Loading…

On multiscale approaches to three-dimensional modelling of morphogenesis

In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical...

Full description

Saved in:

Bibliographic Details
Published in:	Journal of the Royal Society interface 2005-06, Vol.2 (3), p.237-253
Main Authors:	Chaturvedi, R, Huang, C, Kazmierczak, B, Schneider, T, Izaguirre, J.A, Glimm, T, Hentschel, H.G.E, Glazier, J.A, Newman, S.A, Alber, M.S
Format:	Article
Language:	English
Subjects:	Animals Cattle Cell Death Cell Division Cell Dynamics Cell Physiological Phenomena Cellular Potts Model Computational Biology Models, Biological Morphogenesis Morphogenesis - physiology Organogenesis Physiology - methods Systems Biology
Citations:	Items that this one cites Items that cite this one
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

cited_by	cdi_FETCH-LOGICAL-c563t-c52a173e01c855513a90d8b87c6bef551eaf56b0c4b7030687a3997761a974763
cites	cdi_FETCH-LOGICAL-c563t-c52a173e01c855513a90d8b87c6bef551eaf56b0c4b7030687a3997761a974763
container_end_page	253
container_issue	3
container_start_page	237
container_title	Journal of the Royal Society interface
container_volume	2
creator	Chaturvedi, R Huang, C Kazmierczak, B Schneider, T Izaguirre, J.A Glimm, T Hentschel, H.G.E Glazier, J.A Newman, S.A Alber, M.S
description	In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction-diffusion model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex-developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb.
doi_str_mv	10.1098/rsif.2005.0033
format	article
fullrecord	<record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmed_primary_16849182</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>70171932</sourcerecordid><originalsourceid>FETCH-LOGICAL-c563t-c52a173e01c855513a90d8b87c6bef551eaf56b0c4b7030687a3997761a974763</originalsourceid><addsrcrecordid>eNp9kMGP1CAUxhujcdfVq0fTk7eOUAoUDyZm1R2TTfaiG28vlL5OWdsyAlXnv5em4-ge9AI8-H3fe3xZ9pySDSWqfuWD7TYlIXxDCGMPsnMqq7LgQpQPT-danWVPQrhLhGScP87OqKgrRevyPNveTPk4D9EGowfM9X7vnTY9hjy6PPYesWjtiFOwbtJDProWh8FOu9x1qfD73u1wwmDD0-xRp4eAz477Rfb5w_tPl9vi-ubq4-Xb68JwwWJaS00lQ0JNzTmnTCvS1k0tjWiwSxeoOy4aYqpGEkZELTVTSkpBtZKVFOwie7P67udmxNbgFL0eYO_tqP0BnLZw_2WyPezcd6CiVESqZPDyaODdtxlDhDF9Pv1KT-jmAJJQSRUrE7hZQeNdCB67UxNKYAkflvBhCR-W8JPgxd-j_cGPaSeArYB3h5SRMxbjAe7c7FO24d-2xaqyIeLPk6v2X0FIJjnc1hVcVVt---XdFmTi6cr3dtf_sB7hXrtU2Cmi77RBKIFByRbN6_9qlomMS7Ip_tZANw8p97ZjvwAJjMqy</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>70171932</pqid></control><display><type>article</type><title>On multiscale approaches to three-dimensional modelling of morphogenesis</title><source>PubMed Central</source><source>Royal Society Publishing Jisc Collections Royal Society Journals Read & Publish Transitional Agreement 2025 (reading list)</source><creator>Chaturvedi, R ; Huang, C ; Kazmierczak, B ; Schneider, T ; Izaguirre, J.A ; Glimm, T ; Hentschel, H.G.E ; Glazier, J.A ; Newman, S.A ; Alber, M.S</creator><creatorcontrib>Chaturvedi, R ; Huang, C ; Kazmierczak, B ; Schneider, T ; Izaguirre, J.A ; Glimm, T ; Hentschel, H.G.E ; Glazier, J.A ; Newman, S.A ; Alber, M.S</creatorcontrib><description>In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction-diffusion model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex-developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb.</description><identifier>ISSN: 1742-5689</identifier><identifier>EISSN: 1742-5662</identifier><identifier>DOI: 10.1098/rsif.2005.0033</identifier><identifier>PMID: 16849182</identifier><language>eng</language><publisher>London: The Royal Society</publisher><subject>Animals ; Cattle ; Cell Death ; Cell Division ; Cell Dynamics ; Cell Physiological Phenomena ; Cellular Potts Model ; Computational Biology ; Models, Biological ; Morphogenesis ; Morphogenesis - physiology ; Organogenesis ; Physiology - methods ; Systems Biology</subject><ispartof>Journal of the Royal Society interface, 2005-06, Vol.2 (3), p.237-253</ispartof><rights>2005 The Royal Society</rights><rights>2005 The Royal Society 2005</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c563t-c52a173e01c855513a90d8b87c6bef551eaf56b0c4b7030687a3997761a974763</citedby><cites>FETCH-LOGICAL-c563t-c52a173e01c855513a90d8b87c6bef551eaf56b0c4b7030687a3997761a974763</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1629079/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1629079/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,725,778,782,883,27907,27908,53774,53776</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16849182$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chaturvedi, R</creatorcontrib><creatorcontrib>Huang, C</creatorcontrib><creatorcontrib>Kazmierczak, B</creatorcontrib><creatorcontrib>Schneider, T</creatorcontrib><creatorcontrib>Izaguirre, J.A</creatorcontrib><creatorcontrib>Glimm, T</creatorcontrib><creatorcontrib>Hentschel, H.G.E</creatorcontrib><creatorcontrib>Glazier, J.A</creatorcontrib><creatorcontrib>Newman, S.A</creatorcontrib><creatorcontrib>Alber, M.S</creatorcontrib><title>On multiscale approaches to three-dimensional modelling of morphogenesis</title><title>Journal of the Royal Society interface</title><addtitle>J R Soc Interface</addtitle><description>In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction-diffusion model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex-developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb.</description><subject>Animals</subject><subject>Cattle</subject><subject>Cell Death</subject><subject>Cell Division</subject><subject>Cell Dynamics</subject><subject>Cell Physiological Phenomena</subject><subject>Cellular Potts Model</subject><subject>Computational Biology</subject><subject>Models, Biological</subject><subject>Morphogenesis</subject><subject>Morphogenesis - physiology</subject><subject>Organogenesis</subject><subject>Physiology - methods</subject><subject>Systems Biology</subject><issn>1742-5689</issn><issn>1742-5662</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><recordid>eNp9kMGP1CAUxhujcdfVq0fTk7eOUAoUDyZm1R2TTfaiG28vlL5OWdsyAlXnv5em4-ge9AI8-H3fe3xZ9pySDSWqfuWD7TYlIXxDCGMPsnMqq7LgQpQPT-danWVPQrhLhGScP87OqKgrRevyPNveTPk4D9EGowfM9X7vnTY9hjy6PPYesWjtiFOwbtJDProWh8FOu9x1qfD73u1wwmDD0-xRp4eAz477Rfb5w_tPl9vi-ubq4-Xb68JwwWJaS00lQ0JNzTmnTCvS1k0tjWiwSxeoOy4aYqpGEkZELTVTSkpBtZKVFOwie7P67udmxNbgFL0eYO_tqP0BnLZw_2WyPezcd6CiVESqZPDyaODdtxlDhDF9Pv1KT-jmAJJQSRUrE7hZQeNdCB67UxNKYAkflvBhCR-W8JPgxd-j_cGPaSeArYB3h5SRMxbjAe7c7FO24d-2xaqyIeLPk6v2X0FIJjnc1hVcVVt---XdFmTi6cr3dtf_sB7hXrtU2Cmi77RBKIFByRbN6_9qlomMS7Ip_tZANw8p97ZjvwAJjMqy</recordid><startdate>20050622</startdate><enddate>20050622</enddate><creator>Chaturvedi, R</creator><creator>Huang, C</creator><creator>Kazmierczak, B</creator><creator>Schneider, T</creator><creator>Izaguirre, J.A</creator><creator>Glimm, T</creator><creator>Hentschel, H.G.E</creator><creator>Glazier, J.A</creator><creator>Newman, S.A</creator><creator>Alber, M.S</creator><general>The Royal Society</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20050622</creationdate><title>On multiscale approaches to three-dimensional modelling of morphogenesis</title><author>Chaturvedi, R ; Huang, C ; Kazmierczak, B ; Schneider, T ; Izaguirre, J.A ; Glimm, T ; Hentschel, H.G.E ; Glazier, J.A ; Newman, S.A ; Alber, M.S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c563t-c52a173e01c855513a90d8b87c6bef551eaf56b0c4b7030687a3997761a974763</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Animals</topic><topic>Cattle</topic><topic>Cell Death</topic><topic>Cell Division</topic><topic>Cell Dynamics</topic><topic>Cell Physiological Phenomena</topic><topic>Cellular Potts Model</topic><topic>Computational Biology</topic><topic>Models, Biological</topic><topic>Morphogenesis</topic><topic>Morphogenesis - physiology</topic><topic>Organogenesis</topic><topic>Physiology - methods</topic><topic>Systems Biology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chaturvedi, R</creatorcontrib><creatorcontrib>Huang, C</creatorcontrib><creatorcontrib>Kazmierczak, B</creatorcontrib><creatorcontrib>Schneider, T</creatorcontrib><creatorcontrib>Izaguirre, J.A</creatorcontrib><creatorcontrib>Glimm, T</creatorcontrib><creatorcontrib>Hentschel, H.G.E</creatorcontrib><creatorcontrib>Glazier, J.A</creatorcontrib><creatorcontrib>Newman, S.A</creatorcontrib><creatorcontrib>Alber, M.S</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of the Royal Society interface</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chaturvedi, R</au><au>Huang, C</au><au>Kazmierczak, B</au><au>Schneider, T</au><au>Izaguirre, J.A</au><au>Glimm, T</au><au>Hentschel, H.G.E</au><au>Glazier, J.A</au><au>Newman, S.A</au><au>Alber, M.S</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>On multiscale approaches to three-dimensional modelling of morphogenesis</atitle><jtitle>Journal of the Royal Society interface</jtitle><addtitle>J R Soc Interface</addtitle><date>2005-06-22</date><risdate>2005</risdate><volume>2</volume><issue>3</issue><spage>237</spage><epage>253</epage><pages>237-253</pages><issn>1742-5689</issn><eissn>1742-5662</eissn><abstract>In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction-diffusion model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex-developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb.</abstract><cop>London</cop><pub>The Royal Society</pub><pmid>16849182</pmid><doi>10.1098/rsif.2005.0033</doi><tpages>17</tpages><oa>free_for_read</oa></addata></record>
fulltext	fulltext
identifier	ISSN: 1742-5689
ispartof	Journal of the Royal Society interface, 2005-06, Vol.2 (3), p.237-253
issn	1742-5689 1742-5662
language	eng
recordid	cdi_pubmed_primary_16849182
source	PubMed Central; Royal Society Publishing Jisc Collections Royal Society Journals Read & Publish Transitional Agreement 2025 (reading list)
subjects	Animals Cattle Cell Death Cell Division Cell Dynamics Cell Physiological Phenomena Cellular Potts Model Computational Biology Models, Biological Morphogenesis Morphogenesis - physiology Organogenesis Physiology - methods Systems Biology
title	On multiscale approaches to three-dimensional modelling of morphogenesis
url	http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-16T21%3A15%3A46IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=On%20multiscale%20approaches%20to%20three-dimensional%20modelling%20of%20morphogenesis&rft.jtitle=Journal%20of%20the%20Royal%20Society%20interface&rft.au=Chaturvedi,%20R&rft.date=2005-06-22&rft.volume=2&rft.issue=3&rft.spage=237&rft.epage=253&rft.pages=237-253&rft.issn=1742-5689&rft.eissn=1742-5662&rft_id=info:doi/10.1098/rsif.2005.0033&rft_dat=%3Cproquest_pubme%3E70171932%3C/proquest_pubme%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c563t-c52a173e01c855513a90d8b87c6bef551eaf56b0c4b7030687a3997761a974763%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=70171932&rft_id=info:pmid/16849182&rfr_iscdi=true