Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow
Wednesday 25 September 12.00-4.00pm & Thursday 26 September 12.00-4.00pm AEST
The Australian BioCommons / EMBL-ABR is offering a two-part workshop via its hybrid training methodology. Join a group in your home state that will link up with expert lead trainers online to hear presentations and undertake hands on tutorials with the support of trained facilitators in the room.
Large bioinformatics analysis workflows are fragile ecosystems of software tools, scripts and dependencies and can present a challenge to the reproducibility of data analyses. One solution is the use of the workflow management systems which can be seamlessly executed across different computing environments (laptop/desktop to High Performance Computing).
The two-part workshop will implement a common analytical pipeline in both Nextflow and Snakemake, exposing participants to the core concepts of importance to both workflow managers, while also providing a means to compare and contrast the two.
This workshop is intended for researchers who already use bioinformatics workflows in their research, but who do not yet have knowledge of Nextflow or Snakemake. To participate you must be familiar with the Linux command line and have experience with at least one scripting language.
The workshop is free but places are strictly limited. Participants must attend both days: 25 and 26 Sept, 12-4pm AEST. Please follow the link below to register at the location closest to you.
Introduction for phylogenetic trees for beginners
18 October (Part A: Presentation/ hands-on exercises)
4 December 2019 (Part B: Q&A relating to participants’ real life data problems)
12-4pm AEST, 1-5pm ADST, 12.30-4.30pm ACDT, 10am-2pm AWST
Phylogenetics is essential for comparing biological species and understanding biodiversity for conservation. These workshops will introduce researchers to basic methods of phylogenetic inference. Participants will be guided through using Galaxy Australia and other tools, working with examples drawn from the recently published OzMammals data. A subsequent Q&A session will offer the opportunity for participants to receive expert feedback on the application of their new knowledge to their own research data.
The workshop will demonstrate the use of standard tools to estimate phylogenetic trees from aligned sequence data or distance data. It will help participants to better understand basic principles of phylogenetic analysis, including sources of uncertainty, and support them to make reasonably informed decision about which method(s) to use.
Dr Michael Charleston will lead the training from from the University of Tasmania, and the workshop will occur simultaneously in a number of venues across Australia with the assistance of host universities and research institutes.
Participants will gather at a local venue and connect with the lead trainer via an online interactive presentation. The training will comprise a series of short presentations combined with guided hands-on exercises on participants’ own laptops. All hands-on exercises will be supported by trained local Facilitators, with live online help from experienced bioinformaticians.
The workshop will be coordinated by organised by the Australian BioCommons / EMBL-ABR with the assistance of a network of Facilitators from around Australia.
Registrations to open soon…
RECORDINGS OF ALL 2018 TRAINING EVENTS ARE NOW AVAILABLE FOR VIEWING HERE
Galaxy Australia training series
EMBL-ABR is working with the Biosciences Data Enhanced Virtual Lab (DeVL) Galaxy Australia project team to undertake a national training program. Four workshops will introduce Galaxy Australia capabilities to researchers, with demonstrations based around different themes. The training will be led by a Galaxy expert who is available online throughout the hands on sessions that are facilitated by trained locals at participating EMBL-ABR Nodes. All workshops are free, but places are limited.
Introduction to Galaxy Australia – Genome Assembly
Wednesday, 22 Aug 2018 13:00-16:00 AEST
Introduction to Galaxy Australia: Finding genetic variants in bacterial sequence data
Wednesday 12 Sep 2018 13:00-16:00 AEST
Introduction to Galaxy Australia: Differential Gene Expression from Bacterial RNA-seq Data
Tuesday 23 Oct 14:00-17:00 AEDT
Introduction to Galaxy Australia – Metagenomics
Wednesday 14 Nov 13:00-16:00 AEDT
UCSC Genome Browser: a full-featured genomic data system
Lead Trainer: Robert Kuhn, Associate Director of UCSC Genome Browser, Training and Outreach, Genome Browser licensing
8 Nov 2018 12:00 – 3:00 AEDT (Vic, NSW), 11:00 – 2:00 AEST (Qld), 11:30 – 2:30 ACDT (SA)
This workshop provides hands-on instruction in the use of the UCSC Genome Browser, which is a widely used platform for interpreting many types of genome-wide data for a large number of organisms. In the context of human genetics, aggregated data from hundreds of projects are available, including short and long variants (SNPs and CNVs), benign and pathogenic variants from several large databases, and metagenomic data such as histone- and DNA modification. The Browser provides a consistent interface and gene models for mouse and more than 120 other animals.
The workshop will also demonstrate recently added features including display of exons only, display of discontinuous regions of the genome and the simultaneous, joint configuration of multiple wiggle files, such as are used to display RNA-seq data.
This session will be offered at several EMBL-ABR Nodes around Australia, with expert hands-on help provided at each venue.
Prerequisites: two introductory webinars must be viewed prior to attendance: RECORDINGS NOW AVAILABLE FOR VIEWING: Webinar 1: Using the UCSC Genome Browser; and Webinar 2: Advanced features of the Genome Browser.
These events were initiated by Dominique Gorse, Director, QFAB Bioinformatics, and supported by AGTA’s Small Grants scheme.
- Past EMBL-ABR Events: find details and resources from past EMBL-ABR events here.
- WEBINARS link here for details
- In 2018, EMBL-ABR had representation at the following conferences:
useR! 2018, 10-13 July, Brisbane
ISCB-ASC 2018, 26-30 August, Melbourne
Genemappers 2018, 29-31 August, Noosa Heads
AGTA 2018, 4-7 November Adelaide
ABACBS 2018, 27-28 November, Melbourne
Winter School in Mathematical and Computation Biology, 2-6 July, Brisbane.
- Visit the European Bioinformatics Institute’s training site to find many more opportunities to develop your skills.