Literature DB >> 19526065

From Genes to Organisms Via the Cell A Problem-Solving Environment for Multicellular Development.

Trevor Cickovski1, Kedar Aras, Mark S Alber, Jesus A Izaguirre, Maciej Swat, James A Glazier, Roeland M H Merks, Tilmann Glimm, H George E Hentschel, Stuart A Newman.   

Abstract

To gain performance, developers often build scientific applications in procedural languages, such as C or Fortran, which unfortunately reduces flexibility. To address this imbalance, the authors present CompuCell3D, a multitiered, flexible, and scalable problem-solving environment for morphogenesis simulations that's written in C++ using object-oriented design patterns.

Year:  2007        PMID： 19526065      PMCID： PMC2695324          DOI： 10.1109/MCSE.2007.74

Source DB:  PubMed          Journal:  Comput Sci Eng        ISSN： 1521-9615            Impact factor:   2.080


  7 in total

1.  Percolation, morphogenesis, and burgers dynamics in blood vessels formation.

Authors:  A Gamba; D Ambrosi; A Coniglio; A de Candia; S Di Talia; E Giraudo; G Serini; L Preziosi; F Bussolino
Journal:  Phys Rev Lett       Date:  2003-03-17       Impact factor: 9.161

2.  Dynamical mechanisms for skeletal pattern formation in the vertebrate limb.

Authors:  H G E Hentschel; Tilmann Glimm; James A Glazier; Stuart A Newman
Journal:  Proc Biol Sci       Date:  2004-08-22       Impact factor: 5.349

3.  Simulation of biological cell sorting using a two-dimensional extended Potts model.

Authors: 
Journal:  Phys Rev Lett       Date:  1992-09-28       Impact factor: 9.161

4.  Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling.

Authors:  Roeland M H Merks; Sergey V Brodsky; Michael S Goligorksy; Stuart A Newman; James A Glazier
Journal:  Dev Biol       Date:  2005-12-01       Impact factor: 3.582

5.  On multiscale approaches to three-dimensional modelling of morphogenesis.

Authors:  R Chaturvedi; C Huang; B Kazmierczak; T Schneider; J A Izaguirre; T Glimm; H G E Hentschel; J A Glazier; S A Newman; M S Alber
Journal:  J R Soc Interface       Date:  2005-06-22       Impact factor: 4.118

6.  A framework for three-dimensional simulation of morphogenesis.

Authors:  Trevor M Cickovski; Chenbang Huang; Rajiv Chaturvedi; Tilmann Glimm; H George E Hentschel; Mark S Alber; James A Glazier; Stuart A Newman; Jesús A Izaguirre
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2005 Oct-Dec       Impact factor: 3.710

7.  Simulation of the differential adhesion driven rearrangement of biological cells.

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1993-03
  7 in total
  11 in total

1.  VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development.

Authors:  Roeland M H Merks; Michael Guravage; Dirk Inzé; Gerrit T S Beemster
Journal:  Plant Physiol       Date:  2010-12-09       Impact factor: 8.340

2.  A multiscale model of thrombus development.

Authors:  Zhiliang Xu; Nan Chen; Malgorzata M Kamocka; Elliot D Rosen; Mark Alber
Journal:  J R Soc Interface       Date:  2008-07-06       Impact factor: 4.118

3.  Multi-scale modeling of tissues using CompuCell3D.

Authors:  Maciej H Swat; Gilberto L Thomas; Julio M Belmonte; Abbas Shirinifard; Dimitrij Hmeljak; James A Glazier
Journal:  Methods Cell Biol       Date:  2012       Impact factor: 1.441

Review 4.  Normal morphogenesis of epithelial tissues and progression of epithelial tumors.

Authors:  Chun-Chao Wang; Leen Jamal; Kevin A Janes
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2011-09-02

5.  The effects of cell compressibility, motility and contact inhibition on the growth of tumor cell clusters using the Cellular Potts Model.

Authors:  Jonathan F Li; John Lowengrub
Journal:  J Theor Biol       Date:  2013-11-06       Impact factor: 2.691

6.  Systems biology of embryogenesis.

Authors:  Lucas B Edelman; Sriram Chandrasekaran; Nathan D Price
Journal:  Reprod Fertil Dev       Date:  2010       Impact factor: 2.311

7.  Multicell simulations of development and disease using the CompuCell3D simulation environment.

Authors:  Maciej H Swat; Susan D Hester; Ariel I Balter; Randy W Heiland; Benjamin L Zaitlen; James A Glazier
Journal:  Methods Mol Biol       Date:  2009

8.  Ovarian tumor attachment, invasion, and vascularization reflect unique microenvironments in the peritoneum: insights from xenograft and mathematical models.

Authors:  Mara P Steinkamp; Kimberly Kanigel Winner; Suzy Davies; Carolyn Muller; Yong Zhang; Robert M Hoffman; Abbas Shirinifard; Melanie Moses; Yi Jiang; Bridget S Wilson
Journal:  Front Oncol       Date:  2013-05-17       Impact factor: 6.244

9.  Chaste: an open source C++ library for computational physiology and biology.

Authors:  Gary R Mirams; Christopher J Arthurs; Miguel O Bernabeu; Rafel Bordas; Jonathan Cooper; Alberto Corrias; Yohan Davit; Sara-Jane Dunn; Alexander G Fletcher; Daniel G Harvey; Megan E Marsh; James M Osborne; Pras Pathmanathan; Joe Pitt-Francis; James Southern; Nejib Zemzemi; David J Gavaghan
Journal:  PLoS Comput Biol       Date:  2013-03-14       Impact factor: 4.475

10.  Using cellzilla for plant growth simulations at the cellular level.

Authors:  Bruce E Shapiro; Elliot M Meyerowitz; Eric Mjolsness
Journal:  Front Plant Sci       Date:  2013-10-16       Impact factor: 5.753
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