{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T17:24:49Z","timestamp":1776878689426,"version":"3.51.2"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,8,26]],"date-time":"2005-08-26T00:00:00Z","timestamp":1125014400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2005,8,26]],"date-time":"2005-08-26T00:00:00Z","timestamp":1125014400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computational approaches, visualisation techniques are highly important. Biochemical reaction networks, e.g. metabolic pathways are often depicted as graphs and these graphs should be drawn dynamically to provide flexibility in the context of different data. Conventional layout algorithms are not sufficient for every kind of pathway in biochemical research. This is mainly due to certain conventions to which biochemists\/biologists are used to and which are not in accordance to conventional layout algorithms. A number of approaches has been developed to improve this situation. Some of these are used in the context of biochemical databases and make more or less use of the information in these databases to aid the layout process. However, visualisation becomes also more and more important in modelling and simulation tools which mostly do not offer additional connections to databases. Therefore, layout algorithms used in these tools have to work independently of any databases. In addition, all of the existing algorithms face some limitations with respect to the number of edge crossings when it comes to larger biochemical systems due to the interconnectivity of these. Last but not least, in some cases, biochemical conventions are not met properly.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>Out of these reasons we have developed a new algorithm which tackles these problems by reducing the number of edge crossings in complex systems, taking further biological conventions into account to identify and visualise cycles. Furthermore the algorithm is independent from database information in order to be easily adopted in any application. It can also be tested as part of the SimWiz package (free to download for academic users at [1]).<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion<\/jats:title>\n                        <jats:p>The new algorithm reduces the complexity of pathways, as well as edge crossings and edge length in the resulting graphical representation. It also considers existing and further biological conventions to create a drawing most biochemists are familiar with. A lot of examples can be found on [2].<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-6-212","type":"journal-article","created":{"date-parts":[[2005,8,27]],"date-time":"2005-08-27T06:14:13Z","timestamp":1125123253000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["A new dynamical layout algorithm for complex biochemical reaction networks"],"prefix":"10.1186","volume":"6","author":[{"given":"Katja","family":"Wegner","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ursula","family":"Kummer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,8,26]]},"reference":[{"key":"537_CR1","unstructured":"SimWiz download2005. [http:\/\/projects.villa-bosch.de\/bcb\/software\/]"},{"key":"537_CR2","unstructured":"Supplementary material2005. [http:\/\/projects.villa-bosch.de\/bcb\/people\/katja\/examples.html]"},{"key":"537_CR3","first-page":"34","volume":"59","author":"M Kanehisa","year":"1996","unstructured":"Kanehisa M: Toward pathway engineering: a new database of genetic and molecular pathways. Science and Technology Japan 1996, 59: 34\u201338.","journal-title":"Science and Technology Japan"},{"key":"537_CR4","first-page":"24","volume-title":"Proceedings of the Workshop Molekulare Bioinformatik","author":"FJ Brandenburg","year":"1998","unstructured":"Brandenburg FJ, Gruber B, Himsolt M, Schreiber F: Automatische Visualisierung biochemischer Information. In Proceedings of the Workshop Molekulare Bioinformatik. GI Jahrestagung; 1998:24\u201338."},{"key":"537_CR5","first-page":"207","volume-title":"Proceedings of the Third International Conference on Bioinformatics and Genome Research","author":"PD Karp","year":"1994","unstructured":"Karp PD, Paley S: Automated Drawing of Metabolic Pathways. In Proceedings of the Third International Conference on Bioinformatics and Genome Research. Edited by: Hunter L, Searls D, Shavlik J. AAAI Press; 1994:207\u2013215."},{"key":"537_CR6","volume-title":"Silico Biology","author":"F Schreiber","year":"2002","unstructured":"Schreiber F: High quality visualization of biochemical pathways in BioPath. Silico Biology 2002., 6:"},{"key":"537_CR7","first-page":"225","volume-title":"Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology; Mento Park, CA","author":"PD Karp","year":"1993","unstructured":"Karp PD, Paley SM: Representations of Metabolic Knowledge: Pathways. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology; Mento Park, CA. Edited by: Altman R, Brutlag D, Karp PD, Lathrop R, Searls D. AAAI Press; 1993:225\u2013238."},{"key":"537_CR8","first-page":"11","volume-title":"Proceedings of the German Conference on Bioinformatics; Braunschweig","author":"FJ Brandenburg","year":"2001","unstructured":"Brandenburg FJ, Forster M, Pick A, Raitner M, Schreiber F: BioPath \u2013 Visualization of Biochemical Pathways. In Proceedings of the German Conference on Bioinformatics; Braunschweig Edited by: Wingender E, Hofestaedt R, Liebich I. 2001, 11\u201315."},{"key":"537_CR9","volume-title":"Biochemical Pathways (Poster)","author":"G Michal","year":"1993","unstructured":"Michal G: Biochemical Pathways (Poster). Boehringer Mannheim GmbH \u2013 Biochemica; 1993."},{"key":"537_CR10","volume-title":"Biochemical Pathways","author":"G Michal","year":"1999","unstructured":"Michal G: Biochemical Pathways. Spektrum Akademischer Verlag; 1999."},{"issue":"2","key":"537_CR11","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1109\/TSMC.1981.4308636","volume":"11","author":"K Sugiyama","year":"1981","unstructured":"Sugiyama K, Tagawa S, Toda M: Methods for Visual Understanding of Hierarchical System Structures. IEEE Transactions on Systems, Man and Cybernetics SMC 1981, 11(2):109\u2013125.","journal-title":"IEEE Transactions on Systems, Man and Cybernetics SMC"},{"key":"537_CR12","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","volume":"1","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, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 1: 524\u2013531. 10.1093\/bioinformatics\/btg015","journal-title":"Bioinformatics"},{"key":"537_CR13","first-page":"544","volume-title":"Proceedings of Information Visualization","author":"I Rojdestvenski","year":"2003","unstructured":"Rojdestvenski I: Objective and subjectiv relations in data visualization. Examples from molecular biological data collections. In Proceedings of Information Visualization Edited by: Banissi E, Borner K, Chen C, Clapworthy G, Maple C, Lobben A, Moore C, Roberts J, Ursyn A, Zhang J. 2003, 544\u2013548."},{"key":"537_CR14","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/0020-0190(89)90102-6","volume":"31","author":"T Kamada","year":"1989","unstructured":"Kamada T, Kawai S: An algorithm for drawing general undirected graphs. Information Processing Letters 1989, 31: 7\u201315. 10.1016\/0020-0190(89)90102-6","journal-title":"Information Processing Letters"},{"key":"537_CR15","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1093\/bioinformatics\/17.5.461","volume":"17","author":"MY Becker","year":"2001","unstructured":"Becker MY, Rojas I: A graph layout algorithm for drawing metabolic pathways. Bioinformatics 2001, 17: 461\u2013467. 10.1093\/bioinformatics\/17.5.461","journal-title":"Bioinformatics"},{"key":"537_CR16","first-page":"109","volume":"11","author":"NR Quinn","year":"1979","unstructured":"Quinn NR, Breuer MA: A force directed component placement procedure for printed circuit boards. IEEE Transactions on Circuits Systems 1979, 11: 109\u2013125.","journal-title":"IEEE Transactions on Circuits Systems"},{"key":"537_CR17","first-page":"149","volume-title":"Congressus Numerantium","author":"P Eades","year":"1984","unstructured":"Eades P: A heuristic for graph drawing. Congressus Numerantium 1984, 149\u2013160."},{"key":"537_CR18","first-page":"89","volume-title":"Proceedings of the 2nd Workshop on Computation of Biochemical Pathways and Genetic Networks","author":"LF Olsen","year":"2001","unstructured":"Olsen LF: Simulations of Oscillations of NAD(P)H and Reactive Oxygen Species in Neutrophilic Leukocytes. In Proceedings of the 2nd Workshop on Computation of Biochemical Pathways and Genetic Networks Edited by: Gauges R, van Gend C, Kummer U. 2001, 89\u201399."},{"key":"537_CR19","unstructured":"yfiles2003. [http:\/\/www.yworks.com\/en\/products_yfiles_about.htm]"},{"key":"537_CR20","volume-title":"Introduction to Algorithms","author":"TH Cormen","year":"1990","unstructured":"Cormen TH, Leiserson CE, Rivest RL: Introduction to Algorithms. London: MIT Press; 1990."},{"key":"537_CR21","unstructured":"KEGG2004. [http:\/\/www.genome.ad.jp\/kegg\/pathway.html]"},{"key":"537_CR22","unstructured":"BioCyc2004. [http:\/\/www.biocyc.org]"},{"key":"537_CR23","unstructured":"PathDB2004. [http:\/\/www.ncgr.org\/pathdb]"},{"key":"537_CR24","unstructured":"SBML2005. [http:\/\/sbml.org\/models]"},{"key":"537_CR25","unstructured":"Model database2005. [http:\/\/sbml.org\/models]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-212.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-6-212\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-212.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:14:28Z","timestamp":1728303268000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-212"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,8,26]]},"references-count":25,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["537"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-212","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,8,26]]},"assertion":[{"value":"20 October 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 August 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 August 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"212"}}