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Bioinformatics 15: Advanced Bioinformatics workshop for early career researchers, 9-13th November, 2015.

This Workshop is now sold out!

If you wish to be on our waiting list, please contact us here.

The Australian Centre for Ancient DNA (ACAD) is pleased to present its 6th ECR workshop, which will be based on the successful Bioinformatics 2014, 2013 and 2012 workshops.  This program is an intensive 5 day hands-on training course tutored by international experts, utilising the latest available software for the analysis of Next Generation Sequencing (NGS), Genomics and Metagenomics data.  This workshop is generously sponsored by the Bioinformatics Hub.

The course combines seminars and extensive hands-on practicals involving the analysis of a range of model and empirical datasets, focusing on current approaches in field-leading groups.  There will also be a limited opportunity to work on your own dataset with the tutors.  Early registration is essential as seating is limited to 40 places with very strong demand.

Pre-requisites: Delegates must be familiar with UNIX environments and basic command lines, and will require a basic knowledge of the technology and analytical tools of NGS. As a guide, you should know how to write a loop in BASH. Material will be pitched at an intermidate-advanced level.

Registration

Download Rego form.

Venue: University of Adelaide
North Terrace Campus

For enquiries please email or Ph 8 8313 3952

  • Remco Bouckaert

    Remco Bouckaert is affiliated with the University of Auckland and Waikato, and the Max Planck Institute for the Science of Human History. 

    He is one of the main developers of BEAST 2, SNAPP and DensiTree and his interests are in Bayesian analysis of genetic and linguistic data through phylogenemic methods.
  • Martin Kircher

    Martin is a Computational Molecular Biologist by training, and has a broad interest in genomics, epigenetics and evolution as well as the development of sequencing protocols, technolgoies and bioinformatics approaches to advance capabilities in these fields. Martin is currently developing methods for the functional scoring of variants (CADD) and to functionally assess regulartory variants using massively parallel regulatory assays (MPIRA), at the University of Washington, US.

  • Rob Knight

    Rob Knight is a Professor at the Biomedical Sciences Graduate Program at the University of California. Rob heads a lab that investigates techniques that seeks to understand the evolution of the composition of biomolecules, genomes, and communities, specialising in microbes.

  • Paul Stothard

    Paul and his team specialise in analysis and interpretation of huge DNA sequence and genotype data sets, for the purpose of undertanding the genetic underpinnings of important phenotypes. His group has developed advanced software tools for analysing whole-genome sequences and NGS data, and has used these tools to characterise several important microbial and mammalian genomes.

  • Amanda Birmingham

    Amanda is currently a senior software engineer at the University of California, San Diego, with over 10 years technical management experience. She specialises in bioinformatics (the synthesis of biological information using computers and statistical methods), with a focus on the development of microbiome analysis tools and interpretation of high-throughput screening data.

Draft program

Monday 9
Martin Kircher
Tuesday 10
Paul Stothard
Wednesday 11
Remco Bouckaert
Thursday 12
Rob Knight
Friday 13
Amanada Birmingham

9:15-10:00am Welcome, introductions and PC set ups. Venue: Braggs Foyer, see map

~10:00 Venue: Mawson Lecture Theater/computer suite

Introduction to NGS technologies and data pre-processing - Long read and single molecule sequencing, and pipelines & tools.

Hands-on session to include sequences to alignments, alignments to coverage, and variant annotation and functional effects.

~915am Venue: Mawson Lecture Theater/computer suite

Variant discovery, RNA-seq.data set analysis, focusing on comparing gene expression levels and splicing between 2 groups of individuals.

 

Hands on session using Python, FAST, Bowtie, Tophat, R etc.

~915am Venue: Mawson Lecture Theater/computer suite

Phylogenetic algorithms using genomic SNP data.

Multi-species coalescent; SNAPP

Afternnon tutorial on BEAST and species delimitation with SNAPP

~915am Venue: Mawson Lecture Theater/computer suite

Metagenomics

Lecture introducing microbial ecology

Hands on session using the new Qiita database examining existing microbiome studies.

 

~915am Venue: Mawson Lecture Theater/computer suite

Morning lecture on QIIME, statistical testing, preparing manuscript-ready figures, etc. Includes a demonstration on these functionalities.

A couple of hours set aside to work on own datasets with some of the tutors on hand.

Expected finish time 3pm.

Workshop times: 9:15am - ~4:45pm with morning, lunch and afternoon breaks
Evening lectures 5pm-6pm held in the Mawson Lecture Theatre
Paul Stothard: Using sequencing and bioinformatics to link genotype and phenotype. Remco Bouckaert: The origin of Indo-European languages: an evolutionary approach. Rob Knight: How the genes in our microbiome out number our human genes, and can cause or cure disease. Martin Kircher: Tracing cell death throughout the body from cell-free DNA in the blood. -

 

Registration: Early bird rate closes 25th September, 2015. Non early bird rate, closing date 23rd October. No single day registration available. Cancellations after closing date may not guarantee a full refund. CANCELLATIONS 1-3 DAYS PRIOR TO THE START OF WORKSHOP DATE WILL NOT BE REFUNDED.

Adelaide

Venue Hands on session and lectures are in the Mawson Building, Computer Suite ground floor G12, and Mawson Lecture Theatre, ground floor G19 map here.

Adelaide

Accommodation The following is a list of accommodation venues we normaly use for their close proximity to the University and affordability:

Adelaide
  1. Adelaide Riviera Hotel, North Terrace, City. Standard room is around AUD $125.00 and approx 10mins walk to the University. Contact phone +61 8231 8000 or Toll free in Australia only # 1800 061 300.
  2. The Vines or Grand Apartments in North Adelaide City. Standard rooms range from AUD $99-$120. approx 10mins walk to the University. Contact phone Toll free in Australia only #1300 668 400.
  3. The Oaks Embassy 96 North Terrace, Adelaide. 1 bedroom apartment from AUD $135.00.
  4. Try the site Backpacker and Youth/Student Hostels in Adelaide where a listing of local backpackers is provided.
  5. Another site for students who are willing to share accommodation - check EasyRoommate or Adelaide Backpackers.
Australian Centre for Ancient DNA
School of Biological Sciences
Darling Building
North Terrace Campus

The University of Adelaide
South Australia 5005
Australia

Contact

T: +61 8 8313 3952
F: +61 8 8313 4364
Web administrator email