iTOL
allow researchers to visualize evolutionary relationships inferred from sequence alignments. These tools provide interactive displays of phylogenetic trees, highlighting branch lengths, node support values, and evolutionary distances. Genome browser: Genome browsers lik
UCSC Genome Browser
an

provide comprehensive platforms for visualizing sequence alignments across entire genomes. Researchers can explore DNA annotation, regulatory elements, and comparative genomics data within the context of genome sequences. Applications Genomic
sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between ...
visualization is used in various applications, playing a crucial role in various areas of
genomics Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, ...
and
bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...
, enabling researchers to analyze, interpret, and extract valuable insights from genetic data. The applications of
sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between ...
visualization are diverse and encompass a wide range of research fields. Some key applications include:
Comparative genomics Comparative genomics is a branch of biological research that examines genome sequences across a spectrum of species, spanning from humans and mice to a diverse array of organisms from bacteria to chimpanzees. This large-scale holistic approach c ...
:
Sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between ...
visualization is essential for comparative genomics studies, where researchers compare genetic sequences across different
species A species () is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of Taxonomy (biology), ...
to identify evolutionary relationships,
conserved sequence In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids ( DNA and RNA) or proteins across species ( orthologous sequences), or within a genome ( paralogous sequences), or between donor and receptor taxa ...
regions, and functional elements. Visualization tools help in detecting similarities and differences between
genomes 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 genes, other functional regions of the genome such as ...
, aiding in the study of evolutionary processes. Variant analysis: In the field of
genetics Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinians, Augustinian ...
and personalized medicine,
sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between ...
visualization is used for variant analysis to identify
single nucleotide polymorphisms In genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in ...
(SNPs), insertions, deletions, and other
genetic variation Genetic variation is the difference in DNA among individuals or the differences between populations among the same species. The multiple sources of genetic variation include mutation and genetic recombination. Mutations are the ultimate sources ...
. Visualization tools help researchers pinpoint specific variations in genomic sequences and assess their potential impact on phenotypic traits. Phylogenetic analysis:
Phylogenetics In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...
studies rely on
sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between ...
visualization to construct
phylogenetic trees A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In o ...
and analyze genetic relationships between
species A species () is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of Taxonomy (biology), ...
or
population Population is a set of humans or other organisms in a given region or area. Governments conduct a census to quantify the resident population size within a given jurisdiction. The term is also applied to non-human animals, microorganisms, and pl ...
. Visualization tools enable researchers to visualize sequence similarities, calculate evolutionary distances, and infer phylogenetic relationships based on sequence alignments.
Functional genomics Functional genomics is a field of molecular biology that attempts to describe gene (and protein) functions and interactions. Functional genomics make use of the vast data generated by genomic and transcriptomic projects (such as genome sequen ...
: In functional genomics research, sequence alignment visualization is employed to study
gene expression Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...
, regulatory elements, and protein-protein interactions. By visualizing sequence alignments in the context of functional annotations and gene networks, researchers can elucidate the biological functions and regulatory mechanisms of genes. Structural bioinformatics: Sequence alignment visualization is integral to structural bioinformatics, where researchers analyze protein sequences and structures to understand their three-dimensional organization and functional properties. Visualization tools help in aligning protein sequences, predicting
structural motif In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules. A structural motif does not have t ...
, and exploring protein-protein interactions.


Macromolecular A macromolecule is a "molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." Polymers are physi ...

The visualization of macromolecules is critical for an intricate understanding of the multifaceted structures and functionalities that are fundamental to biological systems. Remarkable progress has been made in the three-dimensional portrayal of such macromolecules, spanning carbohydrates, proteins, nucleic acids, and their complexes. Recent advancements in visualization methodologies have precipitated a quantum leap in our ability to discern the subtleties of biological data. These sophisticated visualizations bestow an unprecedented level of clarity and granularity, thereby enhancing our comprehension of the mechanistic underpinnings governing the behavior and interaction of biological entities. Techniques Segmentation enhances biological imaging interpretation, with automated tools improving data analysis. This has led to a rise in web-based visualization for 3D segmentations. Segmentation plays a vital role in deciphering biological imaging data. The advent of sophisticated automated segmentation technologies, along with their incorporation into public imaging data repositories, greatly enhances the interpretation process. Volume rendering reveals internal macromolecular structures without segmentation, providing a non-invasive view inside the molecules. Integrating experimental data into visualizations, like overlaying mutations or binding data, offers richer insights. This can be displayed as heat maps or gradients on the molecule, vital for managing the growing complexity of biomolecular data. Interactive 3D visualization offers hands-on engagement with macromolecules, allowing for manipulation such as rotation and zooming, which enhances comprehension.
Virtual reality Virtual reality (VR) is a Simulation, simulated experience that employs 3D near-eye displays and pose tracking to give the user an immersive feel of a virtual world. Applications of virtual reality include entertainment (particularly video gam ...
and
augmented reality Augmented reality (AR), also known as mixed reality (MR), is a technology that overlays real-time 3D computer graphics, 3D-rendered computer graphics onto a portion of the real world through a display, such as a handheld device or head-mounted ...
present immersive methods to engage with macromolecules, delivering a 3D perspective that screen-based tools can't match. AR app also designed to help students visualize and interact with 3D macromolecular structures, addressing the limitations of traditional 2D images in conveying spatial details and depth perception. Animation of molecular activities illustrates the dynamic behaviors of biomolecules, serving as a powerful educational and research tool. Utilizing Unity3D game engine technology, this approach democratizes the creation of interactive molecular visualization tools, resulting in a user-friendly platform that simplifies complex biological data depiction. High-performance computing visualization enables real-time rendering of massive, intricate datasets, a necessity for advanced macromolecular analysis. Software leveraging high-performance computing dynamically and efficiently analyzes drug-receptor interactions via molecular dynamics simulations, offering profound insights and predictions on drug efficacy, and facilitating visualization. Hybrid visualization techniques merge various methods to provide a multifaceted view of molecules, combining detailed atomic positions with a holistic understanding of structure and volume. Visualization in different types of macromolecular
Carbohydrates A carbohydrate () is a biomolecule composed of carbon (C), hydrogen (H), and oxygen (O) atoms. The typical hydrogen-to-oxygen atomic ratio is 2:1, analogous to that of water, and is represented by the empirical formula (where ''m'' and ''n'' ma ...
visualization Visualizations of the Carbohydrate Binding Module (CBM) of cellulase examine its interactions with cellulose during hydrolysis from three angles: the adsorption of CBM to cellulose, its spatial occupation, and the accessibility of the cellulose surface to CBM.
Proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, re ...
visualization The RCSB Protein Data Bank (RCSB PDB), supported by major US scientific agencies, has been a pivotal resource for structural biologists globally and acts as the US data center within the Worldwide Protein Data Bank (wwPDB) partnership. As the designated Archive Keeper, RCSB PDB ensures the security of PDB data and serves tens of thousands of data depositors annually across all inhabited continents using various structural determination methods. The RCSB.org web portal provides unrestricted access to PDB data to millions globally. This article details the growth and evolution of the archive with advancing experimental techniques, the critical role of data standards and integration, and the introduction of new tools and features for 3D structural analysis and visualization over the past year.
Nucleic acid Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nuclei ...
visualization Researchers have developed a swift, straightforward, and precise method for detecting Infectious Bovine Rhinotracheitis Virus (IBRV) in cattle—a virus known for causing chronic infections and substantial economic impacts. This method integrates recombinant polymerase amplification (RPA) with a vertical flow visualization strip (VF) to form an RPA-VF assay that targets the thymidine kinase gene, ensuring fast detection, high specificity, and zero cross-reactivity with other pathogens. Large non-polymeric molecules The visualization of nanoscale materials is crucial for understanding their structure-function relationships, and it typically requires advanced microscopy and analytical techniques that provide high-resolution and high-magnification images.
Nanoparticles A nanoparticle or ultrafine particle is a particle of matter 1 to 100 nanometres (nm) in diameter. The term is sometimes used for larger particles, up to 500 nm, or fibers and tubes that are less than 100 nm in only two directions. At ...
are tiny particles that measure in the range of 1 to 100 nanometers. Due to their small size and high surface area to volume ratio, they exhibit unique chemical and physical properties. Visualization of nanoparticles is typically achieved using high-resolution techniques like Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), and Dynamic Light Scattering (DLS) for size distribution analysis. Nanocomposites are materials that incorporate nanoparticles within a matrix of another material, such as polymers, ceramics, or metals. These composites often exhibit enhanced properties, such as increased strength or electrical conductivity. Visualization of the distribution and interaction of nanoparticles within the matrix can be carried out using techniques like TEM, SEM, and X-ray diffraction (XRD). Nanotubes, specifically carbon nanotubes (CNTs), are cylindrical structures with diameters as small as 1 nanometer. They have remarkable mechanical, electrical, and thermal properties and are used in various applications from materials science to nanotechnology. Visualization of nanotubes typically requires TEM, SEM, or AFM. Nanofibers are fibers with diameters in the nanometer scale. They are created through processes like electrospinning and have applications in areas such as filtration, textiles, and biomedicine. Nanofibers can be visualized using SEM, which provides detailed images of their morphology and distribution. The visualization section on large non-polymeric molecules demonstrates a comprehensive and clear description of the techniques used to study nanoscale materials. It accurately details the application of advanced microscopy methods like TEM, SEM, AFM, and XRD, along with their relevance to specific nanomaterials such as mesoporous silica nanoparticles, nanocomposites, carbon nanotubes, and nanofibers. Each material is contextualized within its industrial or biomedical applications, emphasizing the importance of these visualization techniques in understanding material properties and behavior. While the section is informative and technically detailed, it could be enhanced by including specific examples of visualization outcomes, discussing the limitations of current techniques, and perhaps introducing emerging methods to provide a more rounded view of the field. Overall, the description is effectively tailored to educate and inform about the critical role of visualization in nanotechnology. Visualize the interactions between macromolecules The interactions of protein-carbohydrae was visulazed by hydrogen atoms in a perdeuterated lectin-fucose complex. Computational docking plays a vital role in structural biology, with software providing a user-friendly web platform for modeling various macromolecular interactions, such as flexible complexes and membrane-associated assemblies. This enhances accessibility and enriches the user experience within the structural biology community. Tools PyMOL, Chimera, ChimeraX, Jmol, VMD, Swiss-PdbViewer, Coot, Biovia Discovery Studio, LightDock and Schrodinger's Maestro are key tools in molecular visualization, each offering unique capabilities ranging from high-quality 3D imaging and interactive analysis to support for virtual reality and large-scale simulations, catering to diverse needs in molecular modeling, publication, and education across both open-source and commercial platforms.


Systems biology

Systems biology Systems biology is the computational modeling, 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 system ...
is a branch of biological data visualization dedicated to analyzing and modeling complex biological systems. Popular computational models used in systems biology include
process calculi In computer science, the process calculi (or process algebras) are a diverse family of related approaches for formally modelling concurrent systems. Process calculi provide a tool for the high-level description of interactions, communications, and ...
, such as stochastic
π-calculus In theoretical computer science, the -calculus (or pi-calculus) is a process calculus. The -calculus allows channel names to be communicated along the channels themselves, and in this matter, it is able to describe concurrent computations whose ...
, and constraint-based reconstruction and analysis (COBRA), a paradigm that considers physical, enzymatic, and topological constraints underlying a
phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (physical form and structure), its developmental processes, its biochemical and physiological propert ...
in a
metabolic network A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell. As such, these networks comprise the chemical reactions of metabolism, the metabolic pathways, as ...
. Most data visualization in systems biology is done using mathematically generated models. Researchers will diagram all of the protein, gene, or metabolic pathways in a given biological system, then determine the speed of the reactions in that system using mass action kinetics or
enzyme kinetics Enzyme kinetics is the study of the rates of enzyme catalysis, enzyme-catalysed chemical reactions. In enzyme kinetics, the reaction rate is measured and the effects of varying the conditions of the reaction are investigated. Studying an enzyme' ...
. These values are used as parameters to construct differential equations representing the system, which can then be used to determine the behavior of the things within that system. Alternative mathematical modeling solutions also exist; for instance, a COBRA method such as flux balance analysis could be used to analyze the flow of metabolites through a particular metabolic network. Another key imaging method in systems biology is
mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...
, which can be used to visualize the spatial distribution of compounds, biomarkers, metabolites, peptides, and/or proteins within the body. This is especially helpful in
metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerpri ...
, a branch of systems biology that uses mass spectrometry to measure metabolite distribution information, then uses the measured intensity to construct an image. Popular software tools used in systems biology modeling includ
massPyCytosim
an
PySB
Further examples may be found at Wikipedia's list of systems biology modeling software.


Microscopy visualization

Other than optical and electron microscopy, other techniques like scanning probe, ultraviolet, infrared, digital holographic, laser, and amateur are also utilize on Visualization. New approaches There is study investigates the use of two-photon microscopy, a technique capable of imaging depths up to 800 μm through two-photon absorption, for visualizing microrobotic agents beneath biological tissue, demonstrating its transformative potential for both in vitro and in vivo microrobotics applications. Researchers used bright-field light microscopy with high-intensity pulsing LED illumination to capture detailed 12-bit-per-channel images of live cells, addressing data distortions caused by optical path interactions and sensor anomalies with a comprehensive spectroscopic calibration approach, allowing for visualization with minimal information loss in 8-bit intensity depth. Researchers explored a community-driven initiative focused on improving the depiction of light microscopy data in scientific publications by adhering to the 'FAIR Data Principles,' which aim to enhance data findability, accessibility, interoperability, and reproducibility. Despite persistent challenges related to data quality and communication, the initiative emphasizes the role of global scientific collaboration in advancing imaging standards and leverages historical insights to guide and promote future advancements in biological imaging.


Magnetic resonance imaging

Magnetic resonance imaging Magnetic resonance imaging (MRI) is a medical imaging technique used in radiology to generate pictures of the anatomy and the physiological processes inside the body. MRI scanners use strong magnetic fields, magnetic field gradients, and ...
(MRI) is a common form of biological data visualization used to form pictures of internal biological processes. Different settings of radiofrequency pulses and gradients result in different image appearances; these combinations are known as MRI sequences. A particularly notable subset of MRI is
magnetic resonance angiography Magnetic resonance angiography (MRA) is a group of techniques based on magnetic resonance imaging (MRI) to image blood vessels. Magnetic resonance angiography is used to generate images of arteries (and less commonly veins) in order to evaluate ...
, which is a group of techniques used to image arteries and veins. MRI's imaging utility is further expanded upon by
diffusion MRI Diffusion-weighted magnetic resonance imaging (DWI or DW-MRI) is the use of specific MRI sequences as well as software that generates images from the resulting data that uses the diffusion of water molecules to generate contrast (vision), contrast ...
and functional MRI, which can be used to capture neuronal tracts and blood flow respectively. Diffusion MRI further relies on diffusion tensor imaging (DTI), which measures water molecule diffusion and directionality, and diffusion basis spectrum imaging (DBSI), which extracts multiple anisotropic and isotropic diffusion tensors. Functional MRI relies on blood-oxygen-level dependent (BOLD) contrast, which measures the proportion of oxygenated hemoglobin in specific areas of the brain; this allows it to measure and model brain activity based on blood flow. Further MRI techniques include saturation pulses (used to reduce motion artifacts), gradient echo (such as dynamic contrast enhancement), spin echo, and diffusion weighting (a signal contrast generation method based on differences in
Brownian motion Brownian motion is the random motion of particles suspended in a medium (a liquid or a gas). The traditional mathematical formulation of Brownian motion is that of the Wiener process, which is often called Brownian motion, even in mathematical ...
). To generate an observable image using MRI, the target is placed in a powerful magnetic field, such as that of an MRI machine. This causes the axes of the hydrogen protons inside the target, which are usually randomly aligned according to equilibrium, to be lined up in the same direction, creating a magnetic vector oriented along the magnet's axis. This orientation also allows the hydrogen protons' spin, or frequency of rotation, to be measured. The alignment is then disrupted using radiofrequency (RF) pulses (RF being a type of non-ionizing electromagnetic radiation). When the magnetic field is removed, the hydrogen protons return to their equilibrium states in a process known as relaxation, and in doing so they emit RF energy. Different tissues relax at different rates, which allows scientists to use specific RF pulse sequences to emphasize particular tissues or abnormalities. After a period of time following the RF pulse, the RF energy signals emitted by the protons are measured to obtain frequency information from each location in the imaged plane. Then Fourier transformation is used to convert this frequency information into intensity levels, which are displayed as shades of grey in the generated image. In general, two aspects of the relaxation process are measured: the time taken for the magnetic vector to return to its resting state (also known as T1 or spin–lattice relaxation), and the time taken for the axial spin of the hydrogen protons to return to its resting state (also known as T2 or spin–spin relaxation). To create a T1-weighted image, the MR signal is measured by changing the amount of time between RF pulses (also known as the time to repeat, or TR). To create a T2-weighted image, the MR signal is measured by changing the amount of time between delivering the RF pulse and receiving the RF energy signals from the hydrogen protons (also known as the time to echo, or TE). The dominant signal intensities of T1 image weighting are fluid (black due to low intensity), muscle (grey due to intermediate signal intensity), and fat (white due to high signal intensity). Fat suppression is applied to many T1 weighted sequences to suppress the brightness of the signal created by it. The dominant signal intensities of T2 image weighting are fluid (white), muscle (grey), and fat (white). T2 signals are also often emphasized or suppressed depending on what the goal of the imaging is; notable examples include fat suppression, fluid attenuation, and susceptibility weighting. Also of note are proton density (PD) weighted images, which are generated using a long TR and a short TE. PD is useful for differentiating between fluid,
hyaline cartilage Hyaline cartilage is the glass-like (hyaline) and translucent cartilage found on many joint surfaces. It is also most commonly found in the ribs, nose, larynx, and trachea. Hyaline cartilage is pearl-gray in color, with a firm consistency and has ...
and
fibrocartilage Fibrocartilage consists of a mixture of white fibrous tissue and cartilaginous tissue in various proportions. It owes its inflexibility and toughness to the former of these constituents, and its elasticity to the latter. It is the only type of ...
, which makes it ideal for imaging joints. Outside of joint imaging it has largely been replaced by fluid attenuated inversion recovery (FLAIR), an
inversion recovery Inversion recovery is a magnetic resonance imaging sequence that provides high contrast between tissue and lesion. It can be used to provide high T1 weighted image, high T2 weighted image, and to suppress the signals from fat, blood, or cerebros ...
sequence that removes the signal from cerebrospinal fluid.


Tomography

Computed tomography A computed tomography scan (CT scan), formerly called computed axial tomography scan (CAT scan), is a medical imaging technique used to obtain detailed internal images of the body. The personnel that perform CT scans are called radiographers or ...
(CT) and
positron emission tomography Positron emission tomography (PET) is a functional imaging technique that uses radioactive substances known as radiotracers to visualize and measure changes in metabolic processes, and in other physiological activities including blood flow, r ...
(PET) scans are similar to MRI, but rely on different imaging techniques (X-rays and ionizing radiation, respectively). A variation of CT known as
contrast CT Contrast CT, or contrast-enhanced computed tomography (CECT), is CT scan, X-ray computed tomography (CT) using radiocontrast. Radiocontrasts for X-ray CT are generally Iodinated contrast, iodine-based types. This is useful to highlight structure ...
also requires the subject to take in a contrast medium called a
radiocontrast Radiocontrast agents are substances used to enhance the visibility of internal structures in X-ray-based imaging techniques such as computed tomography (contrast CT), projectional radiography, and fluoroscopy. Radiocontrast agents are typically iod ...
(typically by oral consumption, enema, or injection). Positive radiocontrast agents such as barium sulfate increase the body's X-ray attenuation, causing the tissue containing them to appear whiter in the X-ray image. Meanwhile, negative agents such as carbon dioxide gas allow X-rays to pass through them easily, causing the tissues containing them to appear darker. Like magnetic resonance imaging, CT scans use numerous methods to display and measure data, including sequential CT (where the CT table steps from location to location), spiral CT (where the entire X-ray tube is spun around the subject), and
electron beam tomography Electron beam computed tomography (EBCT) is a fifth generation computed tomography (CT) scanner in which the X-ray tube is not mechanically spun in order to rotate the source of X-ray photons. This different design was explicitly developed to ...
(where only the electron paths are spun using deflection coils). PET scanners don’t have quite as much hardware variation and instead use different radiotracers depending on what the imaging target is. Note that radiotracers are distinct from radiocontrasts; the former relies on radioactive decay to trace its path while the latter is absorbed into specific tissue and affects that tissue's X-ray attenuation. Because these methods are not mutually exclusive, PET and CT can be performed simultaneously using PET-CT scanners, which are used for the majority of modern PET scans. Either or both of these methods can be used in conjunction with
maximum intensity projection In scientific visualization, a maximum intensity projection (MIP) is a method for 3D data that projects in the visualization plane the voxels with maximum intensity that fall in the way of parallel rays traced from the viewpoint to the plane of ...
(MIP) to convert the scan data into a 3D image. This can be difficult to accomplish due to artifacts created by respiration and bloodflow, which can appear as abnormalities to an untrained eye; however, it's possible to distinguish these artifacts from real disease so long as careful attention is paid to them. When done well, CT and PET scans taken with MIP are excellent for identifying small abnormal tissue growths, especially in the lungs. Scans taken with MIP for this purpose tend to have higher significance than averaged images created with traditional CT. MIP imaging is also used with magnetic resonance angiography, and research has indicated that it could feasibly be used with MRI. At least one study has shown that MIP MRI actually significantly outperforms single-slice MRI when used by neural networks to classify lesions based on malignancy.


Alignment

A sequence alignment is a way of arranging the sequences of protein, RNA or DNA, to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. The concept initially compares only two such sequences in the so called pairwise alignment. Global alignments, which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size. Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context. Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple alignment methods try to align all the sequences in each query set. Multiple alignments are often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related. Purposes of Alignment Visualization: * Aid general understanding of large-scale DNA or protein alignments. When analyzing data, it is helpful to visualize it somehow, to be able to easily spot clear patters or relations. * Visualize alignments for figures and publication. It summarizes the multiple sequence alignment in an easy-to-digest form. * Manually edit and curate automatically generated alignments. Even though there are efficient algorithms, none is perfect and visualization tools provide a way to edit small discrepancies. Regular multiple sequence alignment – Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Many sequence visualization programs also use color to display information about the properties of the individual sequence elements; in DNA and RNA sequences, this equates to assigning each nucleotide its own color. In protein alignments color is often used to indicate amino acid properties to aid in judging the conservation of a given amino acid substitution. For multiple sequences the last row in each column is often the consensus sequence determined by the alignment; the consensus sequence is also often represented in graphical format with a sequence logo in which the size of each nucleotide or amino acid letter corresponds to its degree of conservation. Circular multiple sequence alignment – A common assumption of multiple sequence alignment techniques is that the left- and right-most positions of the input sequences are relevant to the alignment. However, the position where a sequence starts or ends can be totally arbitrary. For instance, when linearizing a circular molecular structure, the start of the sequence is selected randomly. This is relevant, for instance, in the process of multiple sequence alignment of mitochondrial DNA, viroid, viral or other genomes, which have a circular molecular structure. Spiral multiple sequence alignment – Color is used to display information about the properties of the individual sequence elements. There can also be gaps that make the sequences fit better among themselves. In summary, the topology of the spiral sequence alignment is equivalent to a standard linear matrix, with the advantage that it summarizes very long sequences in a practical way. That means that each individual spiral represents one of the sequences being aligned. 3D visualization – A common, one-dimensional, representation of a protein sequence is a list of the amino acids that form it. However, 3-dimensional alignment displays the way sequences may match each other. The 1D-3D Group Alignment Viewer, from the RCSD Protein Data Bank, supports exploration of multiple sequence alignments (MSA) at sequence and structure levels for PDB experimental structures and Computed Structure Models (CSMs). It is possible to select proteins and/or residue regions from the MSA to view their 3D structures aligned. RCSB.org clusters protein entities (PDB experimental structures and CSMs) by sequence identity threshold and UniProt accession. For each cluster, the MSA is calculated using Clustal Omega and displayed in the 1D-3D Group Alignment Viewer using specific color schemes. PDB protein sequence positions are represented in blue if residue was experimentally determined, and in gray if not. CSMs are colored according to their local pLDDT scores.


Phylogenies

A phylogenetic tree is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. It is a visual representation that shows the evolutionary history between a set of species or taxa during a specific time. Two things are implicitly occurring along the branches of a phylogenetic tree. The first is the passage of time. Deeper nodes are older than the shallower nodes to which they are connected. Thus, deeper nodes indicate both more distant relationships among the terminal taxa that they connect, and a greater age for the most recent common ancestor of those taxa. The second thing is evolutionary modification, or the accumulation of hereditary genetic and/or structural changes along these branches. The term "branch length" typically refers to the number of these changes. If the "branch lengths" of the tree measure these changes, we also call the tree a phylogram. Regular phylogenetic tree – Generally called a
dendrogram A dendrogram is a diagram representing a Tree (graph theory), tree graph. This diagrammatic representation is frequently used in different contexts: * in hierarchical clustering, it illustrates the arrangement of the clusters produced by ...
, it is a diagram with straight lines representing a tree. It would show a column of nodes representing individual taxa, and the remaining nodes represent the clusters to which the data belong, with the arrows representing the distance: a way to measure how different they are (dissimilarity). The distance between merged clusters is monotone, increasing with the level of the merger: the height of each node in the plot is proportional to the value of the intergroup dissimilarity between its two branches. Cladogram – It is also a diagram with straight lines representing a tree. The difference between a cladogram and an evolutionary tree is that the cladogram does not show how ancestors are related to descendants, nor does it show how much they have changed. This means that more than one evolutionary tree may correspond to the same cladogram. Circular phylogenetic tree – Circular trees are often used to illustrate relationships among members of major groups of extant organisms, and these trees may have many terminal taxa. It might seem counterintuitive, but the same information given in a regular phylogenetic tree is given in a circular genetic tree. The topology of the structure remains the same, and it only changes shape to better fit a lot of information in less space. 3D Visualization – In a phylogram, the evolutionary distance is represented on one of the axes and the genes on the other. For it to be possible to visualize the paralogs, a third axis can be added. In standard (2D) phylogeny layout it is not always easy to distinguish gene duplication events (paralogs) from speciation branching (species), because only one spatial axis (genes) is available to show the mix of these two kinds of information. By contrast, they can be easily distinguished in 3DPE, because it projects them onto two orthogonal axes: species (X) vs. paralogs (Z). For instance, the evolution of many paralogs is visually obvious in the 3DPE view (in the three eukaryote species, on the right), but this pattern is less clear in the 2D representation.


Visualization software

File:Tree_of_life_SVG.svg, ITOL tree of life File:JMOL-1AER.png, Visualization of exotoxin A created with Jmol File:Metulodontia-Maximum-Likelihood.svg,
Maximum likelihood In statistics, maximum likelihood estimation (MLE) is a method of estimating the parameters of an assumed probability distribution, given some observed data. This is achieved by maximizing a likelihood function so that, under the assumed stati ...
phylogenetic tree A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In ...
created with MEGA6 File:AT-hook PyMol.png, Segment of
DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
depicted by PyMOL File:Cytoscape network visualization1.png, Yeast network data visualized by Cytoscape File:T coffee alignment.png, Multiple sequence alignment of PET hydrolases created with T-Coffee


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)