ACAD Early Career Researcher (ECR) Workshops
ACAD has developed several successful ECR workshops since 2008, and continues to drive innovative training programs as the trends of science expand. Below is a snapshot of previous workshops.
2017 Advanced Bioinformatics Workshop for ECRs
Headlining our workshop in November 13-17 were Allen McRae (methlyation and gene expression: BWA & GATK), Dan Huson (metagenomics, MALT, MEGAN and DIAMOND), Daniel McDonald (Qiita, QIIME) and Blanca Himes (statistics, machine learning, informatics). As with previous workshops, the program consisted of practical hands-on tutorials in a computer lab, as well as lectures. This workshop was sponsored by CABAH.
2016 Advanced Bioinformatics Workshop for ECRsKindly sponsored by the Bioinformatics Hub, this year (7-11 November) we focused on metagenomics with key leaders Rob Knight, Philip Hugenholtz, Laura Weyrich, and Mathieu Fourment presenting a four-day hands-on training course. Topics covered were analysis of amplicon and shotgun metagenomic datasets (QIIME and MALT/MEGAN), along with detailed analysis of bacterial genomic information recovered from metagenomes (genomic mapping, taxonomy, phylogeny, and evolutionary analyses). The program combined 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.
2015 Advanced Bioinformatics Workshop for ECRsOur third advanced level workshop in bioinformatics was held in November 9-13th showcasing the latest available sofware for the analysis of Next Generation Sequencing, genomics and metagenomics data. Sponsored by the Bioinformatics Hub, the expert tutors were Remco Bouchaert (Phylogenetic algorithms using genomic SNP data; BEAST, SNAPP; and multi-species coalescent), Martin Kircher (data pre-processing, long read and single molecule sequencing, including pipelines and tools, Rob Knight (metagenomics; using the new Qiita database), Paul Stothard (Python, FAST, Bowtie, Tophat and R) and Amanda Birmingham (QIIME, statistical testing).
2014 Advanced Bioinformatics Workshop for ECRs
A second advanced level workshop in bioinformatics was held in November 10-14th, 2014 with leading tutors utilising the latest available software for the anlaysis of Next Generation Sequencing (NGS), genomic, methylome and metagenomic data. Delegates were required to have basic command lines knowledge and be familiar with UNIX environments, and have an intermediate knowledge of the technology and analytical tools of NGS. Genome annotation, BASH, Python, MSMC, PSMC AWK and MEGAN were some of the areas covered this year.
Tutors in 2014 were Dr Paul Gardner (genomics), Prof Ryan Lister (epigenetics), A/Prof Daniel Huson (metagenomics) and Dr Stephan Schiffels (population genomics).
2013 Advanced Bioinformatics Workshop for ECRs
As a build up from the successful 2012 Bioinformatics workshop, ACAD presented its 4th workshop at an advanced level. Here, leading experts (Ludovic Orlando, Joe Pickrell, Rob Knight and Stephen Bent) tutored on the latest available software for the analysis of Next Generation Sequencing (NGS), Genomics and Metagenomics data, with the aim of particpants gaining a broad understanding of current bioinformatics tools and methods to handle and analyse NGS and SNP array data. The course combined 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. Day five of the program provided a valuable opportunity for delegates to work on their own dataset with the tutors.
2012 Bioinformatics Workshop for ECRs
In 2012, ACAD tilted its focus to Bioinformatics and the analysis of NGS data with its 3rd ECR workshop held 5-9 November. The workshop offered training in the latest bioinformatics tools and methods to handle and analyse NGS and SNP arrary data, and interpret complex data sets, such as genomic and metagenomic samples. Methods to deal with damaged and low copy number templates were also covered.
The international experts tutoring this sold-out workshop were:
Stephen Bent, University of Adelaide
Ludovic Orlando, University of Copenhagen
Martin Kircher, University of Washington
Laura Wegener Parfrey, University of Colorado; and Bob Schnabel, University of Missouri.
2010 Adelaide Phylogenetics Conference (& ECR Workshop).
The third annual conference, formerly Mathematical & Evolutionary Biology, was held on Port Elliot beachfront, South Australia from April 12-16, 2010. This meeting followed the successful meetings held in Blanche Cave, Naracoorte 2008 and Port Elliot 2009, where topics covered included: Phylogenetics and Networks; Mathematical methods and Algorithms; Macroevolution; Evolutionary rates and dates; Genome analysis; Bioinformatics; Human evolution; and Disease. The conference featured one day devoted to data analysis/recreation with scheduled activities around the Port Elliot area including wine tours, beach activities, or optional data analysis sessions. Important prizes at the Port Elliot meeting included the highly coveted Napkin Award (for the best mathematical solution to a biological problem solved at the conference). We also repeated the extremely successful Phylogenetics Workshop for graduate students, run prior to the conference by ACAD at the University of Adelaide from April 6-10. This workshop featured an intensive 4 day hands-on training from experts, in leading software packages for the analysis of genetic data: Dr. Alexi Drummond (BEAST), Prof. Peter Lockhart (Phylogenetic methods), Christian Anderson (Serial SimCoal), and Andrew Storfer (Landscape Genetics).
2009 Adelaide Conference on Mathematical and Evolutionary Biology, 20-24th April.
This meeting followed the successful inaugural meeting held in Blanche Cave, Naracoorte in 2008. The ACMEB series aimed to bridge the current gap between biologists and mathematicians in Australia, and overseas, by providing a relaxed, informal setting for the discussion of new results. The emphasis is on the development and application of advanced new analytical methods, and building trans-disciplinary collaborations. The conference was designed to allow maximum student and academic interactions, and the analysis of datasets during the meeting itself. In addition to the conference, this year ACAD introduced a 4 day hands-on phylogenetics workshop, 'Methods in Bioinformatics and Molecular Evolution' tailored for early career researchers. The workshop was lead by 4 international experts, in leading software packages for the analysis of genetic data: Peter Lockhart, Massey University; Mark Pagel, University of Reading; Alexi Drummund, University of Auckland (BEAST); and Christian Anderson, University of San Diego (Derial SimCoal).
2008 Adelaide Conference on Mathematical and Evolutionary Biology
Mathematical biology is set to become a key focus of future scientific research in Australia and worldwide, due to the enormous technological advances in our ability to generate genetic data that have occurred over the past 1-2 years. The Adelaide Conference on Mathematical Evolutionary Biology aims to bridge the current gap between the fields of modern biological research and applied mathematical research in Australia, particularly in the study of phylogeny and molecular evolution. This 5 day conference is the first of an annual series which is designed to develop research collaborations within mathematical evolutionary biology, and is closely related to the very successful New Zealand Phylogenetics Meeting series (see http://www.math.canterbury.ac.nz/bio/whitianga08/). The leading researchers from the NZ series will attend the Adelaide meeting to facilitate communication between the mathematical and biological fields - identifying key conceptual and terminology differences, and over-coming the domain barriers which currently prevent interaction of these groups within Australia.
The meeting will featured a mix of general/introductory talks with discussions of work in progress and the presentation of current biological problems/analytical methods. Key topic areas will include phylogenetics, evolutionary rates and dates, coalescent models, population genetics, phylogenetic networks, evolutionary theory/models, search algorithms.
The international presenters were: David Penny, Professor of Theoretical Biology; Allen Rodrigo, Professor of Computational Biology and Bioinformatics and Director of NESCent, ANU; Mike Hendy, Professor of Mathematics at Massey University, Institute of Fundamental Sciences' and Barbara Holland, University of Tasmania.