{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T00:21:18Z","timestamp":1769214078329,"version":"3.49.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2242,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multi-cellular systems in 2D and 3D. It implements an agent-based model that approximates cells as isotropic, elastic and adhesive objects. Cell migration is modeled by an equation of motion for each cell. The software includes many modules specifically tailored to support the simulation and analysis of virtual tissues including real-time 3D visualization and VRML 2.0 support. All cell and environment parameters can be independently varied which facilitates species specific simulations and allows for detailed analyses of growth dynamics and links between cellular and multi-cellular phenotypes.<\/jats:p>\n               <jats:p>Availability: CellSys is freely available for non-commercial use at http:\/\/msysbio.com\/software\/cellsys. The current version of CellSys permits the simulation of growing monolayer cultures and avascular tumor spheroids in liquid environment. Further functionality will be made available ongoing with published papers.<\/jats:p>\n               <jats:p>Contact: \u00a0hoehme@izbi.uni-leipzig.de; dirk.drasdo@inria.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq437","type":"journal-article","created":{"date-parts":[[2010,8,14]],"date-time":"2010-08-14T00:13:54Z","timestamp":1281744834000},"page":"2641-2642","source":"Crossref","is-referenced-by-count":147,"title":["A cell-based simulation software for multi-cellular systems"],"prefix":"10.1093","volume":"26","author":[{"given":"Stefan","family":"Hoehme","sequence":"first","affiliation":[{"name":"1 Interdisciplinary Centre for Bioinformatics, University of Leipzig, Germany and 2Institut National de Recherche en Informatique et en Automatique (INRIA) Unit Rocquencourt B.P.105, 78153 Le Chesnay Cedex, France"}]},{"given":"Dirk","family":"Drasdo","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Centre for Bioinformatics, University of Leipzig, Germany and 2Institut National de Recherche en Informatique et en Automatique (INRIA) Unit Rocquencourt B.P.105, 78153 Le Chesnay Cedex, France"},{"name":"1 Interdisciplinary Centre for Bioinformatics, University of Leipzig, Germany and 2Institut National de Recherche en Informatique et en Automatique (INRIA) Unit Rocquencourt B.P.105, 78153 Le Chesnay Cedex, France"}]}],"member":"286","published-online":{"date-parts":[[2010,8,13]]},"reference":[{"key":"2023012507562559000_B1","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-7643-8123-3","volume-title":"Single-Cell-Based Models in Biology and Medicine.","author":"Anderson","year":"2007"},{"key":"2023012507562559000_B2","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1007\/s00285-008-0212-0","article-title":"Individual-based and continuum models of growing cell populations: a comparison","volume":"58","author":"Byrne","year":"2009","journal-title":"J. Math. Biol."},{"key":"2023012507562559000_B3","doi-asserted-by":"crossref","first-page":"028102","DOI":"10.1103\/PhysRevLett.94.028102","article-title":"Johnson-Kendall-Roberts theory applied to living cells","volume":"94","author":"Chu","year":"2005","journal-title":"Phys. Rev. Lett."},{"key":"2023012507562559000_B4","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1093\/bioinformatics\/btl172","article-title":"BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge","volume":"22","author":"Calzone","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012507562559000_B5","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1007\/s10955-007-9289-x","article-title":"On the role of physics in the growth and pattern formation of multi-cellular systems","volume":"128","author":"Drasdo","year":"2007","journal-title":"J. Stat. Phys."},{"key":"2023012507562559000_B6","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1088\/1478-3975\/2\/3\/001","article-title":"A single-cell-based model of tumor growth in vitro: monolayers and spheroids","volume":"2","author":"Drasdo","year":"2005","journal-title":"Phys. Biol."},{"key":"2023012507562559000_B7","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.cbi.2007.01.010","article-title":"Mathematical modelling of liver regeneration after intoxication with CCl4","volume":"168","author":"Hoehme","year":"2007","journal-title":"Chem. Biol. Interact."},{"key":"2023012507562559000_B8","doi-asserted-by":"crossref","first-page":"10371","DOI":"10.1073\/pnas.0909374107","article-title":"Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration","volume":"107","author":"Hoehme","year":"2010","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012507562559000_B9","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1093\/bioinformatics\/bti820","article-title":"Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment","volume":"22","author":"Missal","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012507562559000_B10","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1529\/biophysj.107.114678","article-title":"Modeling the influence of the E-cadherin-beta-catenin pathway in cancer cell invasion: a multiscale approach","volume":"95","author":"Ramis-Conde","year":"2008","journal-title":"Biophys. J."},{"key":"2023012507562559000_B11","doi-asserted-by":"crossref","first-page":"16008","DOI":"10.1088\/1478-3975\/6\/1\/016008","article-title":"Multi-scale modelling of cancer cell intravasation: the role of cadherins in metastasis","volume":"6","author":"Ramis-Conde","year":"2009","journal-title":"Phys Biol."},{"key":"2023012507562559000_B12","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1073\/pnas.0237333100","article-title":"Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling","volume":"100","author":"Swameye","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012507562559000_B13","doi-asserted-by":"crossref","first-page":"864","DOI":"10.1093\/bioinformatics\/18.6.864","article-title":"Hybrid alignment: high-performance with universal statistics","volume":"18","author":"Yu","year":"2002","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/20\/2641\/48852698\/bioinformatics_26_20_2641.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/20\/2641\/48852698\/bioinformatics_26_20_2641.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:57:00Z","timestamp":1674633420000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/20\/2641\/193478"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,8,13]]},"references-count":13,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2010,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq437","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,10,15]]},"published":{"date-parts":[[2010,8,13]]}}}