The OceanOmics Centre is hiring! Research technician positions available

We are recruiting two new positions for the Minderoo OceanOmics Centre at UWA: a Marine Genomics Research Technician and an eDNA Research Technician / Scientific Officer. These are both full-time two-year positions (with likely opportunities for extension), and applications close 11:55 PM AWST on Sunday, 6 August 2023. Please see the link below to find out more. Informal enquiries are also welcome - please contact Rich Edwards.

We are seeking two new members of the technical support team for the OceanOmics Centre, particularly with respect to all aspects of DNA sequencing (sample extraction, library preparation and setting up sequencing runs). You’ll get to play with the latest sequencing technologies, including Illumina NovaSeq/NextSeq, PacBio Sequel/Revio, and ONT PromethION P24. One role will focus on marine vertebrate reference genomes, and associated techniques (e.g. high molecular weight DNA extract, and HiC proximity ligation). The other role has an environmental DNA (eDNA) focus, with more emphasis on Illumina sequencing and liquid handling robots.

About the team

The Minderoo OceanOmics Centre at UWA is a partnership between UWA and Minderoo Foundation to undertake research and development under the direction of Minderoo’s OceanOmics Program. Part of Minderoo’s Flourishing Oceans initiative, this ambitious program aims to revolutionise ocean conservation through application of novel environmental DNA technologies. This includes the development of innovative laboratory and computational approaches to optimise and scale collection, processing and analysis of environmental DNA (eDNA) from marine environments, as well as generate a comprehensive reference library of marine vertebrate genome data. All data produced as part of the OceanOmics program will be subject to rigorous QA/QC and released publicly through open access repositories.

Located in the Bayliss Building on the UWA Crawley Campus, the OceanOmics Centre combines a joint Ocean Genomes Laboratory, an OceanOmics/eDNA Laboratory, and Computational Biology Services. Equipped with the latest high-throughput sequencing technology, liquid handling robotics, flow cytometry, and computational infrastructure, the centre is staffed by a collaborative team of scientists (from both Minderoo and UWA) and UWA technical staff. Core centre operations support the Minderoo OceanOmics Program, under the direction of senior Minderoo employees.

UWA staff, including this postholder, are part of the UWA Oceans Institute, a multidisciplinary research institution with core offices in the nearby Indian Ocean Marine Research Centre building, and liaise closely with Minderoo employees for day-to-day operations.

For more details, and to apply, visit the UWA jobs site: https://external.jobs.uwa.edu.au/cw/en/job/512661 and https://external.jobs.uwa.edu.au/cw/en/job/514981.

We are also recruiting students for three Pawsey student internships.

Three Pawsey Internship projects available for the Ocean Genomes Project

We have three Pawsey student internships available this summer with the Ocean Genomes Laboratory in the Minderoo OceanOmics Centre at UWA. Closing date: 07 August, 2023 at 17:00 AWST (Perth time). This is a 10-week, paid program open to exceptional undergrad (2nd/3rd year), Honours, Master’s and PhD students. Apply at the CSIRO Application page. Please get in touch if you want to know more and/or are interested in a student research project in the lab.

Optimising workflows for whole genome assembly for marine vertebrates (Project #04)

The biodiversity of marine vertebrates is critical for the health of our ocean’s ecosystem, but is under immediate threat from climate change, pollution, overfishing and habitat destruction. To advance our understanding of how best to protect and sustain our ocean life, global efforts are underway (such as the Vertebrate Genome Project; VGP) to establish a complete library of high-quality reference genomes for all ~22,000 marine vertebrates.

Reference genomes are pivotal not only for answering fundamental questions in marine biology and evolution, but also for guiding the conservation of species most at risk within our changing oceans, and for accurately monitoring biodiversity.

This project utilizes data generated in-house, either by Illumina short-read or PacBio high-fidelity long-read sequencing of Australian marine vertebrate species. The primary objective is to optimize analysis workflows on Pawsey, encompassing the entire life cycle of the data from its raw format to the ultimate outcome of a high-quality assembled genome. We have data across a diverse range of species covering small to large genome sizes.

A containerised Pawsey workflow for Diploidocus (Project #10)

Bioinformatics in general, and genomics specifically, is replete with complex workflows that do not translate easily to HPC. Frequently, genomics pipelines will incorporate many different tools and/or in-built functions with very different computational requirements in terms of multithreading, memory requirements and IO pressures. The Diploidocus genome curation pipeline exemplifies this problem with some lengthy single-processor steps building on data produced by highly parallelised tools, such as minimap2. As well as adapting a specific mission-critical tool, this project will help identify and establish some general principles for optimising genomics code/workflows for running on Setonix.

Diploidocus is a published genome curation and clean-up tool that utilises several different underlying bioinformatics tools and in-built algorithms. Different steps (and tools) in the pipeline have markedly different CPU, IO and memory requirements, including some lengthy non-parallelised portions. This makes it hard to run efficiently on HPC without wasting resource allocation and/or failing to take advantage of parallelisation when available.

The expected outcome of this project is a Nextflow workflow for the deployment of the Diploidocus pipeline on HPC. This will (a) increase in-house efficiency of HPC usage, and (b) make Diploidocus more attractive as a tool to other research groups.

A containerised Pawsey workflow high throughput phylogenomics (Project #14)

This project aims to produce a robust and efficient phylogenomics workflow for whole genome sequencing data.

One important application of genome assemblies is to test and improve the taxonomic classification of species using large-scale genome-wide phylogenetics, known as phylogenomics. There is a previously developed Snakemake workflow for the rapid generation of phylogenomic trees from low- to mid-coverage whole genome shotgun sequencing data. This pipeline (1) creates multiple rapid draft assemblies; (2) identifies an optimal set of orthologous genes per species using BUSCO and BUSCOMP; (3) generates a multiple sequence alignment per gene; (4) generates a phylogenetic tree per gene; and (5) generates a consensus tree from all the individual gene trees.

There is now a requirement to (1) update the pipeline to be optimised for the high-coverage draft and reference genomes created by the Ocean Genomes Project, and (2) convert this pipeline from PBS/Snakemake to SLURM/Nextflow in-line with other genomics workflows being developed at the Minderoo OceanOmics Centre at UWA.

This project will adapt the wgs2tree workflow to optionally start from a set of existing genome assemblies and BUSCO orthologue annotations and implement a Nextflow/SLURM workflow optimised to run efficiently on Pawsey.

The Minderoo OceanOmics Centre at UWA is hiring - lab manager position available

We are recruiting a new lab manager position for the Minderoo OceanOmics Centre at UWA. This is a full-time three-year position, available at Level 6 or 7, depending on experience. Applications close 11:55 PM AWST on Thursday, 13 July 2023. Please see the link below to find out more. Informal enquiries are also welcome - please contact Rich Edwards.

We are seeking a detail-oriented professional who possesses excellent organisational and managerial skills, ideally with a strong scientific background. Your operations experience will ensure smooth functioning of the laboratory, promoting a safe, productive and efficient working environment. As lab manager, you will work closely with the Lead Academic of the OceanOmics Centre to optimise operations to support the goals of Minderoo’s OceanOmics Program.

About the team

The Minderoo OceanOmics Centre at UWA is a partnership between UWA and Minderoo Foundation to undertake research and development under the direction of Minderoo’s OceanOmics Program. Part of Minderoo’s Flourishing Oceans initiative, this ambitious program aims to revolutionise ocean conservation through application of novel environmental DNA technologies. This includes the development of innovative laboratory and computational approaches to optimise and scale collection, processing and analysis of environmental DNA (eDNA) from marine environments, as well as generate a comprehensive reference library of marine vertebrate genome data. All data produced as part of the OceanOmics program will be subject to rigorous QA/QC and released publicly through open access repositories.

Located in the Bayliss Building on the UWA Crawley Campus, the OceanOmics Centre combines a joint Ocean Genomes Laboratory, an OceanOmics/eDNA Laboratory, and Computational Biology Services. Equipped with the latest high-throughput sequencing technology, liquid handling robotics, flow cytometry, and computational infrastructure, the centre is staffed by a collaborative team of scientists (from both Minderoo and UWA) and UWA technical staff. Core centre operations support the Minderoo OceanOmics Program, under the direction of senior Minderoo employees. UWA staff, including this postholder, are part of the UWA Oceans Institute, a multidisciplinary research institution with core offices in the nearby Indian Ocean Marine Research Centre building, and liaise closely with Minderoo employees for day-to-day operations.

For more details, and to apply, visit the UWA jobs site: https://external.jobs.uwa.edu.au/cw/en/job/514000.

Watch this space for some further opportunities coming soon: two laboratory research technicians, and three Pawsey student internships.

Minderoo OceanOmics Centre at UWA Grand Opening

The Grand Opening of the Minderoo OceanOmics Centre at UWA is only a day away! Join the launch of the Centre online from 4:40 to learn more about the inspiration and the vision behind this project, which aims to harness environmental DNA and genomics for marine conservation: https://lnkd.in/gCP4GAhs

You can find out a bit more about the Minderoo OceanOmics Centre at UWA here: https://lnkd.in/gmXKjXNu

And the broader Minderoo OceanOmics program here: https://lnkd.in/gtKHSk7g

Or get in touch if you want to know more!

The Ocean Genomes Lab is hiring - Bioinformatics and Sequencing technicians wanted!

Adding to the recently advertised Sequencing technician posts (closing 27 October), we are now pleased to advertise two bioinformatics research assistant positions to support our creation of marine vertebrate reference genome library. If you have experience with genome assembly or bioinformatics workflows, and are passionate about saving marine biodiversity, come and join us!

Two positions are available at Level 5 or 6, depending on your experience. Both roles will be providing bioinformatics support for our marine vertebrate reference genome project. You’ll get to play with data from the latest sequencing toys, including Illumina NovaSeq 6000, NextSeq 2000 and iSeq 100, the PacBio Sequel IIe, and ONT (probably PromethION and MinION).

Job roles will include developing and applying genome assembly workflows, data curation and QC, data sharing, and development/benchmarking of comparative genomics and genome assembly curation tools. If you have experience or passion for integrating bioinformatics workflows with Laboratory Information Management Systems and/or Electronic Laboratory Notebooks, we’d also love to hear to from you. SQL database skills would not go amiss too.

We’re a new team with lots to do, so there is plenty of scope to make the position your own and play to your strengths.

The closing date for applications is 11:55 PM AWST on Thursday 10 November 2022.

To learn more about these opportunities, please click here or contact Rich Edwards at rich.edwards@uwa.edu.au.

ABOUT THE TEAM

The Minderoo OceanOmics Centre at UWA combines a joint Ocean Genomes Laboratory, an OceanOmics Laboratory, and Computational Biology Services.

Equipped with the latest high-throughput sequencing technology and in collaboration with global partners, the Ocean Genomes Laboratory will generate a comprehensive library of high quality marine vertebrate reference genome assemblies. All such reference genome data will be subject to rigorous QA/QC and all assemblies will be released publicly with open access.

The Ocean Genomes Laboratory will undertake research and development under the direction of Minderoo’s ambitious OceanOmics Program which has the goal of revolutionising ocean conservation through novel marine sampling and genomics approaches and scaling these to significantly advance our knowledge of marine life. The Ocean Genomes Laboratory and Computational Biology Services will include state of the art infrastructure including sample and eDNA preparation areas, flow cytometry, single cell sequencing equipment and the latest bioinformatics and computational biology tools.

The Ocean Genomes Laboratory is hiring!

The Minderoo OceanOmics Centre at UWA Ocean Genomes Laboratory is now hiring our technical team to support high throughput DNA sequencing and genome assembly. We currently have three "wet" lab positions going: a Sequencing Specialist Scientific Officer, and two Sequencing Technician positions. Both roles will be providing technical support in the lab, particularly with respect to all aspects of DNA sequencing (sample extraction, library preparation and setting up sequencing runs). You'll get to play with the latest sequencing toys, including Illumina NovaSeq 6000, NextSeq 2000 and iSeq 100, the PacBio Sequel IIe, and ONT (probably PromethION and MinION).

The closing date for applications is 11:55 PM AWST on Thursday 27 October 2022.

To learn more about these opportunities, please click on the links above or contact Rich Edwards at rich.edwards@uwa.edu.au. We will also be advertising some bioinformatics positions soon.

About the team

The Minderoo OceanOmics Centre at UWA combines a joint Ocean Genomes Laboratory, an OceanOmics Laboratory, and Computational Biology Services.

Equipped with the latest high-throughput sequencing technology and in collaboration with global partners, the Ocean Genomes Laboratory will generate a comprehensive library of high quality marine vertebrate reference genome assemblies. All such reference genome data will be subject to rigorous QA/QC and all assemblies will be released publicly with open access.

The Ocean Genomes Laboratory will undertake research and development under the direction of Minderoo’s ambitious OceanOmics Program which has the goal of revolutionising ocean conservation through novel marine sampling and genomics approaches and scaling these to significantly advance our knowledge of marine life. The Ocean Genomes Laboratory and Computational Biology Services will include state of the art infrastructure including sample and eDNA preparation areas, flow cytometry, single cell sequencing equipment and the latest bioinformatics and computational biology tools.

Senior Postdoc wanted for UWA Ocean Genomes Lab! (Closing soon)

The new Ocean Genomes Laboratory (part of the Minderoo OceanOmics Centre at the UWA Oceans Institute) is hiring a Level B postdoc in marine genomics. (Three-year fixed term full time role, or flexible working equivalent.)

This is a rare opportunity to work as part of a collaborative team in a high-profile state of the art genomics research facility dedicated to studying marine vertebrates. You should have a PhD in bioinformatics, computational biology, molecular genetics or genomics, plus an interest in marine vertebrates and postdoctoral experience in high throughput DNA sequencing and whole genome assembly. The lab is new and there is plenty of scope to shape its direction beyond the core mission creating a marine vertebrate reference genome library as part of the Vertebrate Genome Project. You will also have an important role in helping to supervise the lab staff and research team.

Closing date: 11:55pm AWST, Friday 12 August 2022

Please see the UWA job advert for more details.

About the team

The Minderoo OceanOmics Centre at UWA combines a joint Ocean Genomes Laboratory, an OceanOmics Laboratory, and a Computational Biology Program.

Equipped with the latest high-throughput sequencing technology, and in collaboration with global partners, the Ocean Genomes Laboratory will generate a comprehensive library of high-quality marine vertebrate reference genome assemblies. All reference genome data will be subject to rigorous QA/QC and all assemblies will be released publicly through open access.

The OceanOmics Centre will be located in the Bayliss Building on the UWA Crawley Campus, OceanOmics staff sharing the building with research and teaching staff primarily from the UWA School of Molecular Sciences and interacting with staff in the UWA Oceans Institute in the nearby IOMRC building.

About the opportunity

As a Research Fellow you will join a research group committed to applying modern molecular biological methods to marine research.

Using modern genomic approaches, you will undertake research on marine vertebrates, focussed on the production, QC and assembly of high-quality reference genome data. You will participate in the entire workflow from sample collection and processing, generating genomic sequence data in the laboratory using multiple modern genome sequencing technologies, with a focus on data processing, assembly, curation, analysis and dissemination.

In this unique role you will also be supported to develop your leadership skills. Working closely with the Centre’s UWA Principal Research Fellow, junior postdoctoral academics, the Centre’s Laboratory Manager, and diverse researchers from Minderoo Foundation you will contribute to decision making, oversee the work of technicians and PhD students and provide leadership in modern high-quality genome assembly production and publication.