EMBL-ABR Webinars

EMBL-ABR webinars are open for all to attend.

All our webinars are recorded and uploaded to the EMBL-ABR YouTube channel. Links to the recordings are added to this page within one week of the event.

Our thanks to ARDC (formerly ANDS-Nectar-RDS) for partnering with us to bring the webinar series to the Australian life sciences research community.

Ideas for topics or speaker suggestions are welcome – just email us.

Please subscribe to EMBL-ABR news or follow us on Twitter for news of all upcoming sessions. 


Upcoming Webinars

02 MAY 2019: New opportunities for clinical bioinformatics in GenoVic: The Melbourne Genomics Health Alliance shared clinical system for genomics

This webinar will discuss the evolving landscape of clinical bioinformatics arising from the implementation of GenoVic, an enterprise-grade clinical system for genomics. Delivered and managed by the Melbourne Genomics Health Alliance, GenoVic supports the end-to-end workflow for genomic testing across multiple independent testing laboratories and hospitals. Underpinning GenoVic is a Genomic Orchestration Service (GOS) that provides a single integration point for all laboratories to connect – using a healthcare interoperable messaging standard (HL7 FHIR) – that enables delivery of the genomic testing workflow.

Within the secure on-shore cloud environment of the Amazon Web Services, GenoVic enables the scalable delivery and sharing of high-quality genomic information securely, efficiently, and sustainably. GenoVic is the first implementation of a shared clinical system for genomics in Australia and is designed for the fast and changing pace of genomics. Its flexible, modular nature allows it to evolve as needs change over time.

Join Dr. Natalie Thorne to learn more about:

· The technology behind GenoVic, GOS and the Alliance’s approaches to implementing diagnostic grade bioinformatic pipelines.

· What the clinical bioinformatician of the future looks like (the importance of health informatics, cloud computing, portable pipelines, software testing and deployment, soft skills in collaboration).

Dr Thorne will share her experiences and observations on the changing landscape of translating research bioinformatics into health system innovations, and how the existence of a clinical system like GenoVic provides unique opportunities for Victoria to position itself as a leader in the emerging and important field of clinical bioinformatics.

Date/time: 2 May 2019 12:00-13:00 AEST

Presenter: Natalie Thorne, PhD, Lead Specialist, Clinical Genomics, Melbourne Genomics Health Alliance

Registration: https://register.gotowebinar.com/register/1437958197259367181


Past Webinars

14 MARCH 2019: Nextflow: Scalable, Sharable and Reproducible Computational Workflows across Clouds and Clusters

Large analysis workflows are fragile ecosystems of software tools, scripts and dependencies. This complexity commonly makes these workflows not only irreproducible but sometimes even not re-runnable outside their original development environment. Nextflow is a reactive workflow framework and a domain specific programming language which follows the dataflow paradigm and offers an alternative, and arguably superior, approach to developing, executing and sharing pipelines.

In this webinar we will follow the steps required for developing sharable, version controlled, container-backed workflows, which can be seamlessly executed across different environments from a laptop to cluster to cloud. We will do this by leveraging Nextflow’s integration with code and container image hosting services such as GitHub and Docker Hub, and out of the box support for various HPC cluster schedulers and the Amazon AWS cloud.

Date/time: Thursday 14 March 2019 13:00-14:00 AEDT /12:00-13:00 AEST

Presenter: Radoslaw Suchecki, CSIRO

Registration: https://attendee.gotowebinar.com/register/8408436403729692931


7 FEBRUARY 2019: Snakemake: Reproducible and Scalable Bioinformatic Workflows

Recent years have seen a groundswell of support in the bioscience community for improved reproducibility of data analyses. One solution used by bioinformaticians to achieve this is the use of the Snakemake workflow management system. It is a tool for creating reproducible and scalable data analyses.

This 1-hour webinar will take a look into Snakemake, cover the core concepts and examples required for making your first steps into reproducible Snakemake workflows. Building on this foundation, Nathan will introduce more advanced features which enable workflows to scale seamlessly to server, cluster, grid and cloud environments as well as different software execution environments.

Date/time: Thursday 07 February 2019 13:00-14:00 AEDT /12:00-13:00 AEST

Presenter: Nathan Watson-Haigh, University of Adelaide

Recording: is available on the EMBL-ABR YouTube Channel

Slides and examples: are available on GitHub


30 NOVEMBER 2018: CyVerse – Extensible Cyberinfrastructure for Life Science

Biological research increasingly depends on computational analysis of large and complex data sets. This 1-hour webinar provides a comprehensive look at platforms, tools, and services for large-scale data analysis provided by CyVerse, a cyberinfrastructure (CI) project of the US National Science Foundation.

The webinar will introduce the basic components of CyVerse CI including the Discovery Environment (a simple web portal for managing data, analyses and workflows); the Data Store (scalable, secure, and reliable storage for terabyte-scale data management); Atmosphere (one-click, on-demand cloud computing); and the Visual and Interactive Computing Environment (flexible implementations of Jupyter Labs, Rstudio, and R Shiny).

CyVerse provides a full stack of CI services with entry points for computational novices and software developers. All resources are freely available to the community and free accounts can be obtained at user.cyverse.org

Presenter: Jason Williams. Assistant Director, External Collaborations Cold Spring Harbor Laboratory, DNA Learning Center and Education, Outreach and Training lead for CyVerse.

Recording is available on the EMBL-ABR YouTube Channel

Slides are available on Slideshare


23 OCTOBER 2018: Using the UCSC Genome Browser

This webinar introduced viewers to the UCSC Genome Browser, provided an overview of the browser, what it is, and its history, and covered the following tasks users can perform: Configuring the display; Track settings; Exporting Browser images for publication; How to search for regions/positions, gene names, motifs, other keywords; Saving and sharing sessions; Using the browser to explore microarray data and chromosome imbalances and NGS sequencing data — paired ends, BAM files, variants calling/display; Uploading and displaying your own data; and Custom tracks.

Presenter: Bob Kuhn. Associate Director, UCSC Genome Browser. University of California, Santa Cruz, USA

Recording: is available on the EMBL-ABR YouTube Channel


24 OCTOBER 2018: Advanced features of the UCSC Genome Browser

This webinar showed users how to browse, use and download datasets available in the UCSC Genome Browser. Starting with entry points for browsing UCSC data: Genomic position, Sequence, Variant and gene name.  Track groups and a demo of UCSC’s most popular data sets: Genes and Gene Predictions and Comparative Genomics, Variation, CRISPR, gnomAD, and Gene Interactions.  Useful features include exon-only mode, viewing discontinuous regions together and combining and co-configuring RNA-seq data.

Presenter: Bob Kuhn. Associate Director, UCSC Genome Browser. University of California, Santa Cruz, USA

Recording: is available on the EMBL-ABR YouTube Channel


21 AUGUST 2018: Teaching and training: lessons from education and cognitive science to promote learning

In 2017, Feldon et al. published a study of the results of federally (grant) -funded “bootcamp” type training in data science/technology that was aimed at doctoral-level graduate students in the US. Their results showed that these short/sharp training experiences did not, in fact, lead to any discernable differences between students who did, and those who did not, attend the workshops. This webinar will discuss these results as not surprising – given what is known about adult learners, cognition, and common design characteristics of both short/sharp and longer instructional opportunities. To overcome the difficulties the Feldon et al. results highlighted, we will examine lessons from education; from cognitive science; and from the Data and Software Carpentries. These lessons can be applied to any adult learning experience (“bootcamp”, course, program or curriculum).

Presenter: Prof Rochelle Tractenberg, Georgetown University USA

Dr Rochelle Tractenberg is a tenured professor in the Department of Neurology at Georgetown University (USA), with secondary appointments in the Departments of Biostatistics, Bioinformatics & Biomathematics and Rehabilitation Medicine. She is an accredited professional statistician with over 20 years of experience designing and analysing experimental research; and a research methodologist specialising in designs and analyses with “difficult to measure” outcomes in biomedical and clinical domains. Additionally, with PhDs in psychology/cognitive sciences (1997) and measurement, statistics, and evaluation (2009), she focuses on curriculum development and evaluation in higher (graduate/post graduate and professional) education, training new scientists for ethical practice, and statistical literacy for effective stewardship of the discipline in PhD students/holders in particular.

Prof Tractenberg was elected a Fellow of the American Statistical Association in 2016 and a Fellow of the American Association for the Advancement of Science in 2017. She is involved nationally and internationally in educational and training initiatives that feature the curriculum development, evaluation, and revision tool she created, the Mastery Rubric. In addition to supporting effective curricula (i.e., where intended and actual learning goals are aligned), this construct provides the first way to bring psychometrically-defined validity to curriculum decisions. She maintains active research portfolios in curriculum development, research ethics education, and multiple clinical domains.

Recording: is available on the EMBL-ABR YouTube Channel

Slides: are available from Rochelle Tractenberg’s georgetown.academia.edu website


12 JULY 2018: Bioconda and the Conda Package Manager

Bioconda is the most popular and widely used bioinformatics channel for Conda (the package, dependency and environment management tool for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN). By adding a tool to the Bioconda ecosystem, it becomes widely available as an installable tool package for various operating systems and hardware that is stored in a fully-supported, global repository of bioinformatics tools. This webinar will cover Bioconda basics and how Australian researchers can use it to streamline bioinformatics tool wrapping for use on various systems.

Presenter: Thom Cuddihy, QFAB and University of Queensland RCC

Recording: is on the EMBL-ABR YouTube channel

Slides: are available on EMBL-ABR’s Slideshare


14 JUNE 2018: Galaxy-Australia: Bioinformatics tools without the scripting, and with reference data and compute included.

Galaxy Australia is the open access, free to use portal for Australian life science researchers to perform data manipulation and analysis. Incorporated and accessible through the Australian-made Genomics Virtual Lab, Galaxy Australia has recently been upgraded to incorporate new features, extended compute and quotas and more training resources. This webinar will showcase these new resources and services.


Presenters: Dr Gareth Price, Service Manager of Galaxy Australia and Simon Gladman, System Architect and Tools Expert

Recording: is on the EMBL-ABR YouTube channel

Slides: Gareth Price, Simon Gladman