Literature DB >> 15087311

MathSBML: a package for manipulating SBML-based biological models.

Bruce E Shapiro1, Michael Hucka, Andrew Finney, John Doyle.   

Abstract

UNLABELLED: MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. It converts SBML models into Mathematica data structures and provides a platform for manipulating and evaluating these models. Once a model is read by MathSBML, it is fully compatible with standard Mathematica functions such as NDSolve (a differential-algebraic equations solver). MathSBML also provides an application programming interface for viewing, manipulating, running numerical simulations; exporting SBML models; and converting SBML models in to other formats, such as XPP, HTML and FORTRAN. By accessing the full breadth of Mathematica functionality, MathSBML is fully extensible to SBML models of any size or complexity. AVAILABILITY: Open Source (LGPL) at http://www.sbml.org and http://www.sf.net/projects/sbml

Mesh：

Year:  2004        PMID： 15087311      PMCID： PMC1409765          DOI： 10.1093/bioinformatics/bth271

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


  6 in total

1.  A synthetic oscillatory network of transcriptional regulators.

Authors:  M B Elowitz; S Leibler
Journal:  Nature       Date:  2000-01-20       Impact factor: 49.962

2.  Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades.

Authors:  B N Kholodenko
Journal:  Eur J Biochem       Date:  2000-03

3.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

4.  Systems biology markup language: Level 2 and beyond.

Authors:  A Finney; M Hucka
Journal:  Biochem Soc Trans       Date:  2003-12       Impact factor: 5.407

5.  Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations.

Authors:  Bruce E Shapiro; Andre Levchenko; Elliot M Meyerowitz; Barbara J Wold; Eric D Mjolsness
Journal:  Bioinformatics       Date:  2003-03-22       Impact factor: 6.937

6.  Modeling the cell division cycle: cdc2 and cyclin interactions.

Authors:  J J Tyson
Journal:  Proc Natl Acad Sci U S A       Date:  1991-08-15       Impact factor: 11.205
  6 in total
  19 in total

1.  Comparing simulation results of SBML capable simulators.

Authors:  Frank T Bergmann; Herbert M Sauro
Journal:  Bioinformatics       Date:  2008-06-25       Impact factor: 6.937

2.  A two-way interface between limited Systems Biology Markup Language and R.

Authors:  Tomas Radivoyevitch
Journal:  BMC Bioinformatics       Date:  2004-12-07       Impact factor: 3.169

3.  Quantitative Systems Pharmacology: A Framework for Context.

Authors:  Ioannis P Androulakis
Journal:  Curr Pharmacol Rep       Date:  2016-04-08

4.  Adaptable functionality of transcriptional feedback in bacterial two-component systems.

Authors:  J Christian J Ray; Oleg A Igoshin
Journal:  PLoS Comput Biol       Date:  2010-02-12       Impact factor: 4.475

5.  D-Lactate production as a function of glucose metabolism in Saccharomyces cerevisiae.

Authors:  Benjamin J Stewart; Ali Navid; Kristen S Kulp; Jennifer L S Knaack; Graham Bench
Journal:  Yeast       Date:  2013-01-30       Impact factor: 3.239

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.  PathCase-SB: integrating data sources and providing tools for systems biology research.

Authors:  Sarp A Coskun; Xinjian Qi; Ali Cakmak; En Cheng; A Ercument Cicek; Lei Yang; Rishiraj Jadeja; Ranjan K Dash; Nicola Lai; Gultekin Ozsoyoglu; Zehra Meral Ozsoyoglu
Journal:  BMC Syst Biol       Date:  2012-06-14

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

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

9.  A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation.

Authors:  Mark T Mc Auley; Darren J Wilkinson; Janette J L Jones; Thomas B L Kirkwood
Journal:  BMC Syst Biol       Date:  2012-10-10

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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