Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow

Recent years have seen a groundswell of support in the bioscience community for improved reproducibility of data analyses. Large analysis workflows are fragile ecosystems of software tools, scripts and dependencies. One solution to these issues is the use of the workflow management systems such as Nextflow and Snakemake. Trainees will be exposed to a common analytical pipeline, implemented in both Nextflow and Snakemake, which can be seamlessly executed across different computing environments (laptop/desktop to High Performance Computing).

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Wojtek James Goscinski
Cortical Reconstruction Process using FreeSurfer - Part 2

The University of Sydney is a partner of the CVL project and we are delighted to hold a training on how to use the CVL desktop for The University of Sydney staff and students using FreeSurfer as workflow example. FreeSurfer is an open source software suite for processing and analysing human brain MRI images. This workshop is the second part of a previous workshop , hence previous participants have priority to register.

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Data Fluency: Introduction to HPC Workshop

This workshop will provide an overview of what a High-Performance-Computing system looks like. Users will get hands on experience with a small cluster, and learn how to use Linux command-line tools to write Slurm scripts which they can submit as simple batch jobs. After the workshop, users will be able to use what they learn on much bigger systems.

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Call for Characterisation Community Champions

The Characterisation Virtual Laboratory (CVL) Champions are a community of researchers, university lecturers, and bioimaging professionals taking part in a skills development program. The program is to enhance the national characterisation computing infrastructure and apply FAIR FAIR (Findable, Accessible, Interoperable, Reusable) data principles to research workflows, by upskilling scientists and bioimaging professionals for continuation of these goals.

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MASSIVE M3 DGX User Community Meeting

The MASSIVE team has recently expanded the GPU capability by adding five DGX-1 servers to the resource pool. We are close to completing the integration of these servers into the M3 queue, and we will be expanding this server partition in the future. We are keen to talk to future users of these servers to present how they will be accessed, discuss requirements, and capture any feedback.

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Data Fluency: Introduction to Python workshop

Register now for our upcoming Introduction to Python workshop being held at Clayton campus on Friday 19th July from 10:00am til 3:00pm. This hands-on workshop aims to equip participants with the fundamentals of programming in Python and give them skills needed to apply data analysis approaches to their research questions. The workshop will be taught in a similar style to Data Carpentry workshops. Data Carpentry’s mission is to train researchers in the core data skills for efficient, shareable, and reproducible research practices.

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Data Science and Artificial Intelligence in the Humanities, Arts and Social Sciences

Data Science & AI in HASS, for short, will allow researchers to present new projects that might benefit from further collaboration; discuss the ethical, legal and social issues and challenges in this space; demonstrate tools and services Monash can provide; and encourage opportunities for our researchers to work across the university, or with our partners at Penn State.

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