{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T09:03:30Z","timestamp":1762506210681,"version":"3.37.3"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"S19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,11]]},"DOI":"10.1186\/1471-2105-14-s19-s2","type":"journal-article","created":{"date-parts":[[2013,11,12]],"date-time":"2013-11-12T07:05:11Z","timestamp":1384239911000},"source":"Crossref","is-referenced-by-count":5,"title":["iVUN: interactive Visualization of Uncertain biochemical reaction Networks"],"prefix":"10.1186","volume":"14","author":[{"given":"Corinna","family":"Vehlow","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan","family":"Hasenauer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrei","family":"Kramer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Raue","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabine","family":"Hug","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jens","family":"Timmer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole","family":"Radde","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabian J","family":"Theis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Weiskopf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,11,12]]},"reference":[{"key":"6186_CR1","doi-asserted-by":"publisher","DOI":"10.1002\/3527603603","volume-title":"Systems Biology in Practice","author":"E Klipp","year":"2005","unstructured":"Klipp E, Herwig R, Kowald A, Wierling C, Lehrach H: Systems Biology in Practice. 2005, Wiley-VCH, Weinheim"},{"key":"6186_CR2","doi-asserted-by":"publisher","first-page":"ra31","DOI":"10.1126\/scisignal.2000352","volume":"2","author":"B Sch\u00f6berl","year":"2009","unstructured":"Sch\u00f6berl B: Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis. Science Signaling. 2009, 2: ra31-10.1126\/scisignal.2000352.","journal-title":"Science Signaling"},{"key":"6186_CR3","doi-asserted-by":"publisher","first-page":"20171","DOI":"10.1074\/jbc.M110.106849","volume":"285","author":"C Br\u00e4nnmark","year":"2010","unstructured":"Br\u00e4nnmark C, Palmer R, Glad ST, Cedersund G, Str\u00e5lfors P: Mass and information feedbacks through receptor endocytosis govern insulin signaling as revealed using a parameter-free modeling framework. Journal of Biological Chemistry. 2010, 285: 20171-20179. 10.1074\/jbc.M110.106849.","journal-title":"Journal of Biological Chemistry"},{"key":"6186_CR4","first-page":"493","volume-title":"In Proceedings of IEEE Multi-Conference on Systems and Control (MCS). IEEE","author":"A Kramer","year":"2010","unstructured":"Kramer A, Hasenauer J, Allg\u00f6wer F, Radde N: Computation of the posterior entropy in a Bayesian framework for parameter estimation in biological networks. In Proceedings of IEEE Multi-Conference on Systems and Control (MCS). IEEE. 2010, 493-498."},{"key":"6186_CR5","first-page":"679","volume-title":"In Proceedings of 9th Valencia International Meeting on Bayesian Statistics. Oxford University Press","author":"DJ Wilkinson","year":"2010","unstructured":"Wilkinson DJ: Parameter inference for stochastic kinetic models of bacterial gene regulation: a Bayesian approach to systems biology. In Proceedings of 9th Valencia International Meeting on Bayesian Statistics. Oxford University Press. 2010, 679-705."},{"key":"6186_CR6","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1109\/BioVis.2012.6378598","volume-title":"In Proceedings of IEEE Symposium on Biological Data Visualization (Biovis). IEEE","author":"C Vehlow","year":"2012","unstructured":"Vehlow C, Hasenauer J, Kramer A, Heinrich J, Radde N, Allg\u00f6wer F, Weiskopf D: Uncertainty-aware visual analysis of biochemical reaction networks. In Proceedings of IEEE Symposium on Biological Data Visualization (Biovis). IEEE. 2012, 91-98."},{"key":"6186_CR7","volume-title":"IUPAC Compendium of Chemical Terminology","author":"A McNaught","year":"1997","unstructured":"McNaught A, Wilkinson A: IUPAC Compendium of Chemical Terminology. 1997, Blackwell Science, 2","edition":"2"},{"key":"6186_CR8","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1093\/bib\/bbm007","volume":"8","author":"DJ Wilkinson","year":"2007","unstructured":"Wilkinson DJ: Bayesian methods in bioinformatics and computational systems biology. Briefings in Bioinformatics. 2007, 8: 109-116.","journal-title":"Briefings in Bioinformatics"},{"key":"6186_CR9","volume-title":"Information Theory, Inference, and Learning Algorithms","author":"DJC MacKay","year":"2005","unstructured":"MacKay DJC: Information Theory, Inference, and Learning Algorithms. 2005, Cambridge: Cambridge University Press, 7.2","edition":"7.2"},{"key":"6186_CR10","volume-title":"Illuminating the Path: The Research and Development Agenda for Visual Analytics","author":"JJ Thomas","year":"2005","unstructured":"Thomas JJ, Cook KA: Illuminating the Path: The Research and Development Agenda for Visual Analytics. 2005, IEEE Computer Society Press"},{"key":"6186_CR11","first-page":"168","volume-title":"In Proceedings of the 16th International Parallel and Distributed Processing Symposium. IPDPS '02, IEEE Computer Society","author":"ML Huang","year":"2002","unstructured":"Huang ML: Graph visualization of web data with domain-specific attributes. In Proceedings of the 16th International Parallel and Distributed Processing Symposium. IPDPS '02, IEEE Computer Society. 2002, 168-174."},{"key":"6186_CR12","first-page":"592","volume-title":"In Proceedings of 13th International Conference on Information Visualization, IV. IEEE","author":"F Beck","year":"2009","unstructured":"Beck F, Burch M, Diehl S: Towards an aesthetic dimensions framework for dynamic graph visualisations. In Proceedings of 13th International Conference on Information Visualization, IV. IEEE. 2009, 592-597."},{"key":"6186_CR13","volume-title":"Envisioning Information","author":"ER Tufte","year":"1990","unstructured":"Tufte ER: Envisioning Information. 1990, Cheshire, CT: Graphics Press"},{"key":"6186_CR14","doi-asserted-by":"publisher","first-page":"1253","DOI":"10.1109\/TVCG.2008.117","volume":"14","author":"A Barsky","year":"2008","unstructured":"Barsky A, Munzner T, Gardy J, Kincaid R: Cerebral: visualizing multiple experimental conditions on a graph with biological context. IEEE Transactions on Visualization and Computer Graphics. 2008, 14: 1253-1260.","journal-title":"IEEE Transactions on Visualization and Computer Graphics"},{"key":"6186_CR15","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1111\/j.1467-8659.2009.01710.x","volume":"29","author":"M Meyer","year":"2010","unstructured":"Meyer M, Wong B, Styczynski M, Munzner T, Pfister H: Pathline: a tool for comparative functional genomics. Computer Graphics Forum. 2010, 29: 1043-1052. 10.1111\/j.1467-8659.2009.01710.x.","journal-title":"Computer Graphics Forum"},{"key":"6186_CR16","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1111\/j.1467-8659.2008.01221.x","volume":"27","author":"MA Westenberg","year":"2008","unstructured":"Westenberg MA, van Hijum SAFT, Kuipers OP, Roerdink JBTM: Visualizing genome expression and regulatory network dynamics in genomic and metabolic context. Computer Graphics Forum. 2008, 27: 887-894. 10.1111\/j.1467-8659.2008.01221.x.","journal-title":"Computer Graphics Forum"},{"key":"6186_CR17","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1186\/1471-2105-7-109","volume":"7","author":"B Junker","year":"2006","unstructured":"Junker B, Klukas C, Schreiber F: VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics. 2006, 7: 109-121. 10.1186\/1471-2105-7-109.","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 1","key":"6186_CR18","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1093\/bioinformatics\/18.suppl_1.S225","volume":"18","author":"PD Karp","year":"2002","unstructured":"Karp PD, Paley S, Romero P: The Pathway Tools software. Bioinformatics. 2002, 18 (Suppl 1): 225-232. 10.1093\/bioinformatics\/18.suppl_1.S225.","journal-title":"Bioinformatics"},{"key":"6186_CR19","doi-asserted-by":"publisher","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","volume":"22","author":"S Hoops","year":"2006","unstructured":"Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U: COPASI - a COmplex PAthway SImulator. Bioinformatics. 2006, 22: 3067-3074. 10.1093\/bioinformatics\/btl485.","journal-title":"Bioinformatics"},{"key":"6186_CR20","doi-asserted-by":"publisher","first-page":"1254","DOI":"10.1109\/JPROC.2008.925458","volume":"96","author":"A Funahashi","year":"2008","unstructured":"Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H: CellDesigner 3.5: a versatile modeling tool for biochemical networks. Proceedings of the IEEE. 2008, 96: 1254-1265.","journal-title":"Proceedings of the IEEE"},{"key":"6186_CR21","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1109\/MCG.2004.20","volume":"24","author":"CR Johnson","year":"2004","unstructured":"Johnson CR: Top scientific visualization research problems. IEEE Computer Graphics and Applications: Visualization Viewpoints. 2004, 24: 13-17.","journal-title":"IEEE Computer Graphics and Applications: Visualization Viewpoints"},{"key":"6186_CR22","first-page":"143","volume-title":"In Proceedings of SimVis '06. SCS Publishing House e.V","author":"H Griethe","year":"2006","unstructured":"Griethe H, Schumann H: The visualization of uncertain data: methods and problems. In Proceedings of SimVis '06. SCS Publishing House e.V. 2006, 143-156."},{"key":"6186_CR23","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1109\/MCG.2003.1231171","volume":"23","author":"CR Johnson","year":"2003","unstructured":"Johnson CR, Sanderson AR: A next step: visualizing errors and uncertainty. IEEE Computer Graphics and Applications. 2003, 23: 6-10.","journal-title":"IEEE Computer Graphics and Applications"},{"key":"6186_CR24","volume-title":"Proceedings of the SPIE (Visualization and Data Analysis 2011)","author":"N Cesario","year":"2011","unstructured":"Cesario N, Pang A, Singh L: Visualizing node attribute uncertainty in graphs. Proceedings of the SPIE (Visualization and Data Analysis 2011). 2011"},{"key":"6186_CR25","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1057\/palgrave.ivs.9500157","volume":"6","author":"B Lee","year":"2007","unstructured":"Lee B, Robertson GG, Czerwinski M, Sims Parr C: CandidTree: visualizing structural uncertainty in similar hierarchies. Information Visualization. 2007, 6: 233-246. 10.1057\/palgrave.ivs.9500157.","journal-title":"Information Visualization"},{"key":"6186_CR26","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1007\/s003710050111","volume":"13","author":"AT Pang","year":"1997","unstructured":"Pang AT, Wittenbrink CM, Lodha SK: Approaches to uncertainty visualization. The Visual Computer. 1997, 13: 370-390. 10.1007\/s003710050111.","journal-title":"The Visual Computer"},{"key":"6186_CR27","unstructured":"The Systems Biology Markup Language. 2012, [\n                    http:\/\/sbml.org\/Main_Page\n                    \n                  ]"},{"key":"6186_CR28","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1117\/12.342832","volume":"3643","author":"JC Roberts","year":"1999","unstructured":"Roberts JC: Encouraging coupled views for visualization exploration. Proceedings of SPIE, Visual Data Exploration and Analysis VI. 1999, 3643: 14-24. 10.1117\/12.342832.","journal-title":"Proceedings of SPIE, Visual Data Exploration and Analysis VI"},{"key":"6186_CR29","unstructured":"ColorBrewer. 2011, [\n                    http:\/\/colorbrewer2.org\/\n                    \n                  ]"},{"key":"6186_CR30","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1006\/ijhc.2002.1017","volume":"57","author":"B Tversky","year":"2002","unstructured":"Tversky B, Bauer Morrison J, Betrancourt M: Animation: can it facilitate?. International Journal of Human-Computer Studies. 2002, 57: 247-262. 10.1006\/ijhc.2002.1017.","journal-title":"International Journal of Human-Computer Studies"},{"key":"6186_CR31","doi-asserted-by":"publisher","first-page":"1719","DOI":"10.1111\/j.1467-8659.2011.01898.x","volume":"30","author":"T von Landesberger","year":"2011","unstructured":"von Landesberger T, Kuijper A, Schreck T, Kohlhammer J, van Wijk J, Fekete JD, Fellner D: Visual analysis of large graphs: state-of-the-art and future research challenges. Computer Graphics Forum. 2011, 30: 1719-1749. 10.1111\/j.1467-8659.2011.01898.x.","journal-title":"Computer Graphics Forum"},{"key":"6186_CR32","doi-asserted-by":"publisher","first-page":"1404","DOI":"10.1126\/science.1184913","volume":"328","author":"V Becker","year":"2010","unstructured":"Becker V, Schilling M, Bachmann J, Baumann U, Raue A, Maiwald T, Timmer J, Klingm\u00fcller U: Covering a broad dynamic range: information processing at the erythropoietin receptor. Science. 2010, 328: 1404-1408. 10.1126\/science.1184913.","journal-title":"Science"},{"issue":"516","key":"6186_CR33","first-page":"1","volume":"7","author":"J Bachmann","year":"2011","unstructured":"Bachmann J, Raue A, Schilling M, B\u00f6hm ME, Kreutz C, Kaschek D, Busch H, Gretz N, Lehmann WD, Timmer J, Klingm\u00fcller U: Division of labor by dual feedback regulators controls JAK2\/STAT5 signaling over broad ligand range. Molecular Systems Biology. 2011, 7 (516): 1-15.","journal-title":"Molecular Systems Biology"},{"key":"6186_CR34","volume-title":"Mathematical Biosciences","author":"S Hug","year":"2013","unstructured":"Hug S, Raue A, Hasenauer J, Bachmann J, Klingm\u00fcller U, Timmer J, Theis FJ: High-dimensional Bayesian parameter estimation: case study for a model of JAK2\/STAT5 signaling. Mathematical Biosciences. 2013, [\n                    http:\/\/dx.doi.org\/10.1016\/j.mbs.2013.04.002\n                    \n                  ]"},{"key":"6186_CR35","doi-asserted-by":"publisher","DOI":"10.1137\/1.9780898717921","volume-title":"Inverse Problem Theory and Methods for Model Parameter Estimation","author":"A Tarantola","year":"2005","unstructured":"Tarantola A: Inverse Problem Theory and Methods for Model Parameter Estimation. 2005, SIAM"},{"key":"6186_CR36","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1063\/1.481811","volume":"113","author":"DT Gillespie","year":"2000","unstructured":"Gillespie DT: The chemical Langevin equation. Journal of Chemical Physics. 2000, 113: 297-306. 10.1063\/1.481811.","journal-title":"Journal of Chemical Physics"},{"key":"6186_CR37","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1016\/0378-4371(92)90283-V","volume":"188","author":"DT Gillespie","year":"1992","unstructured":"Gillespie DT: A rigorous derivation of the chemical master equation. Physica A. 1992, 188: 404-425. 10.1016\/0378-4371(92)90283-V.","journal-title":"Physica A"},{"key":"6186_CR38","doi-asserted-by":"publisher","first-page":"1923","DOI":"10.1093\/bioinformatics\/btp358","volume":"25","author":"A Raue","year":"2009","unstructured":"Raue A, Kreutz C, Maiwald T, Bachmann J, Schilling M, Klingm\u00fcller U, Timmer J: Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics. 2009, 25: 1923-1929. 10.1093\/bioinformatics\/btp358.","journal-title":"Bioinformatics"},{"key":"6186_CR39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1752-0509-6-120","volume":"6","author":"C Kreutz","year":"2012","unstructured":"Kreutz C, Raue A, Timmer J: Likelihood based observability analysis and confidence intervals for predictions of dynamic models. BMC Systems Biology. 2012, 6: 1-9. 10.1186\/1752-0509-6-1.","journal-title":"BMC Systems Biology"},{"key":"6186_CR40","unstructured":"Java universal network\/graph framework. 2008, [\n                    http:\/\/jung.sourceforge.net\/\n                    \n                  ]"},{"key":"6186_CR41","unstructured":"JMathPlot: interactive 2D and 3D plots. 2009, [\n                    http:\/\/jmathtools.berlios.de\/\n                    \n                  ]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S19-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T20:26:01Z","timestamp":1548188761000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S19-S2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,11]]},"references-count":41,"journal-issue":{"issue":"S19","published-print":{"date-parts":[[2013,11]]}},"alternative-id":["6186"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s19-s2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2013,11]]},"article-number":"S2"}}