title: The challenges of delivering bioinformatics training in the analysis of high-throughput data.
abstract: High-throughput technologies are widely used in the field of functional genomics and used in an increasing number of applications. For many 'wet lab' scientists, the analysis of the large amount of data generated by such technologies is a major bottleneck that can only be overcome through very specialized training in advanced data analysis methodologies and the use of dedicated bioinformatics software tools. In this article, we wish to discuss the challenges related to delivering training in the analysis of high-throughput sequencing data and how we addressed these challenges in the hands-on training courses that we have developed at the European Bioinformatics Institute.
authors.affiliation: *Functional Genomics Group, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK. Tel.: +44-1223-492539; Fax: +44-1223-494468; gabry@ebi.ac.uk.
authors.forename: Benilton S
authors.initials: BS
authors.lastname: Carvalho
authors.forename: Gabriella
authors.initials: G
authors.lastname: Rustici
mesh_terms: D000047:Academies and Institutes; D019295:Computational Biology / Q000193:education*; D003479:Curriculum; D003627:Data Interpretation, Statistical; D005060:Europe; D005178:Faculty; D023281:Genomics / Q000706:statistics & numerical data*; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data*; D006801:Humans; D012984:Software; D013663:Teaching
keywords: bioinformatics training; high-throughput sequencing analysis; open-source software; practical courses; statistical methodologies
references.citation: Nat Methods. 2009 Nov;6(11 Suppl):S1
references.pmid: 19885970
references.citation: Genome Biol. 2010;11(10):R106
references.pmid: 20979621
references.citation: Nat Rev Genet. 2011 Feb;12(2):87-98
references.pmid: 21191423
references.citation: BMC Bioinformatics. 2010 Aug 10;11:422
references.pmid: 20698981
references.citation: Nat Methods. 2009 Nov;6(11 Suppl):S22-32
references.pmid: 19844228
references.citation: Genome Res. 2012 Oct;22(10):2008-17
references.pmid: 22722343
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D43-7
references.pmid: 22080548
references.citation: Database (Oxford). 2011 Nov 13;2011:bar049
references.pmid: 22083790
references.citation: BMC Bioinformatics. 2011 Dec 17;12:480
references.pmid: 22177264
references.citation: Curr Opin Cell Biol. 2012 Jun;24(3):323-32
references.pmid: 22465326
references.citation: Nature. 2012 Nov 1;491(7422):56-65
references.pmid: 23128226
references.citation: Trends Genet. 2008 Mar;24(3):142-9
references.pmid: 18262676
references.citation: Genome Res. 2011 Feb;21(2):193-202
references.pmid: 20921232
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: Genome Biol. 2011;12(2):R13
references.pmid: 21310039
references.citation: Nat Biotechnol. 2010 May;28(5):511-5
references.pmid: 20436464
references.citation: BMC Bioinformatics. 2010 Feb 18;11:94
references.pmid: 20167110
references.citation: Nature. 2012 Jan 04;481(7381):389-93
references.pmid: 22217937
references.citation: Proc Natl Acad Sci U S A. 2010 May 25;107(21):9546-51
references.pmid: 20460310
references.citation: Nat Rev Genet. 2010 Jan;11(1):31-46
references.pmid: 19997069
references.citation: Genome Res. 2012 Sep;22(9):1813-31
references.pmid: 22955991
references.citation: Nat Methods. 2009 Nov;6(11 Suppl):S2-5
references.pmid: 19844227
references.citation: Nucleic Acids Res. 2008 Sep;36(16):5221-31
references.pmid: 18684996
references.citation: Curr Opin Microbiol. 2009 Oct;12(5):536-46
references.pmid: 19758836
references.citation: Genome Biol. 2010;11(8):R86
references.pmid: 20738864
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: Bioinformatics. 2010 Jan 1;26(1):139-40
references.pmid: 19910308
references.citation: Nat Methods. 2009 Nov;6(11 Suppl):S6-S12
references.pmid: 19844229
references.citation: Bioinformatics. 2009 May 1;25(9):1105-11
references.pmid: 19289445
references.citation: Bioinformatics. 2009 Oct 1;25(19):2607-8
references.pmid: 19654119
references.citation: Genome Biol. 2004;5(10):R80
references.pmid: 15461798
references.citation: Stat Med. 1990 Jul;9(7):811-8
references.pmid: 2218183
references.citation: Genome Biol. 2008;9(9):R137
references.pmid: 18798982
references.citation: Bioinformatics. 2012 Apr 1;28(7):921-8
references.pmid: 22285831
references.citation: Biostatistics. 2012 Apr;13(2):204-16
references.pmid: 22285995
references.citation: PLoS One. 2010 Jul 08;5(7):e11471
references.pmid: 20628599
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D28-31
references.pmid: 20972220
references.citation: Nat Rev Genet. 2012 Jan 18;13(2):77-83
references.pmid: 22251872
references.citation: Brief Bioinform. 2013 Mar;14(2):178-92
references.pmid: 22517427
references.citation: Bioinformatics. 2012 Dec 15;28(24):3169-77
references.pmid: 23060614
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
references.pmid: 19458158