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Results: 1 to 20 of 96

1.

Nestly--a framework for running software with nested parameter choices and aggregating results.

McCoy CO, Gallagher A, Hoffman NG, Matsen FA.

Bioinformatics. 2013 Feb 1;29(3):387-8. doi: 10.1093/bioinformatics/bts696. Epub 2012 Dec 6.

PMID:
23220574
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

A graph-based approach for designing extensible pipelines.

Rodrigues MR, Magalhães WC, Machado M, Tarazona-Santos E.

BMC Bioinformatics. 2012 Jul 12;13:163. doi: 10.1186/1471-2105-13-163.

PMID:
22788675
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology.

Adams R, Clark A, Yamaguchi A, Hanlon N, Tsorman N, Ali S, Lebedeva G, Goltsov A, Sorokin A, Akman OE, Troein C, Millar AJ, Goryanin I, Gilmore S.

Bioinformatics. 2013 Mar 1;29(5):664-5. doi: 10.1093/bioinformatics/btt023. Epub 2013 Jan 17.

PMID:
23329415
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

FSelector: a Ruby gem for feature selection.

Cheng T, Wang Y, Bryant SH.

Bioinformatics. 2012 Nov 1;28(21):2851-2. doi: 10.1093/bioinformatics/bts528. Epub 2012 Aug 31.

PMID:
22942017
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

pymzML--Python module for high-throughput bioinformatics on mass spectrometry data.

Bald T, Barth J, Niehues A, Specht M, Hippler M, Fufezan C.

Bioinformatics. 2012 Apr 1;28(7):1052-3. doi: 10.1093/bioinformatics/bts066. Epub 2012 Feb 2.

PMID:
22302572
[PubMed - indexed for MEDLINE]
Free Article
6.

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations.

Dale RK, Pedersen BS, Quinlan AR.

Bioinformatics. 2011 Dec 15;27(24):3423-4. doi: 10.1093/bioinformatics/btr539. Epub 2011 Sep 23.

PMID:
21949271
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Mobyle: a new full web bioinformatics framework.

Néron B, Ménager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C.

Bioinformatics. 2009 Nov 15;25(22):3005-11. doi: 10.1093/bioinformatics/btp493. Epub 2009 Aug 17.

PMID:
19689959
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines.

Cieślik M, Mura C.

BMC Bioinformatics. 2011 Feb 25;12:61. doi: 10.1186/1471-2105-12-61.

PMID:
21352538
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.

Chaudhury S, Lyskov S, Gray JJ.

Bioinformatics. 2010 Mar 1;26(5):689-91. doi: 10.1093/bioinformatics/btq007. Epub 2010 Jan 7.

PMID:
20061306
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Python as a federation tool for GENESIS 3.0.

Cornelis H, Rodriguez AL, Coop AD, Bower JM.

PLoS One. 2012;7(1):e29018. doi: 10.1371/journal.pone.0029018. Epub 2012 Jan 20.

PMID:
22276101
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

StochHMM: a flexible hidden Markov model tool and C++ library.

Lott PC, Korf I.

Bioinformatics. 2014 Jun 1;30(11):1625-6. doi: 10.1093/bioinformatics/btu057. Epub 2014 Jan 30.

PMID:
24489371
[PubMed - indexed for MEDLINE]
12.

HeFPipe: a complete analytical pipeline for heterozygosity-fitness correlation studies.

Fisher MA.

Mol Ecol Resour. 2014 Jan;14(1):215-7. doi: 10.1111/1755-0998.12160. Epub 2013 Sep 6.

PMID:
24034598
[PubMed - indexed for MEDLINE]
13.

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.

Jossinet F, Ludwig TE, Westhof E.

Bioinformatics. 2010 Aug 15;26(16):2057-9. doi: 10.1093/bioinformatics/btq321. Epub 2010 Jun 18.

PMID:
20562414
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform.

Eckels J, Nathe C, Nelson EK, Shoemaker SG, Nostrand EV, Yates NL, Ashley VC, Harris LJ, Bollenbeck M, Fong Y, Tomaras GD, Piehler B.

BMC Bioinformatics. 2013 Apr 30;14:145. doi: 10.1186/1471-2105-14-145.

PMID:
23631706
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

NGS++: a library for rapid prototyping of epigenomics software tools.

Nordell Markovits A, Joly Beauparlant C, Toupin D, Wang S, Droit A, Gevry N.

Bioinformatics. 2013 Aug 1;29(15):1893-4. doi: 10.1093/bioinformatics/btt312. Epub 2013 Jun 4.

PMID:
23736531
[PubMed - indexed for MEDLINE]
Free Article
16.

Utility library for structural bioinformatics.

Gront D, Kolinski A.

Bioinformatics. 2008 Feb 15;24(4):584-5. doi: 10.1093/bioinformatics/btm627. Epub 2008 Jan 28.

PMID:
18227118
[PubMed - indexed for MEDLINE]
Free Article
17.

p3d--Python module for structural bioinformatics.

Fufezan C, Specht M.

BMC Bioinformatics. 2009 Aug 21;10:258. doi: 10.1186/1471-2105-10-258.

PMID:
19698094
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ.

Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20.

PMID:
19304878
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

OpenStructure: a flexible software framework for computational structural biology.

Biasini M, Mariani V, Haas J, Scheuber S, Schenk AD, Schwede T, Philippsen A.

Bioinformatics. 2010 Oct 15;26(20):2626-8. doi: 10.1093/bioinformatics/btq481. Epub 2010 Aug 23.

PMID:
20733063
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Bioclipse: an open source workbench for chemo- and bioinformatics.

Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JE.

BMC Bioinformatics. 2007 Feb 22;8:59.

PMID:
17316423
[PubMed - indexed for MEDLINE]
Free PMC Article

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