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class="vector-toc-text"> <span class="vector-toc-numb">2</span> <span>Macromolecular</span> </div> </a> <ul id="toc-Macromolecular-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Systems_biology" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Systems_biology"> <div class="vector-toc-text"> <span class="vector-toc-numb">3</span> <span>Systems biology</span> </div> </a> <ul id="toc-Systems_biology-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Microscopy_visualization" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Microscopy_visualization"> <div class="vector-toc-text"> <span class="vector-toc-numb">4</span> <span>Microscopy visualization</span> </div> </a> <ul id="toc-Microscopy_visualization-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Magnetic_resonance_imaging" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Magnetic_resonance_imaging"> <div class="vector-toc-text"> <span class="vector-toc-numb">5</span> <span>Magnetic resonance imaging</span> </div> </a> <ul id="toc-Magnetic_resonance_imaging-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Tomography" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Tomography"> <div class="vector-toc-text"> <span class="vector-toc-numb">6</span> <span>Tomography</span> </div> </a> <ul id="toc-Tomography-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Alignment" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Alignment"> <div class="vector-toc-text"> <span class="vector-toc-numb">7</span> <span>Alignment</span> </div> </a> <ul id="toc-Alignment-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Phylogenies" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Phylogenies"> <div class="vector-toc-text"> <span class="vector-toc-numb">8</span> <span>Phylogenies</span> </div> </a> <ul id="toc-Phylogenies-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Visualization_software" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Visualization_software"> <div class="vector-toc-text"> <span class="vector-toc-numb">9</span> <span>Visualization software</span> </div> </a> <ul id="toc-Visualization_software-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-References" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#References"> <div class="vector-toc-text"> <span class="vector-toc-numb">10</span> <span>References</span> </div> </a> <ul id="toc-References-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-External_links" 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class="vector-body" aria-labelledby="firstHeading" data-mw-ve-target-container> <div class="vector-body-before-content"> <div class="mw-indicators"> </div> <div id="siteSub" class="noprint">From Wikipedia, the free encyclopedia</div> </div> <div id="contentSub"><div id="mw-content-subtitle"></div></div> <div id="mw-content-text" class="mw-body-content"><div class="mw-content-ltr mw-parser-output" lang="en" dir="ltr"><div class="shortdescription nomobile noexcerpt noprint searchaux" style="display:none">Branch of bioinformatics</div> <p><b>Biological data visualization</b> is a branch of <a href="/wiki/Bioinformatics" title="Bioinformatics">bioinformatics</a> concerned with the application of <a href="/wiki/Computer_graphics" title="Computer graphics">computer graphics</a>, <a href="/wiki/Scientific_visualization" title="Scientific visualization">scientific visualization</a>, and <a href="/wiki/Information_visualization" class="mw-redirect" title="Information visualization">information visualization</a> to different areas of the <a href="/wiki/Life_sciences" class="mw-redirect" title="Life sciences">life sciences</a>. This includes visualization of <a href="/wiki/Sequences" class="mw-redirect" title="Sequences">sequences</a>, <a href="/wiki/Genomes" class="mw-redirect" title="Genomes">genomes</a>, <a href="/wiki/Sequence_alignment" title="Sequence alignment">alignments</a>, <a href="/wiki/Phylogenies" class="mw-redirect" title="Phylogenies">phylogenies</a>, <a href="/wiki/Macromolecules" class="mw-redirect" title="Macromolecules">macromolecular structures</a>, <a href="/wiki/Systems_biology" title="Systems biology">systems biology</a>, <a href="/wiki/Microscopy" title="Microscopy">microscopy</a>, and <a href="/wiki/Magnetic_resonance_imaging" title="Magnetic resonance imaging">magnetic resonance imaging</a> data. Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems. </p><p>An emerging trend is the blurring of boundaries between the visualization of 3D structures at atomic resolution, the visualization of larger complexes by <a href="/wiki/Cryo-electron_microscopy" class="mw-redirect" title="Cryo-electron microscopy">cryo-electron microscopy</a>, and the visualization of the location of proteins and complexes within whole cells and tissues.<sup id="cite_ref-1" class="reference"><a href="#cite_note-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> There has also been an increase in the availability and importance of time-resolved data from <a href="/wiki/Systems_biology" title="Systems biology">systems biology</a>, <a href="/wiki/Electron_microscopy" class="mw-redirect" title="Electron microscopy">electron microscopy</a>, and cell and tissue imaging.<sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-4" class="reference"><a href="#cite_note-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="Sequence_alignment"><a href="/wiki/Sequence_alignment" title="Sequence alignment">Sequence alignment</a></h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Biological_data_visualization&action=edit&section=1" title="Edit section: Sequence alignment"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure typeof="mw:File/Thumb"><a href="/wiki/File:WPP_domain_alignment.PNG" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/a/a7/WPP_domain_alignment.PNG/684px-WPP_domain_alignment.PNG" decoding="async" width="684" height="159" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/a/a7/WPP_domain_alignment.PNG 1.5x" data-file-width="921" data-file-height="214" /></a><figcaption>A multiple sequence alignment of the WPP domain. Source: Wikipedia Commons, the free media repository. Retrieved April 20, 2024, from <a class="external free" href="https://commons.wikimedia.org/wiki/File:WPP_domain_alignment.PNG">https://commons.wikimedia.org/wiki/File:WPP_domain_alignment.PNG</a></figcaption></figure> <p>Sequence alignment visualization plays a crucial role in <a href="/wiki/Bioinformatics" title="Bioinformatics">bioinformatics</a> and <a href="/wiki/Genomics" title="Genomics">genomics</a> 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 <a href="/wiki/DNA" title="DNA">DNA</a> or <a href="/wiki/Protein_sequences" class="mw-redirect" title="Protein sequences">protein sequences</a>, aiding in understanding genetic relationships, functional elements, and evolutionary processes. Sequence alignment visualization is essential for several reasons: </p><p><b>Identifying <a href="/wiki/Conserved_sequence" title="Conserved sequence">conserved sequence</a>:</b> Visualization helps researchers identify conserved regions across sequences, which are indicative of functional importance or evolutionary relationships. <sup id="cite_ref-5" class="reference"><a href="#cite_note-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> </p><p><b>Detecting mutations and variations:</b> Visualization tools enable the detection of <a href="/wiki/Mutations" class="mw-redirect" title="Mutations">mutations</a>, insertions, deletions, and other variations within sequences, providing insights into <a href="/wiki/Genetic_diversity" title="Genetic diversity">genetic diversity</a> and disease-causing mutations. <sup id="cite_ref-6" class="reference"><a href="#cite_note-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> </p><p><b>Understanding evolutionary relationships:</b> By visualizing sequence alignments, researchers can infer evolutionary relationships, construct phylogenetic trees, and study the evolutionary history of species or genes. <sup id="cite_ref-7" class="reference"><a href="#cite_note-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> </p><p><b>Predicting functional elements:</b> Visualization aids in predicting functional elements such as protein domains, motifs, and regulatory regions within sequences, facilitating functional genomics studies. <sup id="cite_ref-8" class="reference"><a href="#cite_note-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> </p> <figure typeof="mw:File/Thumb"><a href="/wiki/File:DNA_ORF.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/4/46/DNA_ORF.png/406px-DNA_ORF.png" decoding="async" width="406" height="306" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/4/46/DNA_ORF.png/609px-DNA_ORF.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/4/46/DNA_ORF.png/812px-DNA_ORF.png 2x" data-file-width="1000" data-file-height="754" /></a><figcaption>DNA, ORF (open reading frame). Source: <a rel="nofollow" class="external free" href="http://www.genome.gov/Images/EdKit/bio2b_large.gif">http://www.genome.gov/Images/EdKit/bio2b_large.gif</a></figcaption></figure> <p><b>Comparing genomes</b>: <a href="/wiki/Comparative_genomics" title="Comparative genomics">comparative genomics</a> rely on <a href="/wiki/Sequence_alignment" title="Sequence alignment">sequence alignment</a> visualization to compare <a href="/wiki/Genomes" class="mw-redirect" title="Genomes">genomes</a>, identify orthologous and paralogous genes, and study <a href="/wiki/Genome_evolution" title="Genome evolution">genome evolution</a> across species. <sup id="cite_ref-9" class="reference"><a href="#cite_note-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> To visualize sequence alignments and their features, researchers often rely on popular bioinformatics software tools such as <a rel="nofollow" class="external text" href="https://www.ebi.ac.uk/jdispatcher/msa/clustalo/">Clustal Omega</a>, <a rel="nofollow" class="external text" href="https://www.ebi.ac.uk/jdispatcher/msa/muscle">MUSCLE</a>, <a rel="nofollow" class="external text" href="https://tcoffee.crg.eu/">T-Coffee</a>, and <a rel="nofollow" class="external text" href="https://www.ebi.ac.uk/jdispatcher/msa/mafft">MAFFT</a>. These tools provide interactive platforms for aligning sequences, highlighting conserved regions, displaying sequence variations, and identifying sequence motifs. Additionally, visualization software like <a rel="nofollow" class="external text" href="https://www.jalview.org/">Jalview</a>, <a rel="nofollow" class="external text" href="https://bioedit.software.informer.com/">BioEdit</a>, and <a rel="nofollow" class="external text" href="https://www.geneious.com/">Geneious</a> offer advanced features for visualizing and analyzing sequence alignments, making it easier for researchers to interpret and extract meaningful information from genetic data. </p><p><b>Techniques</b> </p><p>Besides software tools, such as <a rel="nofollow" class="external text" href="https://www.ebi.ac.uk/jdispatcher/msa/clustalo/">Clustal Omega</a>, <a rel="nofollow" class="external text" href="https://www.ebi.ac.uk/jdispatcher/msa/muscle">MUSCLE</a>, <a rel="nofollow" class="external text" href="https://tcoffee.crg.eu/">T-Coffee</a>, and <a rel="nofollow" class="external text" href="https://www.ebi.ac.uk/jdispatcher/msa/mafft">MAFFT</a>, 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: </p> <figure typeof="mw:File/Thumb"><a href="/wiki/File:LexA_gram_positive_bacteria_sequence_logo.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/8/85/LexA_gram_positive_bacteria_sequence_logo.png/408px-LexA_gram_positive_bacteria_sequence_logo.png" decoding="async" width="408" height="113" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/8/85/LexA_gram_positive_bacteria_sequence_logo.png/612px-LexA_gram_positive_bacteria_sequence_logo.png 1.5x, //upload.wikimedia.org/wikipedia/commons/8/85/LexA_gram_positive_bacteria_sequence_logo.png 2x" data-file-width="680" data-file-height="188" /></a><figcaption>A <a href="/wiki/Sequence_logo" title="Sequence logo">sequence logo</a> of the <a href="/wiki/LexA" class="mw-redirect" title="LexA">LexA</a>-binding motif of <a href="/wiki/Gram-positive_bacteria" title="Gram-positive bacteria">Gram-positive bacteria</a>. Source: Wikipedia Commons, the free media repository. Retrieved April 20, 2024, from <a class="external free" href="https://commons.wikimedia.org/wiki/File:LexA_gram_positive_bacteria_sequence_logo.png">https://commons.wikimedia.org/wiki/File:LexA_gram_positive_bacteria_sequence_logo.png</a></figcaption></figure> <p><b><a href="/wiki/Sequence_logo" title="Sequence logo">Sequence logo</a>:</b> 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 <a href="/wiki/Amino_acid" title="Amino acid">amino acid</a> or <a href="/wiki/Nucleotide" title="Nucleotide">nucleotide</a>. Sequence logos provide a compact and informative visualization of <a href="/wiki/Conserved_sequence" title="Conserved sequence">conserved sequence</a> and variability. <sup id="cite_ref-10" class="reference"><a href="#cite_note-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> </p><p><b><a href="/wiki/Multiple_sequence_alignment" title="Multiple sequence alignment">Multiple sequence alignment</a>:</b> Multiple sequence alignment viewers, such as <a rel="nofollow" class="external text" href="https://www.jalview.org/">Jalview</a> and <a rel="nofollow" class="external text" href="https://www.megasoftware.net/">MEGA</a>, provide interactive platforms for visualizing and analyzing <a href="/wiki/Multiple_sequence_alignment" title="Multiple sequence alignment">multiple sequence alignment</a>. These tools offer features for highlighting <a href="/wiki/Conserved_sequence" title="Conserved sequence">conserved sequence</a> regions, identifying motifs, and exploring evolutionary relationships within sequences.<sup id="cite_ref-11" class="reference"><a href="#cite_note-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup> </p> <figure typeof="mw:File/Thumb"><a href="/wiki/File:CYP4F2_protein_structure.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/7/79/CYP4F2_protein_structure.png/411px-CYP4F2_protein_structure.png" decoding="async" width="411" height="270" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/7/79/CYP4F2_protein_structure.png/617px-CYP4F2_protein_structure.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/7/79/CYP4F2_protein_structure.png/822px-CYP4F2_protein_structure.png 2x" data-file-width="2584" data-file-height="1696" /></a><figcaption>CYP4F2 protein structure - Protein structure of Leukotriene-B4 omega-hydroxylase 1 enzyme. Source: Wikipedia Commons, the free media repository. Retrieved April 20, 2024, from <a class="external free" href="https://commons.wikimedia.org/wiki/File:CYP4F2_protein_structure.png">https://commons.wikimedia.org/wiki/File:CYP4F2_protein_structure.png</a></figcaption></figure> <p><b>Protein structure alignment tools:</b> tools like <a rel="nofollow" class="external text" href="https://pymol.org/">PyMOL</a> and <a rel="nofollow" class="external text" href="https://www.cgl.ucsf.edu/chimera/">UCSF Chimera</a> enable the visualization of sequence alignments in the context of protein structures. By superimposing aligned sequences onto <a href="/wiki/Protein_structures" class="mw-redirect" title="Protein structures">protein structures</a>, researchers can analyze the spatial arrangement of conserved residues and functional domains.<sup id="cite_ref-12" class="reference"><a href="#cite_note-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> </p><p><b>Phylogenetic tree visualization:</b> Phylogenetic tree visualization tools, such as <a rel="nofollow" class="external text" href="http://tree.bio.ed.ac.uk/software/figtree/">FigTree</a> and <a rel="nofollow" class="external text" href="https://itol.embl.de/">iTOL</a>, 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.<sup id="cite_ref-13" class="reference"><a href="#cite_note-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> </p><p><b>Genome browser:</b> Genome browsers like <a rel="nofollow" class="external text" href="https://genome.ucsc.edu/">UCSC Genome Browser</a> and <a rel="nofollow" class="external text" href="https://useast.ensembl.org/index.html/">Ensembl</a> provide comprehensive platforms for visualizing sequence alignments across entire genomes. Researchers can explore <a href="/wiki/DNA_annotation" title="DNA annotation">DNA annotation</a>, regulatory elements, and comparative genomics data within the context of genome sequences.<sup id="cite_ref-14" class="reference"><a href="#cite_note-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup> </p> <figure typeof="mw:File/Thumb"><a href="/wiki/File:Protista_taxonomy_vs_phylogeny.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/9/9f/Protista_taxonomy_vs_phylogeny.png/683px-Protista_taxonomy_vs_phylogeny.png" decoding="async" width="683" height="515" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/9/9f/Protista_taxonomy_vs_phylogeny.png/1025px-Protista_taxonomy_vs_phylogeny.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/9/9f/Protista_taxonomy_vs_phylogeny.png/1366px-Protista_taxonomy_vs_phylogeny.png 2x" data-file-width="3000" data-file-height="2260" /></a><figcaption>Prostista taxonomy vs. phylogeny - This diagram shows the phylogeny of eukaryotes based on some recent analyses superimposed over the current kingdom and subkingdom-level taxonomy of protists. The purpose of the image is to demonstrate the paraphyly of most protist groupings, particularly those belonging to kingdom Protozoa: subkingdom Eozoa. Source: Wikipedia Commons, the free media repository. Retrieved April 20, 2024, from <a class="external free" href="https://commons.wikimedia.org/wiki/File:Protista_taxonomy_vs_phylogeny.png">https://commons.wikimedia.org/wiki/File:Protista_taxonomy_vs_phylogeny.png</a></figcaption></figure> <p><b>Applications</b> </p><p>Genomic <a href="/wiki/Sequence_alignment" title="Sequence alignment">sequence alignment</a> visualization is used in various applications, playing a crucial role in various areas of <a href="/wiki/Genomics" title="Genomics">genomics</a> and <a href="/wiki/Bioinformatics" title="Bioinformatics">bioinformatics</a>, enabling researchers to analyze, interpret, and extract valuable insights from genetic data. The applications of <a href="/wiki/Sequence_alignment" title="Sequence alignment">sequence alignment</a> visualization are diverse and encompass a wide range of research fields. Some key applications include: </p><p><b><a href="/wiki/Comparative_genomics" title="Comparative genomics">Comparative genomics</a>:</b> <a href="/wiki/Sequence_alignment" title="Sequence alignment">Sequence alignment</a> visualization is essential for comparative genomics studies, where researchers compare genetic sequences across different <a href="/wiki/Species" title="Species">species</a> to identify evolutionary relationships, <a href="/wiki/Conserved_sequence" title="Conserved sequence">conserved sequence</a> regions, and functional elements. Visualization tools help in detecting similarities and differences between <a href="/wiki/Genomes" class="mw-redirect" title="Genomes">genomes</a>, aiding in the study of evolutionary processes.<sup id="cite_ref-15" class="reference"><a href="#cite_note-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> </p> <figure typeof="mw:File/Thumb"><a href="/wiki/File:EncodeSample.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/2/21/EncodeSample.png/683px-EncodeSample.png" decoding="async" width="683" height="256" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/2/21/EncodeSample.png 1.5x" data-file-width="800" data-file-height="300" /></a><figcaption>View of ENCODE project tracks in the UCSC Genome browser. Source: Wikipedia Commons, the free media repository. Retrieved April 20, 2024, from <a class="external free" href="https://commons.wikimedia.org/wiki/File:EncodeSample.png">https://commons.wikimedia.org/wiki/File:EncodeSample.png</a></figcaption></figure> <p><b>Variant analysis:</b> In the field of <a href="/wiki/Genetics" title="Genetics">genetics</a> and <a href="/wiki/Personalized_medicine" title="Personalized medicine">personalized medicine</a>, <a href="/wiki/Sequence_alignment" title="Sequence alignment">sequence alignment</a> visualization is used for variant analysis to identify <a href="/wiki/Single_nucleotide_polymorphisms" class="mw-redirect" title="Single nucleotide polymorphisms">single nucleotide polymorphisms</a> (SNPs), insertions, deletions, and other <a href="/wiki/Genetic_variation" title="Genetic variation">genetic variation</a>. Visualization tools help researchers pinpoint specific variations in genomic sequences and assess their potential impact on phenotypic traits.<sup id="cite_ref-16" class="reference"><a href="#cite_note-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup> </p><p><b>Phylogenetic analysis:</b> <a href="/wiki/Phylogenetics" title="Phylogenetics">Phylogenetics</a> studies rely on <a href="/wiki/Sequence_alignment" title="Sequence alignment">sequence alignment</a> visualization to construct <a href="/wiki/Phylogenetic_trees" class="mw-redirect" title="Phylogenetic trees">phylogenetic trees</a> and analyze genetic relationships between <a href="/wiki/Species" title="Species">species</a> or <a href="/wiki/Population" title="Population">population</a>. Visualization tools enable researchers to visualize sequence similarities, calculate evolutionary distances, and infer phylogenetic relationships based on sequence alignments.<sup id="cite_ref-17" class="reference"><a href="#cite_note-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> </p><p><b><a href="/wiki/Functional_genomics" title="Functional genomics">Functional genomics</a>:</b> In functional genomics research, sequence alignment visualization is employed to study <a href="/wiki/Gene_expression" title="Gene expression">gene expression</a>, regulatory elements, and <a href="/wiki/Protein-protein_interactions" class="mw-redirect" title="Protein-protein interactions">protein-protein interactions</a>. By visualizing sequence alignments in the context of functional annotations and gene networks, researchers can elucidate the biological functions and regulatory mechanisms of genes.<sup id="cite_ref-18" class="reference"><a href="#cite_note-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup> </p><p><b><a href="/wiki/Structural_bioinformatics" title="Structural bioinformatics">Structural bioinformatics</a>:</b> Sequence alignment visualization is integral to <a href="/wiki/Structural_bioinformatics" title="Structural bioinformatics">structural bioinformatics</a>, where researchers analyze protein sequences and structures to understand their three-dimensional organization and functional properties. Visualization tools help in aligning protein sequences, predicting <a href="/wiki/Structural_motif" title="Structural motif">structural motif</a>, and exploring <a href="/wiki/Protein-protein_interactions" class="mw-redirect" title="Protein-protein interactions">protein-protein interactions</a>.<sup id="cite_ref-19" class="reference"><a href="#cite_note-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Macromolecular"><a href="/wiki/Macromolecular" class="mw-redirect" title="Macromolecular">Macromolecular</a></h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Biological_data_visualization&action=edit&section=2" title="Edit section: Macromolecular"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>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. </p><p><b>Techniques</b> </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:VolRenderShearWarp.gif" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/a/a0/VolRenderShearWarp.gif/220px-VolRenderShearWarp.gif" decoding="async" width="220" height="223" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/a/a0/VolRenderShearWarp.gif/330px-VolRenderShearWarp.gif 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/a/a0/VolRenderShearWarp.gif/440px-VolRenderShearWarp.gif 2x" data-file-width="533" data-file-height="540" /></a><figcaption><b>Volume rendering</b></figcaption></figure> <p><b>Segmentation</b> 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.<sup id="cite_ref-20" class="reference"><a href="#cite_note-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> </p><p><b>Volume rendering</b> reveals internal macromolecular structures without segmentation, providing a non-invasive view inside the molecules. </p><p><b>Integrating experimental data</b> 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.<sup id="cite_ref-21" class="reference"><a href="#cite_note-21"><span class="cite-bracket">[</span>21<span class="cite-bracket">]</span></a></sup> </p><p><b>Interactive 3D visualization</b> offers hands-on engagement with macromolecules, allowing for manipulation such as rotation and zooming, which enhances comprehension. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Side-on_3D_view_of_the_Per-Tau_Shell,_giant_structure_forming_star-forming_molecular_clouds_(with_Sun).png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/a/ac/Side-on_3D_view_of_the_Per-Tau_Shell%2C_giant_structure_forming_star-forming_molecular_clouds_%28with_Sun%29.png/220px-Side-on_3D_view_of_the_Per-Tau_Shell%2C_giant_structure_forming_star-forming_molecular_clouds_%28with_Sun%29.png" decoding="async" width="220" height="232" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/a/ac/Side-on_3D_view_of_the_Per-Tau_Shell%2C_giant_structure_forming_star-forming_molecular_clouds_%28with_Sun%29.png/330px-Side-on_3D_view_of_the_Per-Tau_Shell%2C_giant_structure_forming_star-forming_molecular_clouds_%28with_Sun%29.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/a/ac/Side-on_3D_view_of_the_Per-Tau_Shell%2C_giant_structure_forming_star-forming_molecular_clouds_%28with_Sun%29.png/440px-Side-on_3D_view_of_the_Per-Tau_Shell%2C_giant_structure_forming_star-forming_molecular_clouds_%28with_Sun%29.png 2x" data-file-width="1848" data-file-height="1947" /></a><figcaption><b>Interactive 3D visualization</b></figcaption></figure> <p><b><a href="/wiki/Virtual_reality" title="Virtual reality">Virtual reality</a> and <a href="/wiki/Augmented_reality" title="Augmented reality">augmented reality</a></b> 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.<sup id="cite_ref-22" class="reference"><a href="#cite_note-22"><span class="cite-bracket">[</span>22<span class="cite-bracket">]</span></a></sup> </p><p><b>Animation of molecular activities</b> 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.<sup id="cite_ref-23" class="reference"><a href="#cite_note-23"><span class="cite-bracket">[</span>23<span class="cite-bracket">]</span></a></sup> </p><p><b>High-performance computing visualization</b> 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.<sup id="cite_ref-24" class="reference"><a href="#cite_note-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup> </p><p><b>Hybrid visualization</b> techniques merge various methods to provide a multifaceted view of molecules, combining detailed atomic positions with a holistic understanding of structure and volume. </p><p><b>Visualization in different types of macromolecular</b> </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Carbohydrate_kinase_1KYH.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/2/2d/Carbohydrate_kinase_1KYH.png/220px-Carbohydrate_kinase_1KYH.png" decoding="async" width="220" height="165" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/2/2d/Carbohydrate_kinase_1KYH.png/330px-Carbohydrate_kinase_1KYH.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/2/2d/Carbohydrate_kinase_1KYH.png/440px-Carbohydrate_kinase_1KYH.png 2x" data-file-width="1440" data-file-height="1080" /></a><figcaption>Carbohydrate kinase 1KYH</figcaption></figure> <p><b><a href="/wiki/Carbohydrate" title="Carbohydrate">Carbohydrates</a> visualization</b> </p><p>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. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Human_alfa2beta2_hemoglobin.gif" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/2/27/Human_alfa2beta2_hemoglobin.gif/220px-Human_alfa2beta2_hemoglobin.gif" decoding="async" width="220" height="165" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/2/27/Human_alfa2beta2_hemoglobin.gif 1.5x" data-file-width="300" data-file-height="225" /></a><figcaption>Human alfa2beta2 hemoglobin</figcaption></figure> <p><b><a href="/wiki/Protein" title="Protein">Proteins</a> visualization</b> </p><p>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.<sup id="cite_ref-25" class="reference"><a href="#cite_note-25"><span class="cite-bracket">[</span>25<span class="cite-bracket">]</span></a></sup> </p><p><b><a href="/wiki/Nucleic_acid" title="Nucleic acid">Nucleic acid</a> visualization</b> </p><p>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.<sup id="cite_ref-26" class="reference"><a href="#cite_note-26"><span class="cite-bracket">[</span>26<span class="cite-bracket">]</span></a></sup> </p><p><b>Large non-polymeric molecules</b> </p><p>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. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Mesoporous_Silica_Nanoparticle.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Mesoporous_Silica_Nanoparticle.jpg/220px-Mesoporous_Silica_Nanoparticle.jpg" decoding="async" width="220" height="195" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Mesoporous_Silica_Nanoparticle.jpg/330px-Mesoporous_Silica_Nanoparticle.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Mesoporous_Silica_Nanoparticle.jpg/440px-Mesoporous_Silica_Nanoparticle.jpg 2x" data-file-width="740" data-file-height="657" /></a><figcaption>Mesoporous Silica Nanoparticle</figcaption></figure> <p><b><a href="/wiki/Nanoparticle" title="Nanoparticle">Nanoparticles</a></b> 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.<sup id="cite_ref-27" class="reference"><a href="#cite_note-27"><span class="cite-bracket">[</span>27<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-28" class="reference"><a href="#cite_note-28"><span class="cite-bracket">[</span>28<span class="cite-bracket">]</span></a></sup> </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Nanocomposite_structure_german.svg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/4/4f/Nanocomposite_structure_german.svg/220px-Nanocomposite_structure_german.svg.png" decoding="async" width="220" height="147" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/4/4f/Nanocomposite_structure_german.svg/330px-Nanocomposite_structure_german.svg.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/4/4f/Nanocomposite_structure_german.svg/440px-Nanocomposite_structure_german.svg.png 2x" data-file-width="2436" data-file-height="1627" /></a><figcaption>Nanocomposite structure german</figcaption></figure> <p><b><a href="/wiki/Nanocomposite" title="Nanocomposite">Nanocomposites</a></b> 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). </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Carbon_nanotube_(single-walled_zigzag).gif" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/6/68/Carbon_nanotube_%28single-walled_zigzag%29.gif/220px-Carbon_nanotube_%28single-walled_zigzag%29.gif" decoding="async" width="220" height="220" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/6/68/Carbon_nanotube_%28single-walled_zigzag%29.gif/330px-Carbon_nanotube_%28single-walled_zigzag%29.gif 1.5x, //upload.wikimedia.org/wikipedia/commons/6/68/Carbon_nanotube_%28single-walled_zigzag%29.gif 2x" data-file-width="380" data-file-height="380" /></a><figcaption>Carbon nanotube</figcaption></figure> <p><b><a href="/wiki/Nanotube" title="Nanotube">Nanotubes</a></b>, 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. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Electronspun_Nanofibers_April_2023.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/8/87/Electronspun_Nanofibers_April_2023.jpg/220px-Electronspun_Nanofibers_April_2023.jpg" decoding="async" width="220" height="166" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/8/87/Electronspun_Nanofibers_April_2023.jpg/330px-Electronspun_Nanofibers_April_2023.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/8/87/Electronspun_Nanofibers_April_2023.jpg 2x" data-file-width="422" data-file-height="318" /></a><figcaption>Nanofibers</figcaption></figure> <p><b><a href="/wiki/Nanofiber" title="Nanofiber">Nanofibers</a></b> 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. </p><p>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. </p><p><b>Visualize the interactions between macromolecules</b> </p><p>The interactions of protein-carbohydrae was visulazed by hydrogen atoms in a perdeuterated lectin-fucose complex.<sup id="cite_ref-29" class="reference"><a href="#cite_note-29"><span class="cite-bracket">[</span>29<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-30" class="reference"><a href="#cite_note-30"><span class="cite-bracket">[</span>30<span class="cite-bracket">]</span></a></sup> </p><p><b>Tools</b> </p><p>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. </p> <div class="mw-heading mw-heading2"><h2 id="Systems_biology">Systems biology</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Biological_data_visualization&action=edit&section=3" title="Edit section: Systems biology"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Results_of_FBA_maths.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Results_of_FBA_maths.png/220px-Results_of_FBA_maths.png" decoding="async" width="220" height="125" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Results_of_FBA_maths.png/330px-Results_of_FBA_maths.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Results_of_FBA_maths.png/440px-Results_of_FBA_maths.png 2x" data-file-width="1666" data-file-height="946" /></a><figcaption>A metabolic network before and after flux-balance analysis</figcaption></figure> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Whole_body_by_Mass_Spectrometry_Imaging.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/3/36/Whole_body_by_Mass_Spectrometry_Imaging.jpg/220px-Whole_body_by_Mass_Spectrometry_Imaging.jpg" decoding="async" width="220" height="94" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/3/36/Whole_body_by_Mass_Spectrometry_Imaging.jpg/330px-Whole_body_by_Mass_Spectrometry_Imaging.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/3/36/Whole_body_by_Mass_Spectrometry_Imaging.jpg/440px-Whole_body_by_Mass_Spectrometry_Imaging.jpg 2x" data-file-width="1089" data-file-height="464" /></a><figcaption>A whole-body section of a mouse taken using mass spectrometry, with the green particles representing the distribution of drugs and metabolites within its system<sup id="cite_ref-31" class="reference"><a href="#cite_note-31"><span class="cite-bracket">[</span>31<span class="cite-bracket">]</span></a></sup></figcaption></figure> <p><a href="/wiki/Systems_biology" title="Systems biology">Systems biology</a> is a branch of biological data visualization dedicated to analyzing and modeling complex biological systems. Popular computational models used in systems biology include <a href="/wiki/Process_calculi" class="mw-redirect" title="Process calculi">process calculi</a>, such as stochastic <a href="/wiki/%CE%A0-calculus" title="Π-calculus">π-calculus</a>, and constraint-based reconstruction and analysis (COBRA), a paradigm that considers physical, enzymatic, and topological constraints underlying a <a href="/wiki/Phenotype" title="Phenotype">phenotype</a> in a <a href="/wiki/Metabolic_network" title="Metabolic network">metabolic network</a>.<sup id="cite_ref-32" class="reference"><a href="#cite_note-32"><span class="cite-bracket">[</span>32<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-33" class="reference"><a href="#cite_note-33"><span class="cite-bracket">[</span>33<span class="cite-bracket">]</span></a></sup> </p><p>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 <a href="/wiki/Law_of_mass_action" title="Law of mass action">mass action kinetics</a> or <a href="/wiki/Enzyme_kinetics" title="Enzyme kinetics">enzyme kinetics</a>. These values are used as parameters to construct <a href="/wiki/Biochemical_systems_equation" title="Biochemical systems equation">differential equations</a> 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 <a href="/wiki/Flux_balance_analysis" title="Flux balance analysis">flux balance analysis</a> could be used to analyze the flow of metabolites through a particular metabolic network.<sup id="cite_ref-34" class="reference"><a href="#cite_note-34"><span class="cite-bracket">[</span>34<span class="cite-bracket">]</span></a></sup> </p><p>Another key imaging method in systems biology is <a href="/wiki/Mass_spectrometry" title="Mass spectrometry">mass spectrometry</a>, 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 <a href="/wiki/Metabolomics" title="Metabolomics">metabolomics</a>, a branch of systems biology that uses mass spectrometry to measure metabolite distribution information, then uses the measured intensity to construct an image.<sup id="cite_ref-35" class="reference"><a href="#cite_note-35"><span class="cite-bracket">[</span>35<span class="cite-bracket">]</span></a></sup> </p><p>Popular software tools used in systems biology modeling include <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/33507922/">massPy</a>, <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/17855418/">Cytosim</a>, and <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/23423320/">PySB</a>. Further examples may be found at Wikipedia's <a href="/wiki/List_of_systems_biology_modeling_software" title="List of systems biology modeling software">list of systems biology modeling software</a>. </p> <div class="mw-heading mw-heading2"><h2 id="Microscopy_visualization">Microscopy visualization</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Biological_data_visualization&action=edit&section=4" title="Edit section: Microscopy visualization"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Other than optical and electron microscopy, other techniques like scanning probe, ultraviolet, infrared, digital holographic, laser, and amateur are also utilize on Visualization. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Microbial_imaging_techniques.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/0/0c/Microbial_imaging_techniques.jpg/220px-Microbial_imaging_techniques.jpg" decoding="async" width="220" height="241" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/0/0c/Microbial_imaging_techniques.jpg/330px-Microbial_imaging_techniques.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/0/0c/Microbial_imaging_techniques.jpg/440px-Microbial_imaging_techniques.jpg 2x" data-file-width="2128" data-file-height="2331" /></a><figcaption>Microbial imaging</figcaption></figure> <p>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.<sup id="cite_ref-36" class="reference"><a href="#cite_note-36"><span class="cite-bracket">[</span>36<span class="cite-bracket">]</span></a></sup> </p><p>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.<sup id="cite_ref-37" class="reference"><a href="#cite_note-37"><span class="cite-bracket">[</span>37<span class="cite-bracket">]</span></a></sup> </p><p>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. <sup id="cite_ref-38" class="reference"><a href="#cite_note-38"><span class="cite-bracket">[</span>38<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Magnetic_resonance_imaging">Magnetic resonance imaging</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Biological_data_visualization&action=edit&section=5" title="Edit section: Magnetic resonance imaging"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Magnetic_Resonance_Angiography.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/d/d7/Magnetic_Resonance_Angiography.jpg/220px-Magnetic_Resonance_Angiography.jpg" decoding="async" width="220" height="85" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/d/d7/Magnetic_Resonance_Angiography.jpg/330px-Magnetic_Resonance_Angiography.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/d/d7/Magnetic_Resonance_Angiography.jpg/440px-Magnetic_Resonance_Angiography.jpg 2x" data-file-width="2880" data-file-height="1112" /></a><figcaption>Blood flow in the neck and brain depicted using <a href="/wiki/Magnetic_resonance_angiography" title="Magnetic resonance angiography">magnetic resonance angiography</a></figcaption></figure> <p><a href="/wiki/Magnetic_resonance_imaging" title="Magnetic resonance imaging">Magnetic resonance imaging</a> (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 <a href="/wiki/MRI_sequences" class="mw-redirect" title="MRI sequences">MRI sequences</a>. A particularly notable subset of MRI is <a href="/wiki/Magnetic_resonance_angiography" title="Magnetic resonance angiography">magnetic resonance angiography</a>, which is a group of techniques used to image arteries and veins. MRI's imaging utility is further expanded upon by <a href="/wiki/Diffusion_MRI" class="mw-redirect" title="Diffusion MRI">diffusion MRI</a> and <a href="/wiki/Functional_MRI" class="mw-redirect" title="Functional MRI">functional MRI</a>, which can be used to capture neuronal tracts and blood flow respectively. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:DTI-sagittal-fibers.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/8/82/DTI-sagittal-fibers.jpg/220px-DTI-sagittal-fibers.jpg" decoding="async" width="220" height="205" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/8/82/DTI-sagittal-fibers.jpg/330px-DTI-sagittal-fibers.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/8/82/DTI-sagittal-fibers.jpg/440px-DTI-sagittal-fibers.jpg 2x" data-file-width="1021" data-file-height="952" /></a><figcaption><a href="/wiki/Striatum" title="Striatum">Sagittal fibers</a> depicted using <a href="/wiki/Diffusion_MRI" class="mw-redirect" title="Diffusion MRI">diffusion tensor imaging</a> (DTI)</figcaption></figure> <p>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.<sup id="cite_ref-39" class="reference"><a href="#cite_note-39"><span class="cite-bracket">[</span>39<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-40" class="reference"><a href="#cite_note-40"><span class="cite-bracket">[</span>40<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-41" class="reference"><a href="#cite_note-41"><span class="cite-bracket">[</span>41<span class="cite-bracket">]</span></a></sup> Further MRI techniques include saturation pulses (used to reduce motion artifacts), <a href="/wiki/Gradient_echo" title="Gradient echo">gradient echo</a> (such as dynamic contrast enhancement), <a href="/wiki/Spin_echo" title="Spin echo">spin echo</a>, and diffusion weighting (a signal contrast generation method based on differences in <a href="/wiki/Brownian_motion" title="Brownian motion">Brownian motion</a>).<sup id="cite_ref-42" class="reference"><a href="#cite_note-42"><span class="cite-bracket">[</span>42<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-43" class="reference"><a href="#cite_note-43"><span class="cite-bracket">[</span>43<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-44" class="reference"><a href="#cite_note-44"><span class="cite-bracket">[</span>44<span class="cite-bracket">]</span></a></sup> </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:T1t2PD.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/0/03/T1t2PD.jpg/220px-T1t2PD.jpg" decoding="async" width="220" height="97" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/0/03/T1t2PD.jpg/330px-T1t2PD.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/0/03/T1t2PD.jpg/440px-T1t2PD.jpg 2x" data-file-width="541" data-file-height="239" /></a><figcaption>Examples of T1-weighted, T2-weighted and <a href="/wiki/MRI_sequence#Proton_density" class="mw-redirect" title="MRI sequence">PD-weighted</a> MRI scans</figcaption></figure> <p>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).<sup id="cite_ref-45" class="reference"><a href="#cite_note-45"><span class="cite-bracket">[</span>45<span class="cite-bracket">]</span></a></sup> When the magnetic field is removed, the hydrogen protons return to their equilibrium states in a process known as <a href="/wiki/Relaxation_(NMR)" title="Relaxation (NMR)">relaxation</a>, and in doing so they emit RF energy.<sup id="cite_ref-46" class="reference"><a href="#cite_note-46"><span class="cite-bracket">[</span>46<span class="cite-bracket">]</span></a></sup> Different tissues relax at different rates, which allows scientists to use specific RF pulse sequences to emphasize particular tissues or abnormalities. </p><p>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 <a href="/wiki/Fourier_transform" title="Fourier transform">Fourier transformation</a> is used to convert this frequency information into intensity levels, which are displayed as shades of grey in the generated image. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Morbus_Fabry_Stroke_MRT_01.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/6/6e/Morbus_Fabry_Stroke_MRT_01.jpg/220px-Morbus_Fabry_Stroke_MRT_01.jpg" decoding="async" width="220" height="124" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/6/6e/Morbus_Fabry_Stroke_MRT_01.jpg/330px-Morbus_Fabry_Stroke_MRT_01.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/6/6e/Morbus_Fabry_Stroke_MRT_01.jpg/440px-Morbus_Fabry_Stroke_MRT_01.jpg 2x" data-file-width="1200" data-file-height="678" /></a><figcaption>A FLAIR-weighted axial MRI section showing multiple white matter lesions in the cerebral hemispheres</figcaption></figure> <p>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 T<sub>1</sub> or <a href="/wiki/Spin%E2%80%93lattice_relaxation" title="Spin–lattice relaxation">spin–lattice relaxation</a>), and the time taken for the axial spin of the hydrogen protons to return to its resting state (also known as T<sub>2</sub> or <a href="/wiki/Spin%E2%80%93spin_relaxation" title="Spin–spin relaxation">spin–spin relaxation</a>).<sup id="cite_ref-47" class="reference"><a href="#cite_note-47"><span class="cite-bracket">[</span>47<span class="cite-bracket">]</span></a></sup> To create a T<sub>1</sub>-weighted image, the MR signal is measured by changing the amount of time between RF pulses (also known as the <a href="/wiki/Repetition_time" class="mw-redirect" title="Repetition time">time to repeat</a>, or TR). To create a T<sub>2</sub>-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 <a href="/wiki/Echo_time" class="mw-redirect" title="Echo time">time to echo</a>, or TE). The dominant signal intensities of T<sub>1</sub> 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 T<sub>1</sub> weighted sequences to suppress the brightness of the signal created by it. The dominant signal intensities of T<sub>2</sub> image weighting are fluid (white), muscle (grey), and fat (white). T<sub>2</sub> 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. </p><p>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, <a href="/wiki/Hyaline_cartilage" title="Hyaline cartilage">hyaline cartilage</a> and <a href="/wiki/Fibrocartilage" title="Fibrocartilage">fibrocartilage</a>, which makes it ideal for imaging joints. Outside of joint imaging it has largely been replaced by <a href="/wiki/Fluid_attenuated_inversion_recovery" class="mw-redirect" title="Fluid attenuated inversion recovery">fluid attenuated inversion recovery</a> (FLAIR), an <a href="/wiki/Inversion_recovery" title="Inversion recovery">inversion recovery</a> sequence that removes the signal from cerebrospinal fluid.<sup id="cite_ref-48" class="reference"><a href="#cite_note-48"><span class="cite-bracket">[</span>48<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Tomography">Tomography</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Biological_data_visualization&action=edit&section=6" title="Edit section: Tomography"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:SADDLE_PE.JPG" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/e/ea/SADDLE_PE.JPG/220px-SADDLE_PE.JPG" decoding="async" width="220" height="183" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/e/ea/SADDLE_PE.JPG/330px-SADDLE_PE.JPG 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/e/ea/SADDLE_PE.JPG/440px-SADDLE_PE.JPG 2x" data-file-width="1053" data-file-height="876" /></a><figcaption>A <a href="/wiki/Contrast_CT" title="Contrast CT">contrast CT</a> of a <a href="/wiki/Pulmonary_artery" title="Pulmonary artery">pulmonary artery</a> with an <a href="/wiki/Pulmonary_embolism" title="Pulmonary embolism">embolism</a>. Note the contrast between the embolism (center, grey) and the surrounding blood (black). This is because the blood contains a negative <a href="/wiki/Radiocontrast_agent" title="Radiocontrast agent">radiocontrast agent</a>; without the radiocontrast, the blood and the embolism may be indistinguishable.</figcaption></figure> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Recurrensparese.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/7/7d/Recurrensparese.jpg/220px-Recurrensparese.jpg" decoding="async" width="220" height="219" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/7/7d/Recurrensparese.jpg/330px-Recurrensparese.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/7/7d/Recurrensparese.jpg/440px-Recurrensparese.jpg 2x" data-file-width="825" data-file-height="823" /></a><figcaption>Scans of a bronchial tumor taken using <a href="/wiki/Computed_tomography" class="mw-redirect" title="Computed tomography">CT</a>, <a href="/wiki/Positron_emission_tomography" title="Positron emission tomography">PET</a>, <a href="/wiki/PET-CT" title="PET-CT">PET-CT</a>, and <a href="/wiki/Maximum_intensity_projection" title="Maximum intensity projection">MIP</a> PET</figcaption></figure> <p><a href="/wiki/Computed_tomography" class="mw-redirect" title="Computed tomography">Computed tomography</a> (CT) and <a href="/wiki/Positron_emission_tomography" title="Positron emission tomography">positron emission tomography</a> (PET) scans are similar to MRI, but rely on different imaging techniques (X-rays and ionizing radiation, respectively). A variation of CT known as <a href="/wiki/Contrast_CT" title="Contrast CT">contrast CT</a> also requires the subject to take in a contrast medium called a <a href="/wiki/Radiocontrast_agent" title="Radiocontrast agent">radiocontrast</a> (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.<sup id="cite_ref-49" class="reference"><a href="#cite_note-49"><span class="cite-bracket">[</span>49<span class="cite-bracket">]</span></a></sup> </p><p>Like magnetic resonance imaging, CT scans use numerous methods to display and measure data, including <a href="/wiki/CT_scan" title="CT scan">sequential CT</a> (where the CT table steps from location to location), <a href="/wiki/Operation_of_computed_tomography" title="Operation of computed tomography">spiral CT</a> (where the entire X-ray tube is spun around the subject), and <a href="/wiki/Electron_beam_computed_tomography" title="Electron beam computed tomography">electron beam tomography</a> (where only the electron paths are spun using deflection coils). PET scanners don’t have quite as much hardware variation and instead use different <a href="/wiki/Radioactive_tracer" title="Radioactive tracer">radiotracers</a> 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.<sup id="cite_ref-50" class="reference"><a href="#cite_note-50"><span class="cite-bracket">[</span>50<span class="cite-bracket">]</span></a></sup> </p><p>Either or both of these methods can be used in conjunction with <a href="/wiki/Maximum_intensity_projection" title="Maximum intensity projection">maximum intensity projection</a> (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.<sup id="cite_ref-51" class="reference"><a href="#cite_note-51"><span class="cite-bracket">[</span>51<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-52" class="reference"><a href="#cite_note-52"><span class="cite-bracket">[</span>52<span class="cite-bracket">]</span></a></sup> </p><p>MIP imaging is also used with magnetic resonance angiography, and research has indicated that it could feasibly be used with MRI.<sup id="cite_ref-53" class="reference"><a href="#cite_note-53"><span class="cite-bracket">[</span>53<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-54" class="reference"><a href="#cite_note-54"><span class="cite-bracket">[</span>54<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Alignment">Alignment</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Biological_data_visualization&action=edit&section=7" title="Edit section: Alignment"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>A <b>sequence alignment</b> 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. <b>Multiple sequence alignment</b> 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. </p><p><b>Purposes of Alignment Visualization:</b> </p> <ul><li>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.</li> <li>Visualize alignments for figures and publication. It summarizes the multiple sequence alignment in an easy-to-digest form.</li> <li>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.</li></ul> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:RPLP0_90_ClustalW_aln.gif" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/7/79/RPLP0_90_ClustalW_aln.gif/220px-RPLP0_90_ClustalW_aln.gif" decoding="async" width="220" height="124" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/7/79/RPLP0_90_ClustalW_aln.gif/330px-RPLP0_90_ClustalW_aln.gif 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/7/79/RPLP0_90_ClustalW_aln.gif/440px-RPLP0_90_ClustalW_aln.gif 2x" data-file-width="1250" data-file-height="706" /></a><figcaption>Multiple Sequence Alignment of the protein sequences to the left. Colors are used to display similarities among the sequences.</figcaption></figure> <p><b>Regular multiple sequence alignment</b> – 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. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:The-sequence-alignment-visualization-of-large-gene-sets-analyzed-with-the-AlignStatPlot.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/6/68/The-sequence-alignment-visualization-of-large-gene-sets-analyzed-with-the-AlignStatPlot.png/220px-The-sequence-alignment-visualization-of-large-gene-sets-analyzed-with-the-AlignStatPlot.png" decoding="async" width="220" height="126" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/6/68/The-sequence-alignment-visualization-of-large-gene-sets-analyzed-with-the-AlignStatPlot.png/330px-The-sequence-alignment-visualization-of-large-gene-sets-analyzed-with-the-AlignStatPlot.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/6/68/The-sequence-alignment-visualization-of-large-gene-sets-analyzed-with-the-AlignStatPlot.png/440px-The-sequence-alignment-visualization-of-large-gene-sets-analyzed-with-the-AlignStatPlot.png 2x" data-file-width="850" data-file-height="488" /></a><figcaption>Circular Multiple Sequence Alignment where the start and end of protein sequences can vary to find better matches.</figcaption></figure> <p><b>Circular multiple sequence alignment</b> – 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. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Spiral_Multiple_Sequence_Alignment.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/9/95/Spiral_Multiple_Sequence_Alignment.png/220px-Spiral_Multiple_Sequence_Alignment.png" decoding="async" width="220" height="220" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/9/95/Spiral_Multiple_Sequence_Alignment.png/330px-Spiral_Multiple_Sequence_Alignment.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/9/95/Spiral_Multiple_Sequence_Alignment.png/440px-Spiral_Multiple_Sequence_Alignment.png 2x" data-file-width="1026" data-file-height="1025" /></a><figcaption>Spiral display of an alignment of multiple protein sequences.</figcaption></figure> <p><b>Spiral multiple sequence alignment</b> – 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. </p><p><br /> </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:3D_Multiple_Sequence_Alignment.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/a/aa/3D_Multiple_Sequence_Alignment.png/220px-3D_Multiple_Sequence_Alignment.png" decoding="async" width="220" height="104" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/a/aa/3D_Multiple_Sequence_Alignment.png/330px-3D_Multiple_Sequence_Alignment.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/a/aa/3D_Multiple_Sequence_Alignment.png/440px-3D_Multiple_Sequence_Alignment.png 2x" data-file-width="512" data-file-height="241" /></a><figcaption>3-dimensional multiple sequence alignment, produced on the 1D-3D Group Alignment Viewer, by RCSB Protein Data Bank.</figcaption></figure> <p><b>3D visualization</b> – 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. </p><p>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. <sup id="cite_ref-55" class="reference"><a href="#cite_note-55"><span class="cite-bracket">[</span>55<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Phylogenies">Phylogenies</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Biological_data_visualization&action=edit&section=8" title="Edit section: Phylogenies"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure typeof="mw:File/Thumb"><a href="/wiki/File:Phylogeny_of_Hoplocercinae.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Phylogeny_of_Hoplocercinae.jpg/220px-Phylogeny_of_Hoplocercinae.jpg" decoding="async" width="220" height="291" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Phylogeny_of_Hoplocercinae.jpg/331px-Phylogeny_of_Hoplocercinae.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Phylogeny_of_Hoplocercinae.jpg/440px-Phylogeny_of_Hoplocercinae.jpg 2x" data-file-width="1202" data-file-height="1588" /></a><figcaption>Phylogeny of Hoplocercinae</figcaption></figure><p>A <b>phylogenetic tree</b> 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. </p><p>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. <b>Regular phylogenetic tree</b> – Generally called a <a href="/wiki/Dendrogram" title="Dendrogram">dendrogram</a>, 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. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:CLADOGRAM.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/0/02/CLADOGRAM.jpg/220px-CLADOGRAM.jpg" decoding="async" width="220" height="198" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/0/02/CLADOGRAM.jpg/330px-CLADOGRAM.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/0/02/CLADOGRAM.jpg/440px-CLADOGRAM.jpg 2x" data-file-width="450" data-file-height="406" /></a><figcaption>Cladogram of Primates</figcaption></figure> <p><b>Cladogram</b> – 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. </p><p><br /> </p><p><br /> </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Fig_5_Phylogeny_of_genera_Marnaviridae.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/8/8c/Fig_5_Phylogeny_of_genera_Marnaviridae.jpg/220px-Fig_5_Phylogeny_of_genera_Marnaviridae.jpg" decoding="async" width="220" height="220" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/8/8c/Fig_5_Phylogeny_of_genera_Marnaviridae.jpg/330px-Fig_5_Phylogeny_of_genera_Marnaviridae.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/8/8c/Fig_5_Phylogeny_of_genera_Marnaviridae.jpg/440px-Fig_5_Phylogeny_of_genera_Marnaviridae.jpg 2x" data-file-width="2001" data-file-height="2001" /></a><figcaption>Circular phylogenetic tree of environmental sequences of genera within the Marnaviridae</figcaption></figure> <p><b>Circular phylogenetic tree</b> – 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. </p><p><br /> </p><p><br /> </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Contrast_between_2-dimensional_phylogeny_and_3-dimensional_phylogeny.webp" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/c/c2/Contrast_between_2-dimensional_phylogeny_and_3-dimensional_phylogeny.webp/220px-Contrast_between_2-dimensional_phylogeny_and_3-dimensional_phylogeny.webp.png" decoding="async" width="220" height="182" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/c/c2/Contrast_between_2-dimensional_phylogeny_and_3-dimensional_phylogeny.webp/330px-Contrast_between_2-dimensional_phylogeny_and_3-dimensional_phylogeny.webp.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/c/c2/Contrast_between_2-dimensional_phylogeny_and_3-dimensional_phylogeny.webp/440px-Contrast_between_2-dimensional_phylogeny_and_3-dimensional_phylogeny.webp.png 2x" data-file-width="1200" data-file-height="992" /></a><figcaption>Both trees represent COG1222.</figcaption></figure> <p><b>3D Visualization</b> – 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. <sup id="cite_ref-56" class="reference"><a href="#cite_note-56"><span class="cite-bracket">[</span>56<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Visualization_software">Visualization software</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Biological_data_visualization&action=edit&section=9" title="Edit section: Visualization software"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <table class="wikitable sortable"> <tbody><tr> <th>Name </th> <th>Description </th> <th>Data type </th> <th>Author(s) </th> <th>Year </th></tr> <tr> <td><a href="/wiki/Cytoscape" title="Cytoscape">Cytoscape</a> </td> <td>Open source software platform for visualizing complex biological networks<sup id="cite_ref-57" class="reference"><a href="#cite_note-57"><span class="cite-bracket">[</span>57<span class="cite-bracket">]</span></a></sup></td> <td>Systems biology</td> <td>Cytoscape Team</td> <td>July 2002 </td></tr> <tr> <td>FigTree </td> <td>Java tree viewer able to read multiple tree file formats, color branches, and produce vector artwork</td> <td>Phylogenetic tree</td> <td>Andrew Rambaut</td> <td>Nov 6, 2006 </td></tr> <tr> <td>Interactive Tree Of Life (ITOL) </td> <td>Constructs trees and annotates them with various types of data</td> <td>Phylogenetic tree</td> <td>Ciccarelli FD, et al. <sup id="cite_ref-58" class="reference"><a href="#cite_note-58"><span class="cite-bracket">[</span>58<span class="cite-bracket">]</span></a></sup> </td> <td>Mar 3, 2006 </td></tr> <tr> <td><a href="/wiki/Jmol" title="Jmol">Jmol</a> </td> <td>Free, open-source java applet capable of loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, and crystal symmetry<sup id="cite_ref-59" class="reference"><a href="#cite_note-59"><span class="cite-bracket">[</span>59<span class="cite-bracket">]</span></a></sup></td> <td>Molecular</td> <td>Dan Gezelter</td> <td>2001 </td></tr> <tr> <td>Medical Image Processing, Analysis, and Visualization (MIPAV) </td> <td>Quantitative analysis and visualization of medical images for modalities such as PET, MRI, CT, or microscopy<sup id="cite_ref-60" class="reference"><a href="#cite_note-60"><span class="cite-bracket">[</span>60<span class="cite-bracket">]</span></a></sup></td> <td>Medical imaging</td> <td>National Institutes of Health Center for Information Technology</td> <td>Unknown </td></tr> <tr> <td>Medusa </td> <td>Software to build and analyze ensembles of genome-scale metabolic network reconstructions<sup id="cite_ref-61" class="reference"><a href="#cite_note-61"><span class="cite-bracket">[</span>61<span class="cite-bracket">]</span></a></sup></td> <td>Systems biology</td> <td>Gregory L. Medlock, Thomas J. Moutinho, Jason A. Papin</td> <td>2001 </td></tr> <tr> <td><a href="/wiki/Molecular_Evolutionary_Genetics_Analysis" title="Molecular Evolutionary Genetics Analysis">Molecular Evolutionary Genetics Analysis</a> (MEGA) </td> <td>Provides multiple algorithms to construct phylogenetic trees, including UPGMA, Maximum Likelihood, Maximum Parsimony, etc</td> <td>Phylogenetic tree</td> <td>Masatoshi Nei, Sudhir Kumar, Koichiro Tamura, Glen Stecher, Daniel Peterson, Nicholas Peterson</td> <td>1993 </td></tr> <tr> <td><a href="/wiki/Molecular_Operating_Environment" title="Molecular Operating Environment">Molecular Operating Environment</a> (MOE) </td> <td>Models micro- and macromolecules, protein-ligand complexes, and crystal lattices</td> <td>Molecular</td> <td>Chemical Computing Group</td> <td>Unknown </td></tr> <tr> <td><a href="/wiki/PyMOL" title="PyMOL">PyMOL</a> </td> <td>Open-source Python application for modeling biological macromolecules</td> <td>Molecular</td> <td>Warren Delano</td> <td>2017 </td></tr> <tr> <td><a href="/wiki/T-Coffee" title="T-Coffee">T-Coffee</a> </td> <td>Performs multiple sequence alignment using a progressive approach</td> <td>Sequences</td> <td>Cédric Notredame</td> <td>Oct 15, 2020 </td></tr></tbody></table> <ul class="gallery mw-gallery-traditional" style="max-width: 489px;border:0px; text-align:center; background:transparent;"> <li class="gallerybox" style="width: 155px"> <div class="thumb" style="width: 150px; height: 150px;"><span typeof="mw:File"><a href="/wiki/File:Tree_of_life_SVG.svg" class="mw-file-description" title="ITOL tree of life"><img alt="ITOL tree of life" src="//upload.wikimedia.org/wikipedia/commons/thumb/1/11/Tree_of_life_SVG.svg/120px-Tree_of_life_SVG.svg.png" decoding="async" width="120" height="120" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/1/11/Tree_of_life_SVG.svg/180px-Tree_of_life_SVG.svg.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/1/11/Tree_of_life_SVG.svg/240px-Tree_of_life_SVG.svg.png 2x" data-file-width="1355" data-file-height="1355" /></a></span></div> <div class="gallerytext">ITOL tree of life</div> </li> <li class="gallerybox" style="width: 155px"> <div class="thumb" style="width: 150px; height: 150px;"><span typeof="mw:File"><a href="/wiki/File:JMOL-1AER.png" class="mw-file-description" title="Visualization of exotoxin A created with Jmol"><img alt="Visualization of exotoxin A created with Jmol" src="//upload.wikimedia.org/wikipedia/commons/thumb/c/c5/JMOL-1AER.png/120px-JMOL-1AER.png" decoding="async" width="120" height="59" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/c/c5/JMOL-1AER.png/180px-JMOL-1AER.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/c/c5/JMOL-1AER.png/240px-JMOL-1AER.png 2x" data-file-width="1916" data-file-height="935" /></a></span></div> <div class="gallerytext">Visualization of <a href="/wiki/Pseudomonas_exotoxin" title="Pseudomonas exotoxin">exotoxin A</a> created with Jmol</div> </li> <li class="gallerybox" style="width: 155px"> <div class="thumb" style="width: 150px; height: 150px;"><span typeof="mw:File"><a href="/wiki/File:Metulodontia-Maximum-Likelihood.svg" class="mw-file-description" title="Maximum likelihood phylogenetic tree created with MEGA6"><img alt="Maximum likelihood phylogenetic tree created with MEGA6" src="//upload.wikimedia.org/wikipedia/commons/thumb/2/29/Metulodontia-Maximum-Likelihood.svg/120px-Metulodontia-Maximum-Likelihood.svg.png" decoding="async" width="120" height="100" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/2/29/Metulodontia-Maximum-Likelihood.svg/180px-Metulodontia-Maximum-Likelihood.svg.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/2/29/Metulodontia-Maximum-Likelihood.svg/240px-Metulodontia-Maximum-Likelihood.svg.png 2x" data-file-width="495" data-file-height="414" /></a></span></div> <div class="gallerytext"><a href="/wiki/Maximum_likelihood_estimation" title="Maximum likelihood estimation">Maximum likelihood</a> <a href="/wiki/Phylogenetic_tree" title="Phylogenetic tree">phylogenetic tree</a> created with <a href="/wiki/Molecular_Evolutionary_Genetics_Analysis" title="Molecular Evolutionary Genetics Analysis">MEGA6</a></div> </li> <li class="gallerybox" style="width: 155px"> <div class="thumb" style="width: 150px; height: 150px;"><span typeof="mw:File"><a href="/wiki/File:AT-hook_PyMol.png" class="mw-file-description" title="Segment of DNA depicted by PyMOL"><img alt="Segment of DNA depicted by PyMOL" src="//upload.wikimedia.org/wikipedia/commons/thumb/4/46/AT-hook_PyMol.png/120px-AT-hook_PyMol.png" decoding="async" width="120" height="103" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/4/46/AT-hook_PyMol.png/180px-AT-hook_PyMol.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/4/46/AT-hook_PyMol.png/240px-AT-hook_PyMol.png 2x" data-file-width="1033" data-file-height="887" /></a></span></div> <div class="gallerytext">Segment of <a href="/wiki/DNA" title="DNA">DNA</a> depicted by PyMOL</div> </li> <li class="gallerybox" style="width: 155px"> <div class="thumb" style="width: 150px; height: 150px;"><span typeof="mw:File"><a href="/wiki/File:Cytoscape_network_visualization1.png" class="mw-file-description" title="Yeast network data visualized by Cytoscape"><img alt="Yeast network data visualized by Cytoscape" src="//upload.wikimedia.org/wikipedia/commons/thumb/0/08/Cytoscape_network_visualization1.png/120px-Cytoscape_network_visualization1.png" decoding="async" width="120" height="99" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/0/08/Cytoscape_network_visualization1.png/180px-Cytoscape_network_visualization1.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/0/08/Cytoscape_network_visualization1.png/240px-Cytoscape_network_visualization1.png 2x" data-file-width="1069" data-file-height="883" /></a></span></div> <div class="gallerytext">Yeast network data visualized by Cytoscape</div> </li> <li class="gallerybox" style="width: 155px"> <div class="thumb" style="width: 150px; height: 150px;"><span typeof="mw:File"><a href="/wiki/File:T_coffee_alignment.png" class="mw-file-description" title="Multiple sequence alignment of PET hydrolases created with T-Coffee"><img alt="Multiple sequence alignment of PET hydrolases created with T-Coffee" src="//upload.wikimedia.org/wikipedia/commons/thumb/d/db/T_coffee_alignment.png/120px-T_coffee_alignment.png" decoding="async" width="120" height="45" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/d/db/T_coffee_alignment.png/180px-T_coffee_alignment.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/d/db/T_coffee_alignment.png/240px-T_coffee_alignment.png 2x" data-file-width="855" data-file-height="321" /></a></span></div> <div class="gallerytext"><a href="/wiki/Multiple_sequence_alignment" title="Multiple sequence alignment">Multiple sequence alignment</a> of <a href="/wiki/PETase" title="PETase">PET hydrolases</a> created with <a href="/wiki/T-Coffee" title="T-Coffee">T-Coffee</a></div> </li> </ul> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Biological_data_visualization&action=edit&section=10" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output .reflist-lower-alpha{list-style-type:lower-alpha}.mw-parser-output .reflist-lower-greek{list-style-type:lower-greek}.mw-parser-output .reflist-lower-roman{list-style-type:lower-roman}</style><div class="reflist"> <div class="mw-references-wrap mw-references-columns"><ol class="references"> <li id="cite_note-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-1">^</a></b></span> <span class="reference-text"><style data-mw-deduplicate="TemplateStyles:r1238218222">.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .cs1-maint{color:#18911f}}</style><cite id="CITEREFLucićFörsterBaumeister2005" class="citation journal cs1">Lucić V, Förster F, Baumeister W (2005). 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PLoS Comput Biol.: e1007847. <a href="/wiki/Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2020PLSCB..16E7847M">2020PLSCB..16E7847M</a>. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1371%2Fjournal.pcbi.1007847">10.1371/journal.pcbi.1007847</a></span>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7213742">7213742</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/32348298">32348298</a>.</cite><span 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href="/w/index.php?title=Biological_data_visualization&action=edit&section=11" title="Edit section: External links"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Related_conferences">Related conferences</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Biological_data_visualization&action=edit&section=12" title="Edit section: Related conferences"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><a rel="nofollow" class="external text" href="http://www.biovis.net">BioVis: Symposium on Biological Data Visualization</a></li> <li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20110717081333/http://www.sbforum.org/earchive.php?e_id=45">Applications of Information Visualization in Bioinformatics</a></li> <li><a rel="nofollow" class="external text" href="http://www.pa.icar.cnr.it/sscibb2008/">CIBDV: Computational Intelligence for Biological Data Visualization</a></li> <li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20081218204158/http://www.graphicslink.co.uk/IV09/IVbm.htm">IVBI: Information Visualization in Biomedical Informatics Symposium</a></li> <li><a rel="nofollow" class="external text" href="http://www.faculty.jacobs-university.de/llinsen/vmls/2009">VMLS: Visualization in Medicine & Life Sciences</a></li> <li><a rel="nofollow" class="external text" href="http://vizbi.org">VIZBI: Workshop on Visualizing Biological Data</a></li></ul> <div class="navbox-styles"><style data-mw-deduplicate="TemplateStyles:r1129693374">.mw-parser-output .hlist dl,.mw-parser-output .hlist ol,.mw-parser-output .hlist ul{margin:0;padding:0}.mw-parser-output .hlist dd,.mw-parser-output .hlist dt,.mw-parser-output .hlist li{margin:0;display:inline}.mw-parser-output .hlist.inline,.mw-parser-output .hlist.inline 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imaging">Chemical imaging</a></li> <li><a href="/wiki/Crime_mapping" title="Crime mapping">Crime mapping</a></li> <li><a href="/wiki/Data_visualization" class="mw-redirect" title="Data visualization">Data visualization</a></li> <li><a href="/wiki/Visualization_(graphics)" title="Visualization (graphics)">Educational visualization</a></li> <li><a href="/wiki/Flow_visualization" title="Flow visualization">Flow visualization</a></li> <li><a href="/wiki/Geovisualization" title="Geovisualization">Geovisualization</a></li> <li><a href="/wiki/Information_visualization" class="mw-redirect" title="Information visualization">Information visualization</a></li> <li><a href="/wiki/Mathematical_diagram" title="Mathematical diagram">Mathematical visualization</a></li> <li><a href="/wiki/Medical_imaging" title="Medical imaging">Medical imaging</a></li> <li><a href="/wiki/Molecular_graphics" title="Molecular graphics">Molecular graphics</a></li> <li><a href="/wiki/Visualization_(graphics)" title="Visualization (graphics)">Product visualization</a></li> <li><a href="/wiki/Scientific_visualization" title="Scientific visualization">Scientific visualization</a></li> <li><a href="/wiki/Social_visualization" title="Social visualization">Social visualization</a></li> <li><a href="/wiki/Software_visualization" title="Software visualization">Software visualization</a></li> <li><a href="/wiki/Technical_drawing" title="Technical drawing">Technical drawing</a></li> <li><a href="/wiki/User_interface_design" title="User interface design">User interface design</a></li> <li><a href="/wiki/Visual_culture" title="Visual culture">Visual culture</a></li> <li><a href="/wiki/Volume_rendering" title="Volume rendering">Volume visualization</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Image <br />types</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Chart" title="Chart">Chart</a></li> <li><a href="/wiki/Diagram" title="Diagram">Diagram</a></li> <li><a href="/wiki/Engineering_drawing" title="Engineering drawing">Engineering drawing</a></li> <li><a href="/wiki/Graph_of_a_function" title="Graph of a function">Graph of a function</a></li> <li><a href="/wiki/Ideogram" title="Ideogram">Ideogram</a></li> <li><a href="/wiki/Map" title="Map">Map</a></li> <li><a href="/wiki/Photograph" title="Photograph">Photograph</a></li> <li><a href="/wiki/Pictogram" title="Pictogram">Pictogram</a></li> <li><a href="/wiki/Plot_(graphics)" title="Plot (graphics)">Plot</a></li> <li><a href="/wiki/Sankey_diagram" title="Sankey diagram">Sankey diagram</a></li> <li><a href="/wiki/Schematic" title="Schematic">Schematic</a></li> <li><a href="/wiki/Skeletal_formula" title="Skeletal formula">Skeletal formula</a></li> <li><a href="/wiki/Statistical_graphics" title="Statistical graphics">Statistical graphics</a></li> <li><a href="/wiki/Table_(information)" title="Table (information)">Table</a></li> <li><a href="/wiki/Technical_drawing" title="Technical drawing">Technical drawings</a></li> <li><a href="/wiki/Technical_illustration" title="Technical illustration">Technical illustration</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">People</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%">Pre-19th century</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Edmond_Halley" title="Edmond Halley">Edmond Halley</a></li> <li><a href="/wiki/Charles-Ren%C3%A9_de_Fourcroy" title="Charles-René de Fourcroy">Charles-René de Fourcroy</a></li> <li><a href="/wiki/Joseph_Priestley" title="Joseph Priestley">Joseph Priestley</a></li> <li><a href="/wiki/Gaspard_Monge" title="Gaspard Monge">Gaspard Monge</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">19th century</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Charles_Dupin" title="Charles Dupin">Charles Dupin</a></li> <li><a href="/wiki/Adolphe_Quetelet" title="Adolphe Quetelet">Adolphe Quetelet</a></li> <li><a href="/wiki/Andr%C3%A9-Michel_Guerry" title="André-Michel Guerry">André-Michel Guerry</a></li> <li><a href="/wiki/William_Playfair" title="William Playfair">William Playfair</a></li> <li><a href="/wiki/August_Kekul%C3%A9" title="August Kekulé">August Kekulé</a></li> <li><a href="/wiki/Charles_Joseph_Minard" title="Charles Joseph Minard">Charles Joseph Minard</a></li> <li><a href="/wiki/Francis_Amasa_Walker" title="Francis Amasa Walker">Francis Amasa Walker</a></li> <li><a href="/wiki/John_Venn" title="John Venn">John Venn</a></li> <li><a href="/wiki/Oliver_Byrne_(mathematician)" title="Oliver Byrne (mathematician)">Oliver Byrne</a></li> <li><a href="/wiki/Matthew_Henry_Phineas_Riall_Sankey" title="Matthew Henry Phineas Riall Sankey">Matthew Sankey</a></li> <li><a href="/wiki/Charles_Booth_(social_reformer)" title="Charles Booth (social reformer)">Charles Booth</a></li> <li><a href="/wiki/John_Snow" title="John Snow">John Snow</a></li> <li><a href="/wiki/Florence_Nightingale" title="Florence Nightingale">Florence Nightingale</a></li> <li><a href="/wiki/Karl_Wilhelm_Pohlke" title="Karl Wilhelm Pohlke">Karl Wilhelm Pohlke</a></li> <li><a href="/wiki/Toussaint_Loua" title="Toussaint Loua">Toussaint Loua</a></li> <li><a href="/wiki/Francis_Galton" title="Francis Galton">Francis Galton</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Early 20th century</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Edward_Walter_Maunder" title="Edward Walter Maunder">Edward Walter Maunder</a></li> <li><a href="/wiki/Otto_Neurath" title="Otto Neurath">Otto Neurath</a></li> <li><a href="/wiki/W._E._B._Du_Bois" title="W. E. B. Du Bois">W. E. B. Du Bois</a></li> <li><a href="/wiki/Henry_Gantt" title="Henry Gantt">Henry Gantt</a></li> <li><a href="/wiki/Arthur_Lyon_Bowley" title="Arthur Lyon Bowley">Arthur Lyon Bowley</a></li> <li><a href="/wiki/Howard_G._Funkhouser" title="Howard G. Funkhouser">Howard G. Funkhouser</a></li> <li><a href="/wiki/John_B._Peddle" title="John B. Peddle">John B. Peddle</a></li> <li><a href="/wiki/Ejnar_Hertzsprung" title="Ejnar Hertzsprung">Ejnar Hertzsprung</a></li> <li><a href="/wiki/Henry_Norris_Russell" title="Henry Norris Russell">Henry Norris Russell</a></li> <li><a href="/wiki/Max_O._Lorenz" title="Max O. Lorenz">Max O. Lorenz</a></li> <li><a href="/wiki/Fritz_Kahn" title="Fritz Kahn">Fritz Kahn</a></li> <li><a href="/wiki/Harry_Beck" title="Harry Beck">Harry Beck</a></li> <li><a href="/wiki/Erwin_Raisz" title="Erwin Raisz">Erwin Raisz</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Mid 20th century</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Jacques_Bertin" title="Jacques Bertin">Jacques Bertin</a></li> <li><a href="/wiki/Rudolf_Modley" title="Rudolf Modley">Rudolf Modley</a></li> <li><a href="/wiki/Arthur_H._Robinson" title="Arthur H. Robinson">Arthur H. Robinson</a></li> <li><a href="/wiki/John_Tukey" title="John Tukey">John Tukey</a></li> <li><a href="/wiki/Mary_Eleanor_Spear" title="Mary Eleanor Spear">Mary Eleanor Spear</a></li> <li><a href="/wiki/Edgar_Anderson" title="Edgar Anderson">Edgar Anderson</a></li> <li><a href="/wiki/Howard_T._Fisher" title="Howard T. Fisher">Howard T. Fisher</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Late 20th century</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Borden_Dent" title="Borden Dent">Borden Dent</a></li> <li><a href="/wiki/Nigel_Holmes" title="Nigel Holmes">Nigel Holmes</a></li> <li><a href="/wiki/William_S._Cleveland" title="William S. Cleveland">William S. Cleveland</a></li> <li><a href="/wiki/George_G._Robertson" title="George G. Robertson">George G. Robertson</a></li> <li><a href="/wiki/Bruce_H._McCormick" title="Bruce H. McCormick">Bruce H. McCormick</a></li> <li><a href="/wiki/Catherine_Plaisant" title="Catherine Plaisant">Catherine Plaisant</a></li> <li><a href="/wiki/Stuart_Card" title="Stuart Card">Stuart Card</a></li> <li><a href="/wiki/Pat_Hanrahan" title="Pat Hanrahan">Pat Hanrahan</a></li> <li><a href="/wiki/Edward_Tufte" title="Edward Tufte">Edward Tufte</a></li> <li><a href="/wiki/Ben_Shneiderman" title="Ben Shneiderman">Ben Shneiderman</a></li> <li><a href="/wiki/Michael_Friendly" title="Michael Friendly">Michael Friendly</a></li> <li><a href="/wiki/Howard_Wainer" title="Howard Wainer">Howard Wainer</a></li> <li><a href="/wiki/Clifford_A._Pickover" title="Clifford A. Pickover">Clifford A. Pickover</a></li> <li><a href="/wiki/Lawrence_J._Rosenblum" title="Lawrence J. Rosenblum">Lawrence J. Rosenblum</a></li> <li><a href="/wiki/Thomas_A._DeFanti" title="Thomas A. DeFanti">Thomas A. DeFanti</a></li> <li><a href="/wiki/George_Furnas" title="George Furnas">George Furnas</a></li> <li><a href="/wiki/Sheelagh_Carpendale" title="Sheelagh Carpendale">Sheelagh Carpendale</a></li> <li><a href="/wiki/Cynthia_Brewer" title="Cynthia Brewer">Cynthia Brewer</a></li> <li><a href="/wiki/Jock_D._Mackinlay" title="Jock D. Mackinlay">Jock D. Mackinlay</a></li> <li><a href="/wiki/Alan_MacEachren" title="Alan MacEachren">Alan MacEachren</a></li> <li><a href="/wiki/David_Goodsell" title="David Goodsell">David Goodsell</a></li> <li><a href="/wiki/Kwan-Liu_Ma" title="Kwan-Liu Ma">Kwan-Liu Ma</a></li> <li><a href="/wiki/Michael_Maltz" class="mw-redirect" title="Michael Maltz">Michael Maltz</a></li> <li><a href="/wiki/Leland_Wilkinson" title="Leland Wilkinson">Leland Wilkinson</a></li> <li><a href="/wiki/Alfred_Inselberg" title="Alfred Inselberg">Alfred Inselberg</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Early 21st century</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Ben_Fry" title="Ben Fry">Ben Fry</a></li> <li><a href="/wiki/Jeffrey_Heer" title="Jeffrey Heer">Jeffrey Heer</a></li> <li><a href="/wiki/Jessica_Hullman" title="Jessica Hullman">Jessica Hullman</a></li> <li><a href="/wiki/Gordon_Kindlmann" title="Gordon Kindlmann">Gordon Kindlmann</a></li> <li><a href="/wiki/Aaron_Koblin" title="Aaron Koblin">Aaron Koblin</a></li> <li><a href="/wiki/Christopher_R._Johnson" title="Christopher R. Johnson">Christopher R. Johnson</a></li> <li><a href="/wiki/Manuel_Lima" title="Manuel Lima">Manuel Lima</a></li> <li><a href="/wiki/David_McCandless" title="David McCandless">David McCandless</a></li> <li><a href="/wiki/Mauro_Martino" title="Mauro Martino">Mauro Martino</a></li> <li><a href="/wiki/John_Maeda" title="John Maeda">John Maeda</a></li> <li><a href="/wiki/Miriah_Meyer" title="Miriah Meyer">Miriah Meyer</a></li> <li><a href="/wiki/Tamara_Munzner" title="Tamara Munzner">Tamara Munzner</a></li> <li><a href="/wiki/Ade_Olufeko" class="mw-redirect" title="Ade Olufeko">Ade Olufeko</a></li> <li><a href="/wiki/Hanspeter_Pfister" title="Hanspeter Pfister">Hanspeter Pfister</a></li> <li><a href="/wiki/Hans_Rosling" title="Hans Rosling">Hans Rosling</a></li> <li><a href="/wiki/Claudio_Silva_(computer_scientist)" title="Claudio Silva (computer scientist)">Claudio Silva</a></li> <li><a href="/wiki/Moritz_Stefaner" title="Moritz Stefaner">Moritz Stefaner</a></li> <li><a href="/wiki/Fernanda_Vi%C3%A9gas" title="Fernanda Viégas">Fernanda Viégas</a></li> <li><a href="/wiki/Martin_M._Wattenberg" title="Martin M. Wattenberg">Martin Wattenberg</a></li> <li><a href="/wiki/Bang_Wong" title="Bang Wong">Bang Wong</a></li> <li><a href="/wiki/Hadley_Wickham" title="Hadley Wickham">Hadley Wickham</a></li></ul> </div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Related <br />topics</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Cartography" title="Cartography">Cartography</a></li> <li><a href="/wiki/Chartjunk" title="Chartjunk">Chartjunk</a></li> <li><a href="/wiki/Color_coding_in_data_visualization" class="mw-redirect" title="Color coding in data visualization">Color coding</a></li> <li><a href="/wiki/Computer_graphics" title="Computer graphics">Computer graphics</a> <ul><li><a href="/wiki/Computer_graphics_(computer_science)" title="Computer graphics (computer science)">in computer science</a></li></ul></li> <li><a href="/wiki/CPK_coloring" title="CPK coloring">CPK coloring</a></li> <li><a href="/wiki/Graph_drawing" title="Graph drawing">Graph drawing</a></li> <li><a href="/wiki/Graphic_design" title="Graphic design">Graphic design</a></li> <li><a href="/wiki/Graphic_organizer" title="Graphic organizer">Graphic organizer</a></li> <li><a href="/wiki/Imaging_science" class="mw-redirect" title="Imaging science">Imaging science</a></li> <li><a href="/wiki/Information_art" title="Information art">Information art</a></li> <li><a href="/wiki/Infographic" title="Infographic">Information graphics</a></li> <li><a href="/wiki/Information_science" title="Information science">Information science</a></li> <li><a href="/wiki/Misleading_graph" title="Misleading graph">Misleading graph</a></li> <li><a href="/wiki/Neuroimaging" title="Neuroimaging">Neuroimaging</a></li> <li><a href="/wiki/Patent_drawing" title="Patent drawing">Patent drawing</a></li> <li><a href="/wiki/Scientific_modelling" title="Scientific modelling">Scientific modelling</a></li> <li><a href="/wiki/Spatial_analysis" title="Spatial analysis">Spatial analysis</a></li> <li><a href="/wiki/Visual_analytics" title="Visual analytics">Visual analytics</a></li> <li><a href="/wiki/Visual_perception" title="Visual perception">Visual perception</a></li> <li><a href="/wiki/Volume_cartography" title="Volume cartography">Volume cartography</a></li> <li><a href="/wiki/Volume_rendering" title="Volume rendering">Volume rendering</a></li></ul> </div></td></tr></tbody></table></div>    </div><noscript><img src="https://login.wikimedia.org/wiki/Special:CentralAutoLogin/start?useformat=desktop&type=1x1&usesul3=0" alt="" width="1" height="1" style="border: none; position: absolute;"></noscript> <div class="printfooter" data-nosnippet="">Retrieved from "<a dir="ltr" href="https://en.wikipedia.org/w/index.php?title=Biological_data_visualization&oldid=1274821754">https://en.wikipedia.org/w/index.php?title=Biological_data_visualization&oldid=1274821754</a>"</div></div> <div id="catlinks" class="catlinks" data-mw="interface"><div id="mw-normal-catlinks" class="mw-normal-catlinks"><a href="/wiki/Help:Category" title="Help:Category">Categories</a>: <ul><li><a href="/wiki/Category:Bioinformatics" title="Category:Bioinformatics">Bioinformatics</a></li><li><a href="/wiki/Category:Visualization_(graphics)" title="Category:Visualization (graphics)">Visualization (graphics)</a></li></ul></div><div id="mw-hidden-catlinks" class="mw-hidden-catlinks mw-hidden-cats-hidden">Hidden categories: <ul><li><a href="/wiki/Category:CS1:_long_volume_value" title="Category:CS1: long volume value">CS1: long volume value</a></li><li><a href="/wiki/Category:CS1_errors:_periodical_ignored" title="Category:CS1 errors: periodical ignored">CS1 errors: periodical ignored</a></li><li><a href="/wiki/Category:Articles_with_short_description" title="Category:Articles with short description">Articles with short description</a></li><li><a href="/wiki/Category:Short_description_matches_Wikidata" title="Category:Short description matches Wikidata">Short description matches Wikidata</a></li></ul></div></div> </div> </main> </div> <div class="mw-footer-container"> <footer id="footer" class="mw-footer" > <ul id="footer-info"> <li id="footer-info-lastmod"> This page was last edited on 9 February 2025, at 12:52<span class="anonymous-show"> (UTC)</span>.</li> <li id="footer-info-copyright">Text is available under the <a href="/wiki/Wikipedia:Text_of_the_Creative_Commons_Attribution-ShareAlike_4.0_International_License" title="Wikipedia:Text of the Creative Commons Attribution-ShareAlike 4.0 International License">Creative Commons Attribution-ShareAlike 4.0 License</a>; additional terms may apply. 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id="ca-ve-edit-sticky-header" tabindex="-1" data-event-name="ve-edit-sticky-header"><span class="vector-icon mw-ui-icon-wikimedia-edit mw-ui-icon-wikimedia-wikimedia-edit"></span> <span></span> </a> <a href="#" class="cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet cdx-button--icon-only" id="ca-viewsource-sticky-header" tabindex="-1" data-event-name="ve-edit-protected-sticky-header"><span class="vector-icon mw-ui-icon-wikimedia-editLock mw-ui-icon-wikimedia-wikimedia-editLock"></span> <span></span> </a> </div> <div class="vector-sticky-header-buttons"> <button class="cdx-button cdx-button--weight-quiet mw-interlanguage-selector" id="p-lang-btn-sticky-header" tabindex="-1" data-event-name="ui.dropdown-p-lang-btn-sticky-header"><span class="vector-icon mw-ui-icon-wikimedia-language mw-ui-icon-wikimedia-wikimedia-language"></span> <span>4 languages</span> </button> <a href="#" class="cdx-button cdx-button--fake-button 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