Facile: A command-line network compiler for systems biology

BMC Systems Biology

Volumn 1, Issue , 2007, Pages

  Swain, Peter S ^a,b   Siso Nadal, Fernando ^b   Ollivier, Julien F ^b  

^a Gene Network Sciences Inc   (United States)

^b MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACER;

ARTICLE; BIOLOGICAL MODEL; COMPUTER; COMPUTER PROGRAM; COMPUTER SIMULATION; COMPUTER SYSTEM; INSTRUMENTATION; METABOLISM; METHODOLOGY; NONLINEAR SYSTEM; SYSTEMS BIOLOGY;

COMPUTER SIMULATION; COMPUTER SYSTEMS; COMPUTERS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; NONLINEAR DYNAMICS; SOFTWARE; SYSTEMS BIOLOGY;

EID: 34548706471     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-1-36     Document Type: Article

References (24)

1. The Systems Biology Markup Language http://sbml.org
2. Alves R Antunes F Salvador A Tools for kinetic modeling of biochemical networks Nat Biotechnol 2006, 24:667-672. 10.1038/nbt0606-667 16763599
3. Loew LM The Virtual Cell project Novartis Found Symp 2002, 247:151-160. 12539954
4. Shapiro BE Levchenko A Meyerowitz EM Wold BJ Mjolsness ED Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations Bioinformatics 2003, 19:677-678. 10.1093/ bioinformatics/btg042 12651737
5. Dhar P Meng TC Somani S Ye L Sairam A Chitre M Hao Z Sakharkar K Cellware-a multi-algorithmic software for computational systems biology Bioinformatics 2004, 20:1319-1321. 10.1093/bioinformatics/bth067 14871872
6. Ramsey S Orrell D Bolouri H Dizzy: Stochastic simulation of large-scale genetic regulatory networks J Bioinform Comput Biol 2005, 3:415-436. 10.1142/S0219720005001132 15852513
7. Hoops S Sahle S Gauges R Lee C Pahle J Simus N Singhal M Xu L Mendes P Kummer U COPASI-a COmplex PAthway SImulator Bioinformatics 2006, 22:3067-3074. 10.1093/bioinformatics/btl485 17032683
8. AUTO: Software for continuation and bifurcation problems in ordinary differential equations http://indy.cs.concordia.ca/auto
9. XPPAUT http://www.math.pitt.edu/∼bard/xpp/xpp.html
10. Cell Designer http://www.systems-biology.org/cd
11. JDesigner http://jdesigner.org
12. Rodriguez N Donizelli M Le Novere N SBMLeditor: Effective creation of models in the Systems Biology Markup language BMC Bioinformatics 2007, 8:7-79. 1780060 17212828 10.1186/1471-2105-8-79
13. Shapiro BE Hucka M Finney A Doyle J MathSBML: A package for manipulating SBML-based biological models Bioinformatics 2004, 20:2829-2831. 1409765 15087311 10.1093/bioinformatics/bth271
14. Keating SM Bornstein BJ Finney A Hucka M SBMLToolbox: An SBML toolbox for MATLAB users Bioinformatics 2006, 22:1275-1277. 10.1093/ bioinformatics/btl111 16574696
15. Vass M Allen N Shaffer CA Ramakrishnan N Watson LT Tyson JJ The JigCell model builder and run manager Bioinformatics 2004, 20:3680-3681. 10.1093/ bioinformatics/bth422 15273159
16. Oscill8 Dynamical Systems Toolset http://oscill8.sourceforge.net
17. Sauro HM Ingalls B Conservation analysis in biochemical networks: computational issues for software writers Biophys Chem 2004, 109:1-15. 10.1016/j.bpc.2003.08.009 15059656
18. Octave http://www.octave.org
19. Kaern M Elston TC Blake WJ Collins JJ Stochasticity in gene expression: from theories to phenotypes Nat Rev Genet 2005, 6:451-464. 10.1038/ nrg1615 15883588
20. Gibson MA Bruck J Efficient exact stochastic simulation of chemical systems with many species and many channels J Phys Chem A 2000, 104:1876-1889. 10.1021/jp993732q
21. Gillespie D Exact stochastic simulation of coupled chemical-reactions J Phys Chem 1977, 81:2340-2361. 10.1021/j100540a008
22. Kitano H Biological robustness Nat Rev Genet 2004, 5:826-837. 10.1038/ nrg1471 15520792
23. Lok L Brent R Automatic generation of cellular reaction networks with Moleculizer 1.0 Nat Biotechnol 2005, 23:131-136. 10.1038/nbt1054 15637632
24. Comprehensive Perl Archive Network http://www.cpan.org