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Items: 1 to 20 of 106

1.

SBRML: a markup language for associating systems biology data with models.

Dada JO, Spasić I, Paton NW, Mendes P.

Bioinformatics. 2010 Apr 1;26(7):932-8. doi: 10.1093/bioinformatics/btq069. Epub 2010 Feb 21.

PMID:
20176582
2.

FuGEFlow: data model and markup language for flow cytometry.

Qian Y, Tchuvatkina O, Spidlen J, Wilkinson P, Gasparetto M, Jones AR, Manion FJ, Scheuermann RH, Sekaly RP, Brinkman RR.

BMC Bioinformatics. 2009 Jun 16;10:184. doi: 10.1186/1471-2105-10-184.

3.

GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models.

Bois FY.

Bioinformatics. 2009 Jun 1;25(11):1453-4. doi: 10.1093/bioinformatics/btp162. Epub 2009 Mar 20.

4.

Managing experimental data using FuGE.

Jones AR, Lister AL.

Methods Mol Biol. 2010;604:333-43. doi: 10.1007/978-1-60761-444-9_23.

PMID:
20013382
5.

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

Kyoda K, Tohsato Y, Ho KH, Onami S.

Bioinformatics. 2015 Apr 1;31(7):1044-52. doi: 10.1093/bioinformatics/btu767. Epub 2014 Nov 19.

6.

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

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum.

Bioinformatics. 2003 Mar 1;19(4):524-31.

PMID:
12611808
7.

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.

Zi Z.

Bioinformatics. 2011 Apr 1;27(7):1028-9. doi: 10.1093/bioinformatics/btr038. Epub 2011 Feb 8.

PMID:
21303862
8.

SBMLToolbox: an SBML toolbox for MATLAB users.

Keating SM, Bornstein BJ, Finney A, Hucka M.

Bioinformatics. 2006 May 15;22(10):1275-7. Epub 2006 Mar 30.

PMID:
16574696
9.

Stochastic simulation GUI for biochemical networks.

Vallabhajosyula RR, Sauro HM.

Bioinformatics. 2007 Jul 15;23(14):1859-61. Epub 2007 Jun 22.

PMID:
17586553
10.

Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager.

Shah AR, Singhal M, Klicker KR, Stephan EG, Wiley HS, Waters KM.

Bioinformatics. 2007 Apr 1;23(7):906-9. Epub 2007 Feb 25.

PMID:
17324940
11.

An object model and database for functional genomics.

Jones A, Hunt E, Wastling JM, Pizarro A, Stoeckert CJ Jr.

Bioinformatics. 2004 Jul 10;20(10):1583-90. Epub 2004 May 14.

PMID:
15145818
12.

SED-ED, a workflow editor for computational biology experiments written in SED-ML.

Adams RR.

Bioinformatics. 2012 Apr 15;28(8):1180-1. doi: 10.1093/bioinformatics/bts101. Epub 2012 Feb 25.

PMID:
22368254
13.

Annotation and merging of SBML models with semanticSBML.

Krause F, Uhlendorf J, Lubitz T, Schulz M, Klipp E, Liebermeister W.

Bioinformatics. 2010 Feb 1;26(3):421-2. doi: 10.1093/bioinformatics/btp642. Epub 2009 Nov 17.

PMID:
19933161
14.

Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.

Schmidt H, Jirstrand M.

Bioinformatics. 2006 Feb 15;22(4):514-5. Epub 2005 Nov 29.

PMID:
16317076
15.

Payao: a community platform for SBML pathway model curation.

Matsuoka Y, Ghosh S, Kikuchi N, Kitano H.

Bioinformatics. 2010 May 15;26(10):1381-3. doi: 10.1093/bioinformatics/btq143. Epub 2010 Apr 5.

16.

SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.

Zi Z, Klipp E.

Bioinformatics. 2006 Nov 1;22(21):2704-5. Epub 2006 Aug 22.

PMID:
16926221
17.

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.

Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.

Nat Biotechnol. 2007 Oct;25(10):1127-33.

PMID:
17921998
18.

Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays.

Watanabe L, Myers CJ.

ACS Synth Biol. 2016 Aug 19;5(8):835-41. doi: 10.1021/acssynbio.5b00242. Epub 2016 Mar 8.

PMID:
26912276
19.

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

Hucka M, Finney A, Bornstein BJ, Keating SM, Shapiro BE, Matthews J, Kovitz BL, Schilstra MJ, Funahashi A, Doyle JC, Kitano H.

Syst Biol (Stevenage). 2004 Jun;1(1):41-53. Review.

PMID:
17052114
20.

MOCCASIN: converting MATLAB ODE models to SBML.

Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC.

Bioinformatics. 2016 Jun 15;32(12):1905-6. doi: 10.1093/bioinformatics/btw056. Epub 2016 Feb 9.

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