Literature DB >> 19244386

BISEN: Biochemical Simulation Environment.

J Vanlier1, F Wu, F Qi, K C Vinnakota, Y Han, R K Dash, F Yang, D A Beard.   

Abstract

SUMMARY: The Biochemical Simulation Environment (BISEN) is a suite of tools for generating equations and associated computer programs for simulating biochemical systems in the MATLAB computing environment. This is the first package that can generate appropriate systems of differential equations for user-specified multi-compartment systems of enzymes and transporters accounting for detailed biochemical thermodynamics, rapid equilibria of multiple biochemical species and dynamic proton and metal ion buffering. AVAILABILITY: The software and a user manual (including several tutorial examples) are available at bbc.mcw.edu/BISEN.

Entities:  

Mesh：

Year:  2009        PMID： 19244386      PMCID： PMC2732302          DOI： 10.1093/bioinformatics/btp069

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


  3 in total

1.  Computer modeling of mitochondrial tricarboxylic acid cycle, oxidative phosphorylation, metabolite transport, and electrophysiology.

Authors:  Fan Wu; Feng Yang; Kalyan C Vinnakota; Daniel A Beard
Journal:  J Biol Chem       Date:  2007-06-25       Impact factor: 5.157

2.  Multiple ion binding equilibria, reaction kinetics, and thermodynamics in dynamic models of biochemical pathways.

Authors:  Kalyan C Vinnakota; Fan Wu; Martin J Kushmerick; Daniel A Beard
Journal:  Methods Enzymol       Date:  2009       Impact factor: 1.600

3.  CellML metadata standards, associated tools and repositories.

Authors:  Daniel A Beard; Randall Britten; Mike T Cooling; Alan Garny; Matt D B Halstead; Peter J Hunter; James Lawson; Catherine M Lloyd; Justin Marsh; Andrew Miller; David P Nickerson; Poul M F Nielsen; Taishin Nomura; Shankar Subramanium; Sarala M Wimalaratne; Tommy Yu
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2009-05-28       Impact factor: 4.226
  3 in total
  10 in total

1.  A database of thermodynamic quantities for the reactions of glycolysis and the tricarboxylic acid cycle.

Authors:  X Li; R K Dash; R K Pradhan; F Qi; M Thompson; K C Vinnakota; F Wu; F Yang; D A Beard
Journal:  J Phys Chem B       Date:  2010-05-06       Impact factor: 2.991

2.  Modular modelling with Physiome standards.

Authors:  Michael T Cooling; David P Nickerson; Poul M F Nielsen; Peter J Hunter
Journal:  J Physiol       Date:  2016-08-29       Impact factor: 5.182

Review 3.  Simulation of cellular biochemical system kinetics.

Authors:  Daniel A Beard
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2010-12-17

Review 4.  Computational modeling of mitochondrial energy transduction.

Authors:  J P J Schmitz; J Vanlier; N A W van Riel; Jeroen A L Jeneson
Journal:  Crit Rev Biomed Eng       Date:  2011

5.  Design of experiments for identification of complex biochemical systems with applications to mitochondrial bioenergetics.

Authors:  Kalyan C Vinnakota; Daniel A Beard; Ranjan K Dash
Journal:  Conf Proc IEEE Eng Med Biol Soc       Date:  2009

6.  Closure of VDAC causes oxidative stress and accelerates the Ca(2+)-induced mitochondrial permeability transition in rat liver mitochondria.

Authors:  Andrey Tikunov; C Bryce Johnson; Peter Pediaditakis; Nikolai Markevich; Jeffrey M Macdonald; John J Lemasters; Ekhson Holmuhamedov
Journal:  Arch Biochem Biophys       Date:  2010-01-25       Impact factor: 4.013

7.  Using a genome-scale metabolic network model to elucidate the mechanism of chloroquine action in Plasmodium falciparum.

Authors:  Shivendra G Tewari; Sean T Prigge; Jaques Reifman; Anders Wallqvist
Journal:  Int J Parasitol Drugs Drug Resist       Date:  2017-03-22       Impact factor: 4.077

8.  Modelling the impact of changes in the extracellular environment on the cytosolic free NAD+/NADH ratio during cell culture.

Authors:  Ross A Kelly; Joseph Leedale; Andy Harrell; Daniel A Beard; Laura E Randle; Amy E Chadwick; Steven D Webb
Journal:  PLoS One       Date:  2018-11-29       Impact factor: 3.240

9.  Generating rate equations for complex enzyme systems by a computer-assisted systematic method.

Authors:  Feng Qi; Ranjan K Dash; Yu Han; Daniel A Beard
Journal:  BMC Bioinformatics       Date:  2009-08-04       Impact factor: 3.169

10.  Optimal experiment design for model selection in biochemical networks.

Authors:  Joep Vanlier; Christian A Tiemann; Peter A J Hilbers; Natal A W van Riel
Journal:  BMC Syst Biol       Date:  2014-02-20
  10 in total

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