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Items: 1 to 20 of 63

1.

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.

2.

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.

3.

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.

PMID:
12075668
4.

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.

5.

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.

PMID:
17392333
6.

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.

7.

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.

8.

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.

PMID:
18056069
9.

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
10.

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.

PMID:
22177662
11.

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.

PMID:
25504849
12.

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.

13.

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

Moskovitch R, Shahar Y.

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

PMID:
15537214
14.

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.

15.

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.

PMID:
16527832
16.

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.

PMID:
18174185
17.

Designing and executing scientific workflows with a programmable integrator.

Chagoyen M, Kurul ME, De-Alarcón PA, Carazo JM, Gupta A.

Bioinformatics. 2004 Sep 1;20(13):2092-100. Epub 2004 Apr 1.

PMID:
15059834
18.

PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees.

Fuchsberger C, Falchi M, Forer L, Pramstaller PP.

Bioinformatics. 2008 Jan 15;24(2):279-81. Epub 2007 Nov 22.

PMID:
18033791
19.

Query Chem: a Google-powered web search combining text and chemical structures.

Klekota J, Roth FP, Schreiber SL.

Bioinformatics. 2006 Jul 1;22(13):1670-3. Epub 2006 May 3.

PMID:
16672261
20.

TO-GO: a Java-based Gene Ontology navigation environment.

Yu U, Choi YJ, Choi JK, Kim S.

Bioinformatics. 2005 Sep 1;21(17):3580-1. Epub 2005 Jun 30.

PMID:
15994194

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