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Items: 1 to 20 of 113

1.

Path2Models: large-scale generation of computational models from biochemical pathway maps.

Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.

BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.

2.

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.

Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C.

BMC Syst Biol. 2010 Jun 29;4:92. doi: 10.1186/1752-0509-4-92.

3.

Integration of CellDesigner and SABIO-RK.

Funahashi A, Jouraku A, Matsuoka Y, Kitano H.

In Silico Biol. 2007;7(2 Suppl):S81-90.

PMID:
17822394
4.
5.

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.

Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A.

BMC Syst Biol. 2015 Oct 9;9:68. doi: 10.1186/s12918-015-0212-9.

6.

Editing, validating and translating of SBGN maps.

Czauderna T, Klukas C, Schreiber F.

Bioinformatics. 2010 Sep 15;26(18):2340-1. doi: 10.1093/bioinformatics/btq407. Epub 2010 Jul 13.

7.

An online model composition tool for system biology models.

Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G.

BMC Syst Biol. 2013 Sep 5;7:88. doi: 10.1186/1752-0509-7-88.

8.

Computational modeling of biochemical networks using COPASI.

Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U.

Methods Mol Biol. 2009;500:17-59. doi: 10.1007/978-1-59745-525-1_2.

PMID:
19399433
9.

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.

Schellenberger J, Park JO, Conrad TM, Palsson BØ.

BMC Bioinformatics. 2010 Apr 29;11:213. doi: 10.1186/1471-2105-11-213.

10.

SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks.

Dräger A, Hassis N, Supper J, Schröder A, Zell A.

BMC Syst Biol. 2008 Apr 30;2:39. doi: 10.1186/1752-0509-2-39.

11.

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database.

Moutselos K, Kanaris I, Chatziioannou A, Maglogiannis I, Kolisis FN.

BMC Bioinformatics. 2009 Oct 8;10:324. doi: 10.1186/1471-2105-10-324.

12.

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems.

Costa RS, Veríssimo A, Vinga S.

BMC Syst Biol. 2014 Aug 13;8:85. doi: 10.1186/s12918-014-0085-3.

13.

Conversion of KEGG metabolic pathways to SBGN maps including automatic layout.

Czauderna T, Wybrow M, Marriott K, Schreiber F.

BMC Bioinformatics. 2013 Aug 16;14:250. doi: 10.1186/1471-2105-14-250.

14.

The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks.

Swainston N, Smallbone K, Mendes P, Kell D, Paton N.

J Integr Bioinform. 2011 Nov 18;8(2):186. doi: 10.2390/biecoll-jib-2011-186.

PMID:
22095399
15.

Systematic integration of experimental data and models in systems biology.

Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW.

BMC Bioinformatics. 2010 Nov 29;11:582. doi: 10.1186/1471-2105-11-582.

16.

A graphical method for reducing and relating models in systems biology.

Gay S, Soliman S, Fages F.

Bioinformatics. 2010 Sep 15;26(18):i575-81. doi: 10.1093/bioinformatics/btq388.

17.

GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.

Liao YC, Tsai MH, Chen FC, Hsiung CA.

Bioinformatics. 2012 Jul 1;28(13):1752-8. doi: 10.1093/bioinformatics/bts267. Epub 2012 May 4.

PMID:
22563070
18.

An application programming interface for CellNetAnalyzer.

Klamt S, von Kamp A.

Biosystems. 2011 Aug;105(2):162-8. doi: 10.1016/j.biosystems.2011.02.002. Epub 2011 Feb 21.

PMID:
21315797
19.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD.

Nucleic Acids Res. 2012 Jan;40(Database issue):D742-53. doi: 10.1093/nar/gkr1014. Epub 2011 Nov 18.

20.

PROMOT: modular modeling for systems biology.

Mirschel S, Steinmetz K, Rempel M, Ginkel M, Gilles ED.

Bioinformatics. 2009 Mar 1;25(5):687-9. doi: 10.1093/bioinformatics/btp029. Epub 2009 Jan 15.

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