{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T07:51:54Z","timestamp":1778226714993,"version":"3.51.4"},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Complexity is a key problem when visualizing biological networks; as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visualized meaningfully and with high performance.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We present a new visualization tool, Arena3D, which introduces a new concept of staggered layers in 3D space. Related data \u2013 such as proteins, chemicals, or pathways \u2013 can be grouped onto separate layers and arranged via layout algorithms, such as Fruchterman-Reingold, distance geometry, and a novel hierarchical layout. Data on a layer can be clustered via k-means, affinity propagation, Markov clustering, neighbor joining, tree clustering, or UPGMA ('unweighted pair-group method with arithmetic mean'). A simple input format defines the name and URL for each node, and defines connections or similarity scores between pairs of nodes. The use of Arena3D is illustrated with datasets related to Huntington's disease.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Arena3D is a user friendly visualization tool that is able to visualize biological or any other network in 3D space. It is free for academic use and runs on any platform. It can be downloaded or lunched directly from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/arena3d.org\" ext-link-type=\"uri\">http:\/\/arena3d.org<\/jats:ext-link>. Java3D library and Java 1.5 need to be pre-installed for the software to run.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1752-0509-2-104","type":"journal-article","created":{"date-parts":[[2008,11,28]],"date-time":"2008-11-28T19:13:36Z","timestamp":1227899616000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":92,"title":["Arena3D: visualization of biological networks in 3D"],"prefix":"10.1186","volume":"2","author":[{"given":"Georgios A","family":"Pavlopoulos","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Se\u00e1n I","family":"O'Donoghue","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Venkata P","family":"Satagopam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Theodoros G","family":"Soldatos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Evangelos","family":"Pafilis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reinhard","family":"Schneider","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,11,28]]},"reference":[{"issue":"11","key":"261_CR1","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13 (11): 2498-2504. 10.1101\/gr.1239303","journal-title":"Genome Res"},{"issue":"3","key":"261_CR2","doi-asserted-by":"publisher","first-page":"R22","DOI":"10.1186\/gb-2003-4-3-r22","volume":"4","author":"BJ Breitkreutz","year":"2003","unstructured":"Breitkreutz BJ, Stark C, Tyers M: Osprey: a network visualization system. Genome Biol. 2003, 4 (3): R22- 10.1186\/gb-2003-4-3-r22","journal-title":"Genome Biol"},{"issue":"24","key":"261_CR3","doi-asserted-by":"publisher","first-page":"4432","DOI":"10.1093\/bioinformatics\/bti696","volume":"21","author":"SD Hooper","year":"2005","unstructured":"Hooper SD, Bork P: Medusa: a simple tool for interaction graph analysis. Bioinformatics. 2005, 21 (24): 4432-4433. 10.1093\/bioinformatics\/bti696","journal-title":"Bioinformatics"},{"issue":"2","key":"261_CR4","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1093\/bioinformatics\/bth494","volume":"21","author":"F Iragne","year":"2005","unstructured":"Iragne F, Nikolski M, Mathieu B, Auber D, Sherman D: ProViz: protein interaction visualization and exploration. Bioinformatics. 2005, 21 (2): 272-274. 10.1093\/bioinformatics\/bth494","journal-title":"Bioinformatics"},{"issue":"9","key":"261_CR5","doi-asserted-by":"publisher","first-page":"1455","DOI":"10.1093\/bioinformatics\/bth080","volume":"20","author":"NN Batada","year":"2004","unstructured":"Batada NN: CNplot: visualizing pre-clustered networks. Bioinformatics. 2004, 20 (9): 1455-1456. 10.1093\/bioinformatics\/bth080","journal-title":"Bioinformatics"},{"issue":"11","key":"261_CR6","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1093\/bioinformatics\/btl081","volume":"22","author":"J Kohler","year":"2006","unstructured":"Kohler J, Baumbach J, Taubert J, Specht M, Skusa A, Ruegg A, Rawlings C, Verrier P, Philippi S: Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics. 2006, 22 (11): 1383-1390. 10.1093\/bioinformatics\/btl081","journal-title":"Bioinformatics"},{"issue":"6","key":"261_CR7","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1111\/j.1365-313X.2004.02016.x","volume":"37","author":"O Thimm","year":"2004","unstructured":"Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M: MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004, 37 (6): 914-939. 10.1111\/j.1365-313X.2004.02016.x","journal-title":"Plant J"},{"key":"261_CR8","first-page":"47","volume":"21","author":"V Batagelj","year":"1998","unstructured":"Batagelj V, Mrvar A: Pajek \u2013 Program for Large Network Analysis. Connections. 1998, 21: 47-57.","journal-title":"Connections"},{"issue":"4","key":"261_CR9","doi-asserted-by":"publisher","first-page":"1399","DOI":"10.1093\/nar\/gki285","volume":"33","author":"JW Pinney","year":"2005","unstructured":"Pinney JW, Shirley MW, McConkey GA, Westhead DR: metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic acids research. 2005, 33 (4): 1399-1409. 10.1093\/nar\/gki285","journal-title":"Nucleic acids research"},{"issue":"10","key":"261_CR10","doi-asserted-by":"publisher","first-page":"2032","DOI":"10.1371\/journal.pcbi.0030206","volume":"3","author":"TC Freeman","year":"2007","unstructured":"Freeman TC, Goldovsky L, Brosch M, van Dongen S, Maziere P, Grocock RJ, Freilich S, Thornton J, Enright AJ: Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS computational biology. 2007, 3 (10): 2032-2042. 10.1371\/journal.pcbi.0030206","journal-title":"PLoS computational biology"},{"issue":"2","key":"261_CR11","first-page":"189","volume":"10","author":"S Kumar","year":"1994","unstructured":"Kumar S, Tamura K, Nei M: MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Comput Appl Biosci. 1994, 10 (2): 189-191.","journal-title":"Comput Appl Biosci"},{"key":"261_CR12","doi-asserted-by":"publisher","first-page":"1596","DOI":"10.1093\/molbev\/msm092","volume":"24","author":"K Tamura","year":"2007","unstructured":"Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 2007, 24: 1596-1599. 10.1093\/molbev\/msm092.","journal-title":"Molecular Biology and Evolution"},{"issue":"7","key":"261_CR13","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1109\/MC.2002.1016905","volume":"35","author":"J Seo","year":"2002","unstructured":"Seo J, Shneiderman B: Interactively Exploring Hierarchical Clustering Results. IEEE Computer. 2002, 35 (7): 80-86.","journal-title":"IEEE Computer"},{"key":"261_CR14","volume-title":"IBM Internal Report, November 17","author":"TT Tanimoto","year":"1957","unstructured":"Tanimoto TT: Tanimoto. IBM Internal Report, November 17. 1957"},{"issue":"7\u20138","key":"261_CR15","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/j.drudis.2006.02.011","volume":"11","author":"RA Erhardt","year":"2006","unstructured":"Erhardt RA, Schneider R, Blaschke C: Status of text-mining techniques applied to biomedical text. Drug Discov Today. 2006, 11 (7\u20138): 315-325. 10.1016\/j.drudis.2006.02.011","journal-title":"Drug Discov Today"},{"key":"261_CR16","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1002\/spe.4380211102","volume":"21","author":"TMJ Fruchterman","year":"1991","unstructured":"Fruchterman TMJ, Reingold EM: Graph Drawing by Force-Directed Placement. Software, Practice and Experience. 1991, 21: 1129-1164. 10.1002\/spe.4380211102.","journal-title":"Software, Practice and Experience"},{"key":"261_CR17","volume-title":"Distance Geometry and Molecular Conformation","author":"GM Crippen","year":"1988","unstructured":"Crippen GM, Havel TF: Distance Geometry and Molecular Conformation. 1988, New York: Wiley"},{"issue":"1","key":"261_CR18","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038\/75556","journal-title":"Nat Genet"},{"issue":"Suppl 1","key":"261_CR19","doi-asserted-by":"publisher","first-page":"i169","DOI":"10.1093\/bioinformatics\/bth921","volume":"20","author":"CA Joslyn","year":"2004","unstructured":"Joslyn CA, Mniszewski SM, Fulmer A, Heaton G: The gene ontology categorizer. Bioinformatics. 2004, 20 (Suppl 1): i169-177. 10.1093\/bioinformatics\/bth921","journal-title":"Bioinformatics"},{"key":"261_CR20","first-page":"281","volume-title":"5-th Berkeley Symposium on Mathematical Statistics and Probability: 1967","author":"JB MacQueen","year":"1967","unstructured":"MacQueen JB: Kmeans Some Methods for classification and Analysis of Multivariate Observations. 5-th Berkeley Symposium on Mathematical Statistics and Probability: 1967. 1967, 281-297. Berkeley: University of California Press"},{"issue":"5814","key":"261_CR21","doi-asserted-by":"publisher","first-page":"972","DOI":"10.1126\/science.1136800","volume":"315","author":"BJ Frey","year":"2007","unstructured":"Frey BJ, Dueck D: Clustering by passing messages between data points. Science. 2007, 315 (5814): 972-976. 10.1126\/science.1136800","journal-title":"Science"},{"issue":"7","key":"261_CR22","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","volume":"30","author":"AJ Enright","year":"2002","unstructured":"Enright AJ, van Dongen S, Ouzounis CA: An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002, 30 (7): 1575-1584. 10.1093\/nar\/30.7.1575","journal-title":"Nucleic Acids Res"},{"key":"261_CR23","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1007\/BF02289588","volume":"2","author":"SC Johnson","year":"1967","unstructured":"Johnson SC: Hierarchical Clustering Schemes. Psychometrika. 1967, 2: 241-254. 10.1007\/BF02289588.","journal-title":"Psychometrika"},{"key":"261_CR24","first-page":"58","volume":"4","author":"R D'andrade","year":"1978","unstructured":"D'andrade R: U-Statistic Hierarchical Clustering. Psychometrika. 1978, 4: 58-67.","journal-title":"Psychometrika"},{"issue":"4","key":"261_CR25","first-page":"406","volume":"4","author":"NM Saitou","year":"1987","unstructured":"Saitou NM: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987, 4 (4): 406-425.","journal-title":"Mol Biol Evol"},{"key":"261_CR26","first-page":"230","volume-title":"Numerical Taxonomy","author":"PHA Sneath","year":"1973","unstructured":"Sneath PHA, Sokal RR: Unweighted Pair Group Method with Arithmetic Mean. Numerical Taxonomy. 1973, 230-234. San Francisco: Freeman"},{"issue":"3","key":"261_CR27","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1093\/bib\/6.3.222","volume":"6","author":"H Shatkay","year":"2005","unstructured":"Shatkay H: Hairpins in bookstacks: information retrieval from biomedical text. Brief Bioinform. 2005, 6 (3): 222-238. 10.1093\/bib\/6.3.222","journal-title":"Brief Bioinform"},{"key":"261_CR28","unstructured":"The Newick tree format. 2005, http:\/\/evolution.genetics.washington.edu\/phylip\/newicktree.html"},{"issue":"1","key":"261_CR29","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","volume":"23","author":"I Letunic","year":"2007","unstructured":"Letunic I, Bork P: Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 2007, 23 (1): 127-128. 10.1093\/bioinformatics\/btl529","journal-title":"Bioinformatics"},{"issue":"1","key":"261_CR30","first-page":"49","volume":"9","author":"T Etzold","year":"1993","unstructured":"Etzold T, Argos P: SRS \u2013 an indexing and retrieval tool for flat file data libraries. Computer Applications in the Biosciences. 1993, 9 (1): 49-57.","journal-title":"Computer Applications in the Biosciences"},{"key":"261_CR31","doi-asserted-by":"publisher","first-page":"D358","DOI":"10.1093\/nar\/gkl825","volume":"35","author":"C von Mering","year":"2006","unstructured":"von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kr\u00fcger B, Snel B, Bork P: STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 2006, 35: D358-62. 10.1093\/nar\/gkl825","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"261_CR32","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic acids research. 2000, 28 (1): 235-242. 10.1093\/nar\/28.1.235","journal-title":"Nucleic acids research"},{"key":"261_CR33","first-page":"D115","volume-title":"Nucleic acids research","author":"M Hucka","year":"2004","unstructured":"Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS: UniProt: the Universal Protein knowledgebase. Nucleic acids research. 2004, D115-119. 32 Database","edition":"32"},{"issue":"4","key":"261_CR34","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","volume":"19","author":"M Hucka","year":"2003","unstructured":"Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003, 19 (4): 524-531. 10.1093\/bioinformatics\/btg015","journal-title":"Bioinformatics"},{"issue":"2","key":"261_CR35","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1038\/nbt926","volume":"22","author":"H Hermjakob","year":"2004","unstructured":"Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B: The HUPO PSI's molecular interaction format \u2013 a community standard for the representation of protein interaction data. Nat Biotechnol. 2004, 22 (2): 177-183. 10.1038\/nbt926","journal-title":"Nat Biotechnol"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-2-104.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T01:58:19Z","timestamp":1630461499000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-2-104"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,11,28]]},"references-count":35,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["261"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-2-104","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,11,28]]},"assertion":[{"value":"10 June 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 November 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 November 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"104"}}