Literature DB >> 11331245

A-Cell: graphical user interface for the construction of biochemical reaction models.

K Ichikawa1.   

Abstract

SUMMARY: A-Cell is a tool for constructing models of complex and complicated biochemical reactions. An important feature of A-Cell is its graphical user interface for constructing biochemical reactions. In addition, it has a capability of importing previously constructed models, combining them, and constructing a comprehensive model. The simulation program for the model is automatically generated by A-cell.

Mesh：

Year:  2001        PMID： 11331245     DOI： 10.1093/bioinformatics/17.5.483

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  13 in total

1.  CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle.

Authors:  Hiroyuki Kurata; Nana Matoba; Natsumi Shimizu
Journal:  Nucleic Acids Res       Date:  2003-07-15       Impact factor: 16.971

2.  A modeling environment with three-dimensional morphology, A-Cell-3D, and Ca2+ dynamics in a spine.

Authors:  Kazuhisa Ichikawa
Journal:  Neuroinformatics       Date:  2005

3.  Molecular properties of rhodopsin and rod function.

Authors:  Hiroo Imai; Vladimir Kefalov; Keisuke Sakurai; Osamu Chisaka; Yoshiki Ueda; Akishi Onishi; Takefumi Morizumi; Yingbin Fu; Kazuhisa Ichikawa; Kei Nakatani; Yoshihito Honda; Jeannie Chen; King-Wai Yau; Yoshinori Shichida
Journal:  J Biol Chem       Date:  2006-12-28       Impact factor: 5.157

4.  Regulation of signal transduction by spatial parameters: a case in NF-κB oscillation.

Authors:  Kazuhisa Ichikawa; Daisuke Ohshima; Hiroshi Sagara
Journal:  IET Syst Biol       Date:  2015-04       Impact factor: 1.615

5.  Roles of spatial parameters on the oscillation of nuclear NF-κB: computer simulations of a 3D spherical cell.

Authors:  Daisuke Ohshima; Jun-ichiro Inoue; Kazuhisa Ichikawa
Journal:  PLoS One       Date:  2012-10-03       Impact factor: 3.240

6.  Postsynaptic signal transduction models for long-term potentiation and depression.

Authors:  Tiina Manninen; Katri Hituri; Jeanette Hellgren Kotaleski; Kim T Blackwell; Marja-Leena Linne
Journal:  Front Comput Neurosci       Date:  2010-12-13       Impact factor: 2.380

7.  Establishment and validation of computational model for MT1-MMP dependent ECM degradation and intervention strategies.

Authors:  Daisuke Hoshino; Naohiko Koshikawa; Takashi Suzuki; Vito Quaranta; Alissa M Weaver; Motoharu Seiki; Kazuhisa Ichikawa
Journal:  PLoS Comput Biol       Date:  2012-04-12       Impact factor: 4.475

8.  Regulation of NF-κB Oscillation by Nuclear Transport: Mechanisms Determining the Persistency and Frequency of Oscillation.

Authors:  Daisuke Ohshima; Kazuhisa Ichikawa
Journal:  PLoS One       Date:  2015-06-04       Impact factor: 3.240

9.  Mathematical modeling of cancer invasion: the role of membrane-bound matrix metalloproteinases.

Authors:  Niall E Deakin; Mark A J Chaplain
Journal:  Front Oncol       Date:  2013-04-03       Impact factor: 6.244

10.  Critical role of transient activity of MT1-MMP for ECM degradation in invadopodia.

Authors:  Ayako Watanabe; Daisuke Hoshino; Daisuke Hosino; Naohiko Koshikawa; Motoharu Seiki; Takashi Suzuki; Kazuhisa Ichikawa
Journal:  PLoS Comput Biol       Date:  2013-05-30       Impact factor: 4.475
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