title: Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia.
abstract: The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show-style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.
authors.affiliation: The Australian Centre for Plant Functional Genomics, University of Adelaide, SA 5064, Australia. nathan.haigh@acpfg.com.au.
authors.forename: Nathan S
authors.initials: NS
authors.lastname: Watson-Haigh
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Shang
authors.forename: Matthias
authors.initials: M
authors.lastname: Haimel
authors.forename: Myrto
authors.initials: M
authors.lastname: Kostadima
authors.forename: Remco
authors.initials: R
authors.lastname: Loos
authors.forename: Nandan
authors.initials: N
authors.lastname: Deshpande
authors.forename: Konsta
authors.initials: K
authors.lastname: Duesing
authors.forename: Xi
authors.initials: X
authors.lastname: Li
authors.forename: Annette
authors.initials: A
authors.lastname: McGrath
authors.forename: Sean
authors.initials: S
authors.lastname: McWilliam
authors.forename: Simon
authors.initials: S
authors.lastname: Michnowicz
authors.forename: Paula
authors.initials: P
authors.lastname: Moolhuijzen
authors.forename: Steve
authors.initials: S
authors.lastname: Quenette
authors.forename: Jerico Nico De Leon
authors.initials: JN
authors.lastname: Revote
authors.forename: Sonika
authors.initials: S
authors.lastname: Tyagi
authors.forename: Maria V
authors.initials: MV
authors.lastname: Schneider
mesh_terms: D001315:Australia; D019295:Computational Biology / Q000193:education*; D003194:Computer-Assisted Instruction / Q000379:methods; D003299:Cooperative Behavior; D003479:Curriculum; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data*; D013663:Teaching
keywords: NGS; cloud; next-generation sequencing; training; workshop
references.citation: BMC Bioinformatics. 2012 Mar 19;13:42
references.pmid: 22429538
references.citation: Source Code Biol Med. 2012 Feb 15;7(1):1
references.pmid: 22333270
references.citation: Brief Bioinform. 2012 May;13(3):383-9
references.pmid: 22110242
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W729-32
references.pmid: 16845108
references.citation: Genome Res. 2005 Oct;15(10):1451-5
references.pmid: 16169926
references.citation: PLoS Comput Biol. 2011 Oct;7(10):e1002245
references.pmid: 22046119