ACAD Bioinformatics Early Career Researcher Workshop, 5th - 9th November, 2012
The University of Adelaide, North Terrace Campus

Organising Committee

Members of the Australian Centre for Ancient DNA, School of Earth & Environmental Sciences:
Professor Alan Cooper
Dr Bastien Llamas
Dr Julien Soubrier
Ms Maria Lekis.

Acknowledgement goes to Dr Stephen Bent and Dr Nathan Watson-Haigh for their invaluable IT assistance.

Presenters

Stephen Bent

Stephen received his PhD in Bioinformatics and Computational Biology from the University of Idaho, working on problems in microbial ecology. Research on pathogen population genetics in tick-borne disease followed at the Yale School of Public Health, and since arriving in Adelaide, he has been working with prokaryotic and eukaryotic second-generation sequencing data sets and performing transcriptome, genome, and metagenome analyses. Stephen's principal intersts lie in facilitating "aha!" moments and understanding microbial population patterns and processes.

Ludovic Orlando

Ludovic is leading a research group at the Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, where his group is developing integrative approaches in ancient DNA research, promoting the field of palaeomics by merging together biochemsitry, molecular biology, genomics and computational biology. These novel approaches have recently specifically been used to study the evolutionary history of one iconic mammal: the horse.

Martin Kircher

Martin's training was in Computational Molecular Biology and entered the field of ancient DNA at a time where high-throughput sequencing completely transformed Svante Pääbo's department at the Max Planck Institute for Evolutionary Anthropology. He developed a base caller for the Illumina/Solexa systems, implemented the analysis pipelines that underlie the Neandertal and Denisova genomes and analyzed NGS data for comparative gene expression studies. Currently, Martin is currently at the University of Washington with Jay Shendure's group.

Laura Wegener Parfrey

Laura did her PhD at the University of Massachusetts and focused on resolving the eukaryotic tree of life by incorporating diverse microbial lineages into phylogenetic analyses. Laura is currently a Postdoc at the University of Colorado where is is using her experitse in eukaryotes to incorporate them into Qimme, where she has used this software extensively for analyses of microbial communities using 16S and 18S marker genes.

Bob Schnabel

A geneticist by training, Bob Schnabel has increasingly moved into a bioinformatics role to support the large amount of data being generated by SNP chips and NGS. Bob was a member of the consortia that developed the Illumina BovineSNP50, BovineHD and Affymetrix BOS-1 genotyping arrays. He was also a leader for the QA/QC group for the Bovine HapMap Consortium."

Program

	Mon 5th Nov	Tue 6th Nov	Wed 7th Nov	Thu 8th Nov	Fri 9th Nov
Includes morning tea break, lecture and hands on sessons	Welcome, Introductions and set up of PC logons. Stephen Bent: Referesher on command lines and UNIX Environment (grep, awk, other shell one-liners and pipelines). Includes outlines on public databases (UCSC, ENSEMBL)	Martin Kircher: Introduction on NGS platforms, data acquisition and analyses	Ludovic Orlando: Brief introduction on ancient DNA, with the problems of contamination, low endogenous contents and post-mortem damage. Use of 2nd + 3rd generation sequencing for the anlysis of ancient DNA.	Laura Wegener Parfrey: Metagenomics: Assessing microbial community patterns using Qiime (quantitative insights into microbial ecology).	Bob Schnabel: Introduction to SNP quality analysis: Managing data (SNP and NGS) and quality control issues prior to analysis.
Lunch break
Hands on sessions, includes afternoon tea break	Stephen Bent: Practical application of the morning's topics.	Martin Kircher: NGS pipelines and tools.	Ludovic Orlando: Mapping ancient DNA Illumina reads to reference genomes to highlight damage patterns and SNP variation. Published data on the Black Death will be used to illustrate this session.	Laura Wegener Parfrey: Particpants will go through tutorial data using Qiime to process raw data and then assess diversity patterns in microbial communities.	Debrief on the essential sessions of the workshop.
PUBLIC LECTURES 5-6pm Mawson L.T.	Martin Kircher: A high coverage Denisovan genome - what 30x coverage from a more than 50,000 old pinky bone tells us about her and our past.	Ludovic Orlando: The last million years of horse evolution.	Laura Wegener-Parfrey: The eukaryotic tree of life as a framework for eukaryotic community analyses.	Bob Schnabel: Application of whole genome sequencing to identify Mendelian disease candidates in dogs using a 1-case + N-control design.	-

Registration

Registration now closed. Seats have sold out.

Registration fees:

Early Bird registration AUD $400.00 (includes training manual and welcome breakfast). Deadline date 3rd September, 2012
Non Early Bird registration AUD $450.00 (includes training manual and welcome breakfast).
For Environment Institute members, there is a special Early Bird offer, please contact Raeleen Day to apply for the reduced rate.
NO SINGLE DAY REGISTRATION AVAILABLE

Payment registration form download here. Regisration form plus full payment must reach our office no later than 30 September, 2012. Late payment does not guarantee a placing.

Completed registration payment form can be returned via scanned pdf only and emailed as an attachment to:
Maria Lekis
c/- Australian Centre for Ancient DNA or delivered by hand at the Centre office, Room 209a Darling Building
North Terrace Campus
The Universsity of Adelaide

For enquiries phone +61 8 8313 3952 | Email Maria here

Venue details and Map

This 5 day workshop is held at the University of Adelaide, North Terrace Campus
Lectures/presentations are held in the Mawson Lecture Theatre, Ground Floor, Mawson Building
Hands on sessions are held in the Mawson Computer Suite, Ground floor, Rm G12, Mawson Building

Click campus map left for enlarged image. Mawson Building map reference 11B

Adelaide Accommodation

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

1) Mantra on Frome. approx 10mins walk to the University. Contact phone +61 8 8412 3333. Standard rooms range from AUD$110-130

2) 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

3) The Vines or Grand Apartments in North Adelaide City. Standard rooms range from AUD $79-$100. approx 10mins walk to the University. Contact phone Toll free in Australia only #1300 668 400

4) The Oaks Embassy 96 North Terrace, Adelaide. 1 bedroom apartment from AUD $134.00.

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 Accommodation

ACAD Bioinformatics Early Career Researcher Workshop, 5th - 9th November, 2012 The University of Adelaide, North Terrace Campus

Sponsored by the Environment Institute