System for Quality-Assured Data Analysis: Flexible, reproducible scientific workflows.
bioinformatics
cancer genomics
computer software
reproducibility
workflow
Journal
Genetic epidemiology
ISSN: 1098-2272
Titre abrégé: Genet Epidemiol
Pays: United States
ID NLM: 8411723
Informations de publication
Date de publication:
03 2019
03 2019
Historique:
received:
02
05
2018
revised:
12
07
2018
accepted:
28
07
2018
pubmed:
20
12
2018
medline:
2
4
2019
entrez:
20
12
2018
Statut:
ppublish
Résumé
The reproducibility of scientific processes is one of the paramount problems of bioinformatics, an engineering problem that must be addressed to perform good research. The System for Quality-Assured Data Analysis (SyQADA), described here, seeks to address reproducibility by managing many of the details of procedural bookkeeping in bioinformatics in as simple and transparent a manner as possible. SyQADA has been used by persons with backgrounds ranging from expert programmer to Unix novice, to perform and repeat dozens of diverse bioinformatics workflows on tens of thousands of samples, consuming over 80 CPU-months of computing on over 300,000 individual tasks of scores of projects on laptops, computer servers, and computing clusters. SyQADA is especially well-suited for paired-sample analyses found in cancer tumor-normal studies. SyQADA executable source code, documentation, tutorial examples, and workflows used in our lab is available from http://scheet.org/software.html.
Identifiants
pubmed: 30565316
doi: 10.1002/gepi.22178
pmc: PMC6571143
mid: NIHMS1013394
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
227-237Subventions
Organisme : NCI NIH HHS
ID : P30 CA016672
Pays : United States
Organisme : NCI NIH HHS
ID : P30CA016672
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG005859
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01HG005859
Pays : United States
Informations de copyright
© 2018 Wiley Periodicals, Inc.
Références
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
Curr Protoc Bioinformatics. 2008 Jun;Chapter 7:Unit 7.12
pubmed: 18551415
Nat Genet. 2008 Oct;40(10):1253-60
pubmed: 18776909
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Genome Biol. 2010;11(8):R86
pubmed: 20738864
Bioinformatics. 2010 Nov 1;26(21):2778-9
pubmed: 20847218
Genet Epidemiol. 2010 Dec;34(8):816-34
pubmed: 21058334
Bioinformatics. 2011 Sep 15;27(18):2601-2
pubmed: 21803805
BMC Genomics. 2011 Oct 14;12:507
pubmed: 21999641
Bioinformatics. 2012 Feb 1;28(3):421-2
pubmed: 22138362
Genome Res. 2012 Mar;22(3):568-76
pubmed: 22300766
Bioinformatics. 2012 Jun 1;28(11):1525-6
pubmed: 22500002
Nat Rev Genet. 2012 Sep;13(9):667-72
pubmed: 22898652
Genome Res. 2013 Jan;23(1):152-8
pubmed: 23028187
PLoS Comput Biol. 2012;8(9):e1002687
pubmed: 23028285
Nat Biotechnol. 2013 Mar;31(3):213-9
pubmed: 23396013
PLoS Comput Biol. 2013 Oct;9(10):e1003285
pubmed: 24204232
Bioinformatics. 2014 May 15;30(10):1471-2
pubmed: 24470576
PLoS Comput Biol. 2014 Aug 28;10(8):e1003765
pubmed: 25166618
Surgery. 2014 Dec;156(6):1351-7; discussion 1357-8
pubmed: 25456907
Bioinformatics. 2015 Jun 1;31(11):1724-8
pubmed: 25637560
Methods Mol Biol. 2016;1374:339-61
pubmed: 26519415
BMC Bioinformatics. 2016 Feb 01;17:53
pubmed: 26830846
Brief Bioinform. 2017 May 1;18(3):530-536
pubmed: 27013646
Cancer Res. 2016 Jul 1;76(13):3676-83
pubmed: 27216194
Cancer Prev Res (Phila). 2016 Jun;9(6):417-27
pubmed: 27221540
Bioinformatics. 2016 Oct 1;32(19):3015-7
pubmed: 27288500
Genome Biol. 2016 Dec 16;17(1):260
pubmed: 27986083
BMC Bioinformatics. 2018 Jan 04;19(1):5
pubmed: 29301485
PLoS One. 2018 Apr 25;13(4):e0194100
pubmed: 29694348