Literature DB >> 16410323

Tools for the SBML Community.

Colin S Gillespie1, Darren J Wilkinson, Carole J Proctor, Daryl P Shanley, Richard J Boys, Thomas B L Kirkwood.   

Abstract

MOTIVATION: SBML is quickly becoming the standard format to exchange biochemical models. The tools presented in this paper are loosely-coupled, and are intended to be incorporated into SBML aware applications. The rationale for this is to reduce the amount of repeated work carried out within the community and to create tools that offer a greater number of features to the end-user. AVAILABILITY: All tools described are available from http://www.basis.ncl.ac.uk/software and are licensed under GNU General Public License.

Entities:  

Mesh:

Year:  2006        PMID: 16410323     DOI: 10.1093/bioinformatics/btk042

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


  25 in total

1.  Antimony: a modular model definition language.

Authors:  Lucian P Smith; Frank T Bergmann; Deepak Chandran; Herbert M Sauro
Journal:  Bioinformatics       Date:  2009-07-03       Impact factor: 6.937

2.  Synthetic biology: a foundation for multi-scale molecular biology.

Authors:  Adam G Bower; Maria K McClintock; Stephen S Fong
Journal:  Bioeng Bugs       Date:  2010 Sep-Oct

3.  GSK3 and p53 - is there a link in Alzheimer's disease?

Authors:  Carole J Proctor; Douglas A Gray
Journal:  Mol Neurodegener       Date:  2010-01-26       Impact factor: 14.195

4.  Efficient stochastic simulation of reaction-diffusion processes via direct compilation.

Authors:  Mieszko Lis; Maxim N Artyomov; Srinivas Devadas; Arup K Chakraborty
Journal:  Bioinformatics       Date:  2009-07-03       Impact factor: 6.937

5.  Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways.

Authors:  Graham R Smith; Daryl P Shanley
Journal:  PLoS One       Date:  2010-06-14       Impact factor: 3.240

6.  Modelling the checkpoint response to telomere uncapping in budding yeast.

Authors:  C J Proctor; D A Lydall; R J Boys; C S Gillespie; D P Shanley; D J Wilkinson; T B L Kirkwood
Journal:  J R Soc Interface       Date:  2007-02-22       Impact factor: 4.118

7.  Computational systems biology in cancer: modeling methods and applications.

Authors:  Wayne Materi; David S Wishart
Journal:  Gene Regul Syst Bio       Date:  2007-09-17

8.  Feedback between p21 and reactive oxygen production is necessary for cell senescence.

Authors:  João F Passos; Glyn Nelson; Chunfang Wang; Torsten Richter; Cedric Simillion; Carole J Proctor; Satomi Miwa; Sharon Olijslagers; Jennifer Hallinan; Anil Wipat; Gabriele Saretzki; Karl Lenhard Rudolph; Tom B L Kirkwood; Thomas von Zglinicki
Journal:  Mol Syst Biol       Date:  2010-02-16       Impact factor: 11.429

9.  Computational modelling of the regulation of Insulin signalling by oxidative stress.

Authors:  Graham R Smith; Daryl P Shanley
Journal:  BMC Syst Biol       Date:  2013-05-24

10.  Systems modelling of NHEJ reveals the importance of redox regulation of Ku70/80 in the dynamics of dna damage foci.

Authors:  David Dolan; Glyn Nelson; Anze Zupanic; Graham Smith; Daryl Shanley
Journal:  PLoS One       Date:  2013-02-06       Impact factor: 3.240

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