From 22-25 July 2024 (Online only)

The workshop will deliver a basic training in Nextflow (https://www.nextflow.io), a workflow management system that enables the development of robust, reproducible, and scalable workflows for scientific and data analysis. Additionally, participants will be introduced to the nf-core initiative (https://nf-co.re), a framework for collaborative work toward reproducible and reusable bioinformatics pipelines (Ewels et al. Nat Biotech 2020). Currently, the nf-core framework and tooling include over 50 pipelines for the reproducible analysis of genomics and transcriptomics data, with over 30 more pipelines under development.

Specifically, the workshop will cover the following sections.

 Session 1 (Monday 22 July 2024)

• • Introduction to Nextflow and nf-core (45 min)

  • Break (15 min)

  • Introduction to Gitpod (30 min)

  • Nextflow in the command line (15 min)

  • Questions (15 min)

• Session 2 (Tuesday 23 July 2024)

• • Hello Nextflow Part 1 (45 min)

  • Break (15 min)

  • Hello Nextflow Part 2 (45 min)

  • Questions (15 min)

• Session 3 (Wednesday 24 July 2024)

• • nf-core customize (45 min)

  • Break (15 min)

  • nf-core customize (45 min)

  • Questions (15 min)

• Session 4 (Thursday 25 July 2024)

• • Ampliseq pipeline

Time: 1-3 pm AWST (Perth time) - 3-5 pm (AEST).

Instructors.

Dr Chris Hakkaard (Developer Advocate at Seqera labs)

Dr Patricia Agudelo-Romero (Computational Biologist at Telethon Kids Institute.

Dr Jose A Caparros-Martin (Telethon Kids Institute)

Requisites.

• A GitHub account (necessary for accessing GitPod and the hands-on over the entire workshop.

• Basic knowledge working on command line

If you are interested, please send an email to info@microbiome-research.net by Sunday 21st.

A virtual catch-up for those looking to meet like-minded researchers with an interest in FMT.

In this meeting Dr Nadia Lopes Amorim shared her expertise in designing FMT pre-clinical studies.

You can view the slides of the presentation by clicking this link. 

Commencing May 2022 (Online only)

Ran over four weeks, this group course will provide structure and guidance as attendees work through an online microbial analysis course together.

Find more information and register by clicking this link.

We kicked off 2022 by diving straight into the deep end, with an event focused on new ideas in microbiome research.

In this event, Dr Mireia Valles-Colomer and Dr Archita Mishra take us through their exciting research areas. 

A virtual catch-up for those looking to meet like-minded researchers with an interest in FMT.

In this meeting Dr Hannah Wardill presented the new and exciting GRAFT guidelines of which she is senior author. Hannah's presentation sparked some discussion points and attendees had the chance to ask questions and discuss points of interest.

An online lightning talk event where our members shared their microbiome super powers for the greater good.

• Svetlina Vasileva, Queensland Brain Institute

• Dr Carolina Gubert, The Florey Institute of Neuroscience & Mental Health

• Samantha Dawson, Food & Mood Centre, Deakin University

• Ghayah Al-Qadami, School of Biomedicine, University of Adelaide

• Prof Mark Nicol, University of Western Australia

• Dr Guillaume Meric, Systems Genomics Lab, Baker Heart & Diabetes Institute

• Prof Nicolas Rasmussen, University of New South Wales

The Australasian Human Microbiome Research Network’s inaugural event.

• Georgina Hold: “Who’s who of the human microbiome: an introduction to key microbes”

• A/Prof Andy Holmes: “What is lost and gained with 16S sequencing relative to shotgun? Is shotgun always better?”

• Dr Thom Quinn: “Appropriate statistics and data transformation for compositional data”