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Items 1 - 20 of 152
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1:

A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems.

Cook DL, Farley JF, Tapscott SJ.

Genome Biol. 2001;2(4):RESEARCH0012. Epub 2001 Mar 22.

PMID: 11305940 [PubMed - indexed for MEDLINE]

2:

Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases.

Srdanovic M, Schenk U, Schwieger M, Campagne F.

BMC Bioinformatics. 2005 Jan 10;6:5.

PMID: 15642112 [PubMed - indexed for MEDLINE]

3:

MILANO--custom annotation of microarray results using automatic literature searches.

Rubinstein R, Simon I.

BMC Bioinformatics. 2005 Jan 20;6:12.

PMID: 15661078 [PubMed - indexed for MEDLINE]

4:

MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

Cai JJ, Smith DK, Xia X, Yuen KY.

BMC Bioinformatics. 2005 Mar 22;6:64.

PMID: 15780146 [PubMed - indexed for MEDLINE]

5:

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 [PubMed - indexed for MEDLINE]

6:

Modeling biochemical transformation processes and information processing with Narrator.

Mandel JJ, Fuss H, Palfreyman NM, Dubitzky W.

BMC Bioinformatics. 2007 Mar 27;8:103.

PMID: 17389034 [PubMed - indexed for MEDLINE]

7:

BioDataServer: a SQL-based service for the online integration of life science data.

Freier A, Hofestädt R, Lange M, Scholz U, Stephanik A.

In Silico Biol. 2002;2(2):37-57.

PMID: 12066840 [PubMed - indexed for MEDLINE]

8:

Using the Unified Modelling Language (UML) to guide the systemic description of biological processes and systems.

Roux-Rouquié M, Caritey N, Gaubert L, Rosenthal-Sabroux C.

Biosystems. 2004 Jul;75(1-3):3-14.

PMID: 15245800 [PubMed - indexed for MEDLINE]

9:

Integration of the Gene Ontology into an object-oriented architecture.

Shegogue D, Zheng WJ.

BMC Bioinformatics. 2005 May 10;6:113.

PMID: 15885145 [PubMed - indexed for MEDLINE]

10:

UML as a cell and biochemistry modeling language.

Webb K, White T.

Biosystems. 2005 Jun;80(3):283-302. Epub 2005 Feb 17.

PMID: 15888343 [PubMed - indexed for MEDLINE]

11:

Design of a description language for generating wrapper to collect biological data.

Lim M, Chung M, Bae M, Park S.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii31-2.

PMID: 16204120 [PubMed - indexed for MEDLINE]

12:

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 [PubMed - indexed for MEDLINE]

13:

Computer support for physiological cell modelling using an ontology on cell physiology.

Takao S, Kazuhiro K, Akira A, Takeshi I, Masanori K, Tetsuya M.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:4171-4.

PMID: 17946607 [PubMed - indexed for MEDLINE]

14:

Atlas - a data warehouse for integrative bioinformatics.

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

BMC Bioinformatics. 2005 Feb 21;6:34.

PMID: 15723693 [PubMed - indexed for MEDLINE]

15:

BIOZON: a system for unification, management and analysis of heterogeneous biological data.

Birkland A, Yona G.

BMC Bioinformatics. 2006 Feb 15;7:70.

PMID: 16480510 [PubMed - indexed for MEDLINE]

16:

Simulating complex intracellular processes using object-oriented computational modelling.

Johnson CG, Goldman JP, Gullick WJ.

Prog Biophys Mol Biol. 2004 Nov;86(3):379-406. Review.

PMID: 15302205 [PubMed - indexed for MEDLINE]

17:

BioLingua: a programmable knowledge environment for biologists.

Massar JP, Travers M, Elhai J, Shrager J.

Bioinformatics. 2005 Jan 15;21(2):199-207. Epub 2004 Aug 12.

PMID: 15308539 [PubMed - indexed for MEDLINE]

18:

Efficient decoding algorithms for generalized hidden Markov model gene finders.

Majoros WH, Pertea M, Delcher AL, Salzberg SL.

BMC Bioinformatics. 2005 Jan 24;6:16.

PMID: 15667658 [PubMed - indexed for MEDLINE]

19:

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 [PubMed - indexed for MEDLINE]

20:

JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases.

Feng G, Burton N, Hill B, Davidson D, Kerwin J, Scott M, Lindsay S, Baldock R.

BMC Bioinformatics. 2005 Mar 9;6:47.

PMID: 15757508 [PubMed - indexed for MEDLINE]

Items 1 - 20 of 152
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