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Items: 1 to 20 of 86


LibKiSAO: a Java library for Querying KiSAO.

Zhukova A, Adams R, Laibe C, Le Novère N.

BMC Res Notes. 2012 Sep 24;5:520. doi: 10.1186/1756-0500-5-520.


Controlled vocabularies and semantics in systems biology.

Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N.

Mol Syst Biol. 2011 Oct 25;7:543. doi: 10.1038/msb.2011.77.


A semantic proteomics dashboard (SemPoD) for data management in translational research.

Jayapandian CP, Zhao M, Ewing RM, Zhang GQ, Sahoo SS.

BMC Syst Biol. 2012;6 Suppl 3:S20. doi: 10.1186/1752-0509-6-S3-S20. Epub 2012 Dec 17.


Building a bioinformatics ontology using OIL.

Stevens R, Goble C, Horrocks I, Bechhofer S.

IEEE Trans Inf Technol Biomed. 2002 Jun;6(2):135-41.


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.


FERN - a Java framework for stochastic simulation and evaluation of reaction networks.

Erhard F, Friedel CC, Zimmer R.

BMC Bioinformatics. 2008 Aug 29;9:356. doi: 10.1186/1471-2105-9-356.


Cyclone: java-based querying and computing with Pathway/Genome databases.

Le Fèvre F, Smidtas S, Schächter V.

Bioinformatics. 2007 May 15;23(10):1299-300. Epub 2007 Mar 28.


A comparison of common programming languages used in bioinformatics.

Fourment M, Gillings MR.

BMC Bioinformatics. 2008 Feb 5;9:82. doi: 10.1186/1471-2105-9-82.


XML schemas for common bioinformatic data types and their application in workflow systems.

Seibel PN, Krüger J, Hartmeier S, Schwarzer K, Löwenthal K, Mersch H, Dandekar T, Giegerich R.

BMC Bioinformatics. 2006 Nov 6;7:490.


Automated manipulation of systems biology models using libSBML within Taverna workflows.

Li P, Oinn T, Soiland S, Kell DB.

Bioinformatics. 2008 Jan 15;24(2):287-9. Epub 2007 Dec 1.


ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

Huan T, Sivachenko AY, Harrison SH, Chen JY.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S5. doi: 10.1186/1471-2105-9-S9-S5.


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.


Visually defining and querying consistent multi-granular clinical temporal abstractions.

Combi C, Oliboni B.

Artif Intell Med. 2012 Feb;54(2):75-101. doi: 10.1016/j.artmed.2011.10.004. Epub 2011 Dec 15.


MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.

Marchetti L, Manca V.

Bioinformatics. 2015 Apr 15;31(8):1328-30. doi: 10.1093/bioinformatics/btu814. Epub 2014 Dec 10.


OptFlux: an open-source software platform for in silico metabolic engineering.

Rocha I, Maia P, Evangelista P, Vilaça P, Soares S, Pinto JP, Nielsen J, Patil KR, Ferreira EC, Rocha M.

BMC Syst Biol. 2010 Apr 19;4:45. doi: 10.1186/1752-0509-4-45.


A multiple-ontology customizable search interface for retrieval of clinical guidelines.

Moskovitch R, Shahar Y.

Stud Health Technol Inform. 2004;101:127-31.


The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications.

Moreland JL, Gramada A, Buzko OV, Zhang Q, Bourne PE.

BMC Bioinformatics. 2005 Feb 6;6:21.


The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.

Machné R, Finney A, Müller S, Lu J, Widder S, Flamm C.

Bioinformatics. 2006 Jun 1;22(11):1406-7. Epub 2006 Mar 9.


Automated programming for bioinformatics algorithm deployment.

Alterovitz G, Jiwaji A, Ramoni MF.

Bioinformatics. 2008 Feb 1;24(3):450-1. doi: 10.1093/bioinformatics/btm602. Epub 2008 Jan 3.


An ontology-based comparative anatomy information system.

Travillian RS, Diatchka K, Judge TK, Wilamowska K, Shapiro LG.

Artif Intell Med. 2011 Jan;51(1):1-15. doi: 10.1016/j.artmed.2010.10.001. Epub 2010 Dec 10.

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