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Public 4.0 Attribution Commons Creative the under licensed is work This Sommer Bjorn Abstract: oa olg fAt colo ein noainDsg niern,Lno W E,U,E-mail: UK, 2EU, SW7 London Engineering, Design Innovation Design, of School Art, of College Royal [email protected] a h ai o h olwu rjcs[] trigfo nerycl iulzto rttp hc was which prototype visualization cell early an from Starting [1]. projects follow-up the for basis the lay fcus,drn h eetyas ubro te ebaeadcl oeln prahshv been have approaches modelling cell and membrane other of number a years, recent the during course, Of Bioin- Integrative major two the on precisely more part, development software the on laid is focus the Here, 10.1515/jib-2019-0057 ELircso ebaedtr(CmME). MembraneEditor CELLmicrocosmos uy2,2019; 29, July 09 jr omr ulse yWle eGutrGb,Berlin/Boston. GmbH, Gruyter de Walter by published Sommer, Bjorn 2019, © nertv iifrais elMdlig oeua oeln,Jv,Oe oreSoftware Source Open Java, Modelling, Molecular Modelling, Cell Bioinformatics, Integrative stecrepnigauthor. corresponding the is 1 sacl oeln n iulzto rjc ihrosgigbc oteya 03we a when 2003 year the to back going roots with project visualization and modelling cell a is Accepted: – etme ,2019 9, September eurn h nerto fmn ifrn aasources. data different many of integration the requiring ELircso elxlrrwt h ahaItgain(CmPI) PathwayIntegration the with CellExplorer CELLmicrocosmos ntecneto hspoet nertv iifraiscan Bioinformatics Integrative project, this of context the In – nMdaIfraisadDsg tBeeedUniversity Bielefeld at Design and Informatics Media in ora fItgaieBonomtc.21;20190057 2019; Bioinformatics. 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[45]. correlated the the visualization is of network, hybrid-dimensional context mitochondrion KEGG-derived as spatial a known classical the of detail a in structure a structure showing 3D network cell, is the the the beds visualization centre, of structure 2D the internal in the the 6: While shows Figure network. 9 in Figure shown network. cell metabolic the the one, of other the on and ponents, molecules. different between differentiation best the enables 5 Figure overview. in better structure a shape provides diamond lipids neighboring the Still, the and Right protein lipids; the between only differentiate showing to impossible nearly is protein transmembrane it a and surrounding membrane the of visualization 8: Figure codes colour the effectivelipid showing showing the left the on graphs table the with the as well distribution as thecombination lipid right) 5 the (Figure with approaches visualization, graphic these of scientific information While an differentiation. is field easy distribution the an enable in 5 lipid structures more different Figure atomic are between in the differentiate visualization to of impossible diamond-like visualization nearly The be the molecules. will occlusion it ambient still However, is nearly and improved. drastically shading structures be of different e.g. could using, differentiation by (Figure the lipids course, whereas higher, surrounding Of much the impossible. is with (Fig- detail protein molecules of transmembrane level all the the Obviously, only of shows right). structure Mode 8 atomic Align the the shows whereas visualization left), Waals 8 der Van ure the 5: Figure in potential[44]. shown membrane large account. currently into which has disciplines both afield take is here presented tools Visualization main Information Both and Scientific of combination The Discussion and Results 5 GRUYTER DE iulzto ftesm EGctaecycle. citrate KEGG same the of visualization Left 6): Figure 9: Figure mIcmie tutrlwt nomto iulzto:o n ad h pta tutr ftecl com- cell the of structure spatial the hand, one on visualization: information with structural combines CmPI the tovisualize ways alternative shows 8 Figure membranes. tovisualize modes different provides CmME ELircso ebaedtr w lentv ast iulz h ebae Left membrane: the visualize to ways alternative Two MembraneEditor: CELLmicrocosmos ELircso elxlrrwt h ahaItgainHbi-iesoa iulzto adti of detail (a visualization PathwayIntegration/Hybrid-dimensional the with CellExplorer CELLmicrocosmos – Dvsaiaino h iohnro ntecne soitdwt h EGctaecce Right cycle; citrate KEGG the with associated center the in mitochondrion the of visualization 3D – h aeclu oe r sdfrtecluigo h Dlipids. 3D the of colouring the for used are codes colour same the – h lg oeve ftetasebaeprotein, transmembrane the of view mode Align the – l tm r iil,laigt oso overview of loss a to leading visible, are atoms all – a e Waals der Van Sommer – 2D 13 Automatically generated rough PDF by ProofCheck from River Valley Technologies Ltd 4 atnzL nrd ,Bri G atnzJ.Pcml akg o uligiiilcngrtosfrmlclrdnmc simula- dynamics molecular for configurations initial building for package a Packmol: JM. Martínez EG, Birgin R, Andrade L, Struct Martínez Comput [4] tools. and methods modelling membrane computational on review short a problems: packing Membrane B. Sommer [3] CELLmicrocosmos B. Sommer [2] CELLmicrocosmos B. Sommer [1] References work. scientific present the to applicable parts journal its the all at with available comply statement they malpractice publication and ethics cation Statement: of Interest Conflict Gouesse Julien 2010 questions Harrison, forum until Harvey especially community 1.5.X, Kon- the Java3D of to to University Java alternative and provided University Falk Monash who to su- at company also stay first go the – my my thanks of during was Many tools memory vision. who the initial In Lorenz my maintain stanz. Dieter develop to freely to me to as allowed me well who enabled as Schreiber and University, thesis Bielefeld supported Bachelor at my who of time Hofestädt pervisor my Ralf pipeline all to the during go realize development thanks to the Special helped https://team.CELLmicrocosmos.org. who project: project the CELLmicrocosmos years porting the many over in involved paper this people in all discussed thank to like would I not Acknowledgements does and Oracle by restricted be will development. Java software of Source versions Open future of to vision access the follow because especially evaluated, be to [47]. project modelling cell whole a of to part future as the behaviour antibiotics/membrane in analyse extended to be might approaches important is These this [46]. supported; [26], is interaction capabilities CmME. 3D Analytics as Immersive well provide as tracking to head hardware compatible visualization, if stereoscopic CmCX/CmPI, accessible, of is case In visualization. 3D Stereoscopic porting merging the direction into future a levels 2). one. be three might Figure into implementation these projects prototype also merging this all (see of tools, (CmPI) extension these The level [2]. all functional (CmX) (1) level combining (3) integrative on exists and modelling implementation (CmCX) and prototype mesoscopic visualization unreleased (2) cell An CmME), supporting (with tools level CELLmicrocosmos molecular main the two the discussed we Here, Outlook 6 14 2008;29:1859 Chem Comput J CHARMM. for interface user graphical web-based a GUI: CHARMM W. Im VG, Iyer T, Kim S, Jo [5] a for funding be must there so, do only to is able is not it who developer is course, main leader Of task. a project this is it. the over there extend take If if other can and years code. the who improve of the developer on period students, software maintain code, long other and a source over of interpret new projects to code write of able variety and the large ideas interpret this new develop to to realize learn possible and to develop have to they how hand learn students hand, one On ol iet hn h eeoeso OLJv3 . n . o podn h prtb rvdn an providing by spirit the upholding for 1.7 and 1.6 JOGL/Java3D of developers the thank to like would I in.JCmu hm2009;30:2157 Chem Comput J tions. 2013;5:e201302014. J Biotec 2012. University, Bielefeld Germany: has versions Java new of use future the Therefore, 8. direction. Java educational workflow with an a run into of tools developed Cm part further the as be currently mentioned, might previously it project As using Cm the are we of aspects projects, certain external Moreover, of number a by used is CmME the While sup- by visualization Reality-related Virtual semi-immersive provide approaches software discussed All iue1soe led htanme fdfeetsuetpoet n hsslytebssfrthis work. for basis the lay theses and projects student different of number a that already showed 1 Figure Sommer – swl so oreSe Goethel/Jausoft. Sven course of as well as – – elniulseug ahlrret ahlrtei.Beeed emn:BeeedUiest,2004. University, Bielefeld Germany: Bielefeld, thesis. Bachelor Bachelorarbeit. zellenvisualisierung. nertv elmdliga h oeua,mssoi n ucinllvl otrt hss Bielefeld, thesis. Doctorate level. functional and mesoscopic molecular, the at modelling cell integrative – uhr tt ocnlc fitrs.Alatoshv edtejournal the read have authors All of interest. conflict no state Authors 64. – seilytesuet,btas h aycoeainprnr sup- partners cooperation many the also but students, the especially – h eeawy eyrsosv to responsive very always were who ’ est n eeycnimthat confirm hereby and website s – u irsses Inc. Microsystems, Sun – uha h zSpace the as such – EGRUYTER DE 65. ’ Publi- s ® – Automatically generated rough PDF by ProofCheck from River Valley Technologies Ltd 3]TplT omirB lse ,HfsätR iDH aawrhuektfrlf cec aaitgain nerBonom2008;5:93. Bioinform Integr J integration. data science life for kit warehouse data a BioDWH: R. Hofestädt A, Klassen B, Kormeier T, Töpel [38] sys- computer ANDCell the of Application existence. NA. of Kolchanov year VA, Ivanisenko 25th OS, Konovalova its PS, in Demenkov developments EE, Yarkova exciting OA, 2015: Podkolodnaya in [37] BRENDA al. et M, Xiao M, Ulbrich 2013;41:D43 Res L, Acids Jeske S, Nucleic Placzek 2013. I, in Schomburg (UniProt) A, resource Chang protein [36] universal the at activities on Update U. Consortium [35] integrating to approach interactive an 4.1: CELLmicrocosmos B. Kormeier M, Rumming A, Husemann N, Sand multi-level J, through Künsemöller B, simulations Sommer molecular [34] performance high GROMACS: al. et B, Hess JC, Smith S, Páll R, Schulz T, Murtola bank. MJ, Abraham data protein [33] the in proteins transmembrane of localization membrane and selection PDB_TM: I. in Simon proteins Z, of Dosztányi positioning GE, for Tusnády resources [32] server: web 2000;28:235 PPM Res and Acids database Nucleic OPM bank. AL. data Lomize protein HI, The Mosberg al. H, Joo et ID, H, Pogozheva Weissig MA, TN, Lomize Bhat [31] G, Gilliland Z, Feng J, Uni- Westbrook Monash HM, at Berman projects [30] analytics immersive 3D-stereoscopic al. et T, Czauderna M, Cordeil T, Chandler S, Boyd biology DG, systems Barnes for B, framework Sommer a [29] v2: VANTED al. et M, Klapperstück H, Treutler E, Grafahrend-Belau A, Hartmann A, Junker H, Rohn Technol-[28] It-Information VANTED. and CmPI with data biomedical of exploration reality virtual and Integration F. Schreiber B, Sommer [27] map space Stereoscopic al. et N, Biere M, Klapperstück T, Czauderna O, Kaluza A, Hamacher B, Model Sommer Inf [26] Chem J trajectories. GROMACS for tool analysis membrane Voronoi-based a APL@Voro: B. Sommer J, interactive Krüger modular G, Lukat a membraneEditor: [25] 2.2 CELLmicrocosmos al. et J, Krüger S, Rubert SE, Schneider C, Gamroth T, Dingersen B, three- Sommer of [24] modelling in applications and advancements 2.2: CELLmicrocosmos C. Gamroth S, Rubert S, Schneider T, Dingersen B, mem- Sommer PDB [23] three-dimensional of modelling the for approach software a 2.1: CELLmicrocosmos 2018 S. 3D, Schneider T, in Dingersen structures B, chemical Sommer for [22] viewer java open-source an Jmol: 3D. in structures chemical for viewer a java of open-source visualization an stereoscopic Jmol: 3D Jmol. and [21] modelling Heuristic al. et BM, Friedrich N, Rothe D, Jäger A, Doebbe M, analysis. Ghaffar biological-image N, for Biere platform [20] open-source an Fiji: al. et T, Pietzsch M, Longair V, Kaynig E, extended Frise for I, platform Arganda-Carreras informatics J, Schindelin bioimage [19] open an Icy: al. et T, Provoost S, 2005;38:749 Pop Handbook N, Hervé Visualization N, analysis. Chenouard data S, visual Dallongeville F, for system Chaumont interactive De highly [18] a Amira: H-C. Hege M, Westerhoff D, Stalling [17] user Amira Berlin. Institute Zuse 2014, [16] Austria, Vienna, visualization. cell molecular and mesoscopic combining mapping: Membrane M. Botsch B, Sommer T, Waltemate [15] CELLmicrocosmos B. 2003;33:169 Sommer Med [14] Biol Comput visualizer. network metabolic Bioin- VRML reality. I. virtual Rojdestvenski in [13] expression gene and networks metabolic of Integration JA. Arabidopsis. Dickerson of C, lattice Cruz-Neira biogenetic ES, Wurtele the L, model Engin and Y, Yang build [12] to software MetNet: al. et B, Fatland CM, Foster 2017;356:806 H, Science Zhang biology. L, cell Diao 21st-century J, for Li course ES, Wurtele a [11] chart Pro- maps In: cell datasets. Whole GT. biomolecular Johnson large R, of Horwitz rendering [10] multi-scale and illustrative for tool a cellVIEW: I. Viola J, Parulek L, sys- Autin structural M, visualize Muzic and Le model [9] to mesoscope virtual a cellPACK: AJ. Olson MF, Sanner DS, Goodsell M, Al-Alusi 2019;431:1889 L, Biol Autin Mol GT, J Johnson dynamics. [8] and organization membrane biological J Visualizing systems. M. complex Baaden protein/micelle [7] and micelle pure/mixed for builder micelle CHARMM-GUI W. Im JB, Klauda HS, Lee S, Jo X, Cheng [6] GRUYTER DE 3]O [39] e orcntuto n nlsso soitv ewrsdsrbn oeta eainhp ewe ypaadgacm.Rs J Russ glaucoma. and myopia between 2011;1:21 relationships Res potential Appl Genet describing networks associative of analysis and reconstruction to tem 2014:gku1068. Res Acids Nucleic Technolo- and Systems Engineering 90 Biomedical 2010, on 2010), Conference (BIOSTEC Joint gies International 3rd the of 2010 part BIOINFORMATICS Bioinformatics, In: on environment. Conference cell tional 3D virtual a into networks metabolic localized spatially 2015;1:19 SoftwareX supercomputers. to laptops from parallelism 2005;33:D275 Res Acids Nucleic 2012;40:D370 Res Acids Nucleic membranes. 2017;2017:179 Imaging Electron Konstanz. of University and versity 2012;6:139. Biol Syst BMC applications. 2016. ogy, Applications and Displays Stereoscopic of 2016;2016:1 Proceedings XXVII Imaging, Electronic In: environments. multi-display in tours 3D-stereoscopic of 2013;53:2908 2011;5:1165 Model Inf Chem J problems. packing membrane heterogeneous solve to approach software shape-based 2010;2:O21. Cheminformatics J membranes. PDB dimensional 2009;3:P72. J Cent Chem branes. 05-Mar-2013]. [Accessed: http://www.jmol.org. from: Available [Online]. reinhardtii domonas 2012;9:676 Methods Nat 2012;9:690 Methods Nat research. reproducible 89 2005;21:3645 formatics 2003;4:239 Genom Funct Comp 2015:61 medicine and biology for computing visual on workshop eurographics the of ceedings 2015;12:85 Methods Nat biology. tems 2013;53:2171 Model Inf Chem 2006. 2003. ’ aahi ,Fse ,WieS oyY h ug(aauieslntokgah rmwr.Ivn,Clfri:Uiest fCalifornia, of University California: Irvine, framework. network/graph) universal (java jung The Y. Boey S, White D, Fisher J, Madadhain – 96. – 25. – el nerBonom2018;15. Bioinform Integr J cell. 9. – – – 50. 8. 82. – – – 80. 5. – – neatv DZlVsaiirn.Mseabi.Mse hss ilfl,Gray ilfl University, Bielefeld Germany: Bielefeld, Thesis. Master Masterarbeit. 3D-ZellVisualisierung. interaktive ’ 8. 45. ud:Aia30 ueIsiueBri,2002. Berlin, Institute Zuse 3.0. Amira guide: s – 91. – 6. – 6. – 25. – 87. – 82. – 70. – 919. – rceig fte1tInterna- 1st the of Proceedings – – eiimrieconfiguration semi-immersive 7. – – 7. 82. Sommer – chlamy- 42. – 67. 15 Automatically generated rough PDF by ProofCheck from River Valley Technologies Ltd 4]ZuY zuen ,Za ,KaprtekM afihMM a -,e l eoesaemtblcmdligo epne to responses of modelling metabolic Genome-scale al. et 2018;15. M-L, Bioinform Han Integr MHM, J Maifiah bioinformatics. M, in Klapperstueck analytics J, immersive Zhao to T, reality Czauderna Y, virtual Zhu From [47] A. Woods M, Krone M, Baaden B, Sommer [46] interaction and visualization Hybrid-dimensional F. Schreiber 2014;34:69 M, Graph Chen Comput L, IEEE biology. Xu SJ, systems Wang from B, example Sommer An SBML. [45] SciVis? with and working InfoVis integrate for Why F. library java Schreiber flexible A, Kerren a [44] JSBML: al. et N, Novère Le C, Wrzodek A, Dörr M, Dumousseau N, Rodriguez A, Dräger [43] Ko AS, Rose D, Sehnal [42] J scenarios. localization cytological of exploration and visualization hybrid-dimensional Web-based B. Sommer M, Electronic Ghaffar In: G, scale. Kovanci molecular [41] to mesoscopic from visualization: cell Stereoscopic L. Jelonek C, Gamroth T, Hoppe C, Bender B, Sommer [40] 16 oyyisin polymyxins 2015;2015:1 (BDVA) Anal Visual Data Big techniques. navigation semi-immersive with 2011;27:2167 Bioinformatics 2018:29 data, molecular of analysis visual and graphics molecular on workshop the of 2016;13:298. Bioinform Integr 2014;23:011007-1 XXVIII Applications and Displays Stereoscopic of Proceedings Imaging, Sommer suooa aeruginosa Pseudomonas č ,Bre K eakrS o* oad omnlbayadtosfrwbmlclrgahc.I:Proceedings In: graphics. molecular web for tools and library common a towards Mol*: S. Velankar SK, Burley J, a – 8. iacec 2018;7:giy021. GigaScience . – – 33. 8. – 10. – nertn Dad3 visualization 3D and 2D integrating – 73. EGRUYTER DE