How is genomics relevant to data science? Many of the steps in the genomic testing pathway use pipelines and database developed by data scientists. This event hosted by Melbourne Genomics on 05 Dec 2022 hopes to highlight how closely they are intertwined. To register, please contact Amy Nisselle.

Microscopy Australia is organising a two-half-day masterclass on the use of high-performance computing (HPC) and virtual research environments (VRE) available to the Australian research community for data processing and data analysis.

The masterclass will include an introduction to HPC (including cloud computing) and Virtual Research Environments, and describe capabilities available in Australia. Data transfer will also be covered (available tools, and network performance measurements). Experts from various organisations, including ARDC Nectar Research Cloud, NCI, the Queensland Cyber Infrastructure Foundation, The University of Queensland, AARNet and the Pawsey Supercomputing Centre will present their services and answer questions from the audience. The masterclasses will be held online on Monday 5 December (HPC) and Tuesday 6 December (VREs).

The program and registration links are available here. Interested participants can register for one day or both days. The masterclass is open to everyone within and outside Microscopy Australia.

Join Australian BioCommons on 06 Dec 2022 for a consultation workshop to review draft principles and recommendations around effective, inclusive and career-spanning short-format training. This is your opportunity take a deep dive into making training in bioinformatics and digital research skills for biologists more equitable, scalable and sustainable. For more information, please visit this website.

IMNIS Engage (Industry Mentoring Network in STEM) is a high impact program of industry mentoring, professional development and networking from the Australian Academy of Technological Sciences and Engineering. This one-year national program prepares Australia’s early-stage STEM researchers from leading research organisations to engage with industry.

IMNIS Engage programs connect motivated mentees with an influential industry mentor who can provide pragmatic career advice, support professional skills development and facilitate broad, cross-sector professional networking to enhance mentees’ capacity to engage with industry, understand commercialization and regulatory processes related to innovating their research, and engage with confidence.

To find out more about becoming either a mentee or a mentor, please visit the IMNIS website.

Intersect have released a report titled "Novel study elucidates the long-term behavioural change & impact of digital skills training on researchers’ workflows", if you are interested in a copy, please go to this link.

Intersect released a training impact study, which demonstrates the long-term impact of training to researchers based on a survey that Intersect gathered from over 1,100 responses from HDR students, researchers and academics. See the full report and story here.

Registration is now open for CarpentryCon 2022: Expanding Data Frontiers and is happening 1-12 Aug 2022. CarpentryCon is an exciting and free way to connect with The Carpentries community and “level up” data science skills.

NCI is supporting four pioneering parallel computing researchers from our community to present at the OpenACC and Hackathon Summit held online 23-25 Aug 2022. Register for your FREE ticket today: https://bit.ly/3aXaZJa

This webinar hosted by Australian BioCommons sees Georgina Samaha from the Sydney Informatics Hub joining them to walk through essential steps and considerations for running and building reproducible whole genome sequencing mapping and variant calling pipelines at the command line interface. She will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need. It is being held on 24 Aug 2022 at 3pm AEST / 2:30pm ACST / 1pm AWST. Please visit this BioCommons page for more details and to register.

This 3-hour online webinar co-organized by the Australian Text Analytics Platform (ATAP), FIN-CLARIAH and its UEF representatives, and the Australian Digital Observatory around Computational Thinking in the Humanities is to be held on 1 Sep 2022 5-8pm AEST. Please see this page for more details.

A 12-week online, collaboratively taught course by internationally renowned professors and scientists for Australian HDR students, ECRs, MCRs and beyond. The purposefully designed curriculum, including hands-on HPC tutorials, aims to support researchers working in the space between HPC/Big Data and drug design and delivery. Starts 6 Sep 2022. If you want more information, please visit the Intersect website.

This webinar hosted by Australian BioCommons sees Nandan Deshpande from the Sydney Informatics Hub, University of Sydney, show how you can deploy a freely available nf-co.re bioinformatics workflows with a single command and will also show you how to can use Nextflow to build your own workflows that save you time and support reproducible, portable and scalable analysis. In the latter half of the webinar, Sarah Beecroft from the Pawsey Supercomputing Research Centre will talk about their Nimbus Cloud systems. She will describe why using Nimbus with Nextflow is a brilliant option for many bioinformatics projects. It is being held on 20 Sep 2022 at 12pm AEST / 11:30am ACST / 10am AWST. Please visit this BioCommons page for more details and to register.

Australian BioCommons has a workshop coming up on RNAseq analysis in partnership with the Sydney Informatics Hub and Pawsey Supercomputing Research Centre. You will learn about the fundamental concepts of RNA sequencing experiments and how to take the data from reads to functional analysis and pathway enrichment. You will get hands-on using nf-core/rnaseq - a portable, scalable, reproducible and publicly available workflow on Pawsey Nimbus Cloud. In the second part of the workshop you will use the count data you created to identify differential genes and pathways using R/Rstudio. By the end of the workshop, you should be able to perform your own RNA-seq analysis for differential gene expression and pathway analysis. It takes place on 27-28 Sep 2022. Please visit this BioCommons page for more details and to apply.

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This online hands-on workshop hosted by Australian Centre of Excellence for Antarctic Science will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. It takes place 11, 13, 18 & 20 Oct 2022. For more details and to register, please see this page.

Abstract

Cloud computing is changing the computing infrastructure landscape by providing on-demand resources with ultra-high scalability. Advancements in virtualisation technology and defining infrastructure using code have revolutionised how cloud computing is applied in day-to-day applications, including research.

Traditionally, compute-intensive research work such as bioinformatics, AI/ML and simulations (MD and CFD) were conducted using on-premise high-performance computing resources. The advancements in network virtualisation and the ability to operate bare-metal computers with RDMA interconnect on the cloud are currently getting popular among compute-intensive research. It is expected that within the next 5 - 10 years, majority of research computing will be using cloud computing compared to on-premise computing.

The transition from on-premise to cloud could be a challenge for some researchers. The key to being successful is to start simple and grow gradually. Oracle for research is here to support you during that journey.

About the speaker

Dr Harinda Rajapaksha is a solutions architect at Oracle for Research. Dr Rajapaksha specialises in computational biology and high-performance computing and has over 15 years of experience in industry and academia. His primary interest is in the development of software solutions for scientists.

This talk takes place 3 Nov 2022 at 2-3pm (AEDT). If you would like to register, please click this link.

Are you interested in joining this year’s BioHackathon Europe but can’t travel to Paris? Australian BioCommons are putting together a team who will join from Australia, working with the international participants in their time zone - but from a city close to home. This is a unique opportunity to participate in a significant global event and network with your international peers while working intensively on practical coding challenges. We will fly you to a central point (TBC) to meet other Australian participants and set you up in a hotel for the duration of ELIXIR’s BioHackathon, 7-11 November 2022. If you want more information, please visit the BioCommons website.

AMSI BioInfoSummer is aimed at advanced undergraduate and postgraduate students, researchers, and professionals working in the fields of mathematics, statistics, data science, complex systems analysis, engineering and biological, chemical and medical sciences. It takes place 21-24 Nov 2022. If you would like more information, please visit this website, if you would like to register, please click this link. 

Installing scientific software on HPC often requires substantial amounts of work. In this Tech Talk, ARDC would like to get input from the community on their idea for a community-led system that makes building and distributing scientific software more sustainable. Their goal is to collect container recipes in a GitHub repository, containers are then automatically built and tested and pushed to a container registry. The containers are security rated and HPC admins can select which container subset they would like to offer to their users. The software containers will be available via a national CVMFS server infrastructure. This takes place 22 Nov 2022. If you would like more information, please visit this ARDC website. 

• COMBINE Symposium 2022 is creeping up [28/11/2022]! Check out our guests for the event - featuring Torsten Seemann, Shila Ghazanfar, Natalie Twine, Milicia Ng and Tony Papenfuss
• Register for COMBINE here: https://www.abacbs.org/registration#!event-register/2022/11/28/abacbs-2022
• Please contact symposium@combine.org.au for any questions.