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Oxford Nanopore workshop — UTAS, Thursday 5 November
by Nicholas Blackburn 14 Oct '26

14 Oct '26

Hi all, Please see flyer attached. We're hosting Oxford Nanopore Technologies for a free, in-person bioinformatics workshop at UTAS in November. It's a hands-on day focused on getting more out of nanopore sequencing data using the EPI2ME desktop application and its analysis workflows. Date: Thursday 5 November 2026 Time: 9:30 am – 4:30 pm Venue: The Forest Room, 2038 (Level 2), 83 Melville Street, Hobart Nanopore experts will introduce us to: * Nanopore data and EPI2ME * EPI2ME metagenomics workflow * EPI2ME human variation workflow The two hands-on sessions cover metagenomics and human variant calling, so it should suit anyone working with (or considering) long-read data. Places are limited. Register here: https://nanoporetech.swoogo.com/ONT_BioIT_WOrkshop_TAS/begin Please forward to anyone in your group who might be interested. Regards, Nick Dr Nicholas Blackburn Senior Research Fellow – Computational Genomics Neurogenomics Group Lead Menzies Institute for Medical Research University of Tasmania +61 3 6226 4244<tel:+61362264244> msresearchflagship.org.au<https://msresearchflagship.org.au/> menzies.utas.edu.au [A red and black logo Description automatically generated] This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Registration is up and ready for Phylomania 2026
by Michael Charleston 06 Oct '26

06 Oct '26

Please go to http://www.maths.utas.edu.au/phylomania/phylomania2026.html to register! And pay! 🙂 Michael Charleston [cid:3c7d6a12-4dcd-4164-969c-efcbe716b3eb] Mathematical Biology Group Professor in Bioinformatics Coordinator, Dean's Summer Research Programme School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Fwd: Same-day RNA-Seq: Real-world experiences with Illumina Rapid RNA Prep
by Michael Charleston 10 Sep '26

10 Sep '26

This might be of interest! School of Natural Sciences University of Tasmania Begin forwarded message: From: Illumina <apac(a)illumina.com> Date: 10 September 2026 at 14:23:10 GMT+10 To: Michael Charleston <michael.charleston(a)utas.edu.au> Subject: Same-day RNA-Seq: Real-world experiences with Illumina Rapid RNA Prep [illumina]<https://url.au.m.mimecastprotect.com/s/sV2BCWLJ2zf6wOBOgF6fkkionyke?domain=…> VIEW IN BROWSER<https://url.au.m.mimecastprotect.com/s/ziTmCk8vzVfk39Q96h3inniGC2tB?domain=…> [Faster workflows. Flexible application. Trusted Illumina performance.]<https://url.au.m.mimecastprotect.com/s/jR-7CXLK3Af472Y2yTVhLLiWdr-P?domain=…> From RNA to sequencing-ready libraries in as little as 2 hours Just launched, Illumina Rapid RNA Prep is the fastest and easiest RNA library prep Research workflow in the Illumina portfolio - designed to minimize hands-on time, standardize mRNA, total RNA, and targeted RNA-Seq through a core workflow, and enable same-day sequencing without compromising performance. In this webinar, Illumina experts are joined by early-access users who will share real-world data, workflow insights, and practical considerations from working labs. Date: 23rd September 2026, Wednesday Time: 09:30am - 10:30am (New Delhi) 11:00am – 12:00pm (Bangkok/ Jakarta) 12:00pm – 1:00pm (Singapore/ Kuala Lumpur) 01:00pm – 2:00pm (Tokyo/ Seoul) 3:00pm – 4:00pm (Melbourne) 5:00pm – 6:00pm (Auckland) Hear directly from early-access users: [speakerPhoto_OscarTorres] Oscar Enrique Torres, PhD Research Fellow, Great Ormond Street Institute of Child Health University College London (UCL), UK Oscar Enrique Torres, PhD (Great Ormond Street Institute of Child Health, UK) presents a rapid hybridization capture workflow for targeted metagenomics of respiratory infections and how streamlined RNA-Seq workflows support application-driven research. [speakerPhoto_ThomasBrabbs] Thomas Brabbs, PhD Senior Scientist, Technical Genomics Group, Earlham Institute, UK Thomas Brabbs, PhD (Earlham Institute, UK) discusses evaluating Rapid RNA Prep for low-cost transcriptomics, with a focus on workflow efficiency, turnaround time, and fit within real lab schedules. [speakerPhoto_MichaelAbdo] Michael Abdo, PhD Business Unit Lead, Strategic Growth APAC - Microbiology, Infectious Disease & Agrigenomics, Illumina Michael Abdo, PhD (Illumina) updates about Illumina Rapid RNA Prep- a new, streamlined RNA library prep workflow designed to support mRNA, total RNA, and targeted RNA-Seq through a single, unified approach. What you will learn: * How the Rapid RNA workflow is designed to enable same-day sequencing through reduced steps and hands-on time * How the workflow fits into established RNA-Seq pipelines and supports faster turnaround in routine research * Real-world insights from early-access users on workflow efficiency and practical performance considerations Register Now<https://url.au.m.mimecastprotect.com/s/jR-7CXLK3Af472Y2yTVhLLiWdr-P?domain=…> For Research Use Only. Not for use in diagnostic procedures (except as specifically noted). © 2026 Illumina, Inc. All rights reserved. All trademarks are the property of Illumina, Inc. or their respective owners. For specific trademark information, see www.illumina.com/company/legal.html<https://url.au.m.mimecastprotect.com/s/feQ6CYWL4BsDoMxMJT9iJJix3i80?domain=…>. [Twitter]<https://url.au.m.mimecastprotect.com/s/HvVfC1WZ5zs6w3Y3DFYtppiVLWs0?domain=…> [Facebook] <https://url.au.m.mimecastprotect.com/s/g2vRC3Q870UXYqQqJHYCZZiQSZ5m?domain=…> [Instagram] <https://url.au.m.mimecastprotect.com/s/IkZVC5QZjEUMYEGEQh4HqqikldC6?domain=…> [LinkedIn] <https://url.au.m.mimecastprotect.com/s/oP8nC71Zl7fzjlklxCrS33ioHce7?domain=…> Sent by Illumina Australia Level 3, 535 Elizabeth Street | Melbourne VIC 3000 www.illumina.com<https://url.au.m.mimecastprotect.com/s/VTU_C91Zn7fzVQBQgC2UNNiqk-La?domain=…> Unsubscribe<https://url.au.m.mimecastprotect.com/s/cLTQCgZovVCq5929xc8fkki4LvOm?domain=…> Update Profile<https://url.au.m.mimecastprotect.com/s/kZhxCjZryVCY18q8MTzhAAim1d2E?domain=…> Update Profile<https://url.au.m.mimecastprotect.com/s/cLTQCgZovVCq5929xc8fkki4LvOm?domain=…> [https://prdt.illumina.com/r/551052/1/1622036960/open/1] This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Fwd: Help sharing long reads workshop with your networks
by Michael Charleston 09 Sep '26

09 Sep '26

School of Natural Sciences University of Tasmania Begin forwarded message: From: Giorgia Mori <giorgia(a)biocommons.org.au> Date: 9 September 2026 at 16:19:59 GMT+10 To: National Bioinformatics Training Cooperative <cooperative(a)biocommons.org.au> Subject: Help sharing long reads workshop with your networks Hello everyone, I’m reaching out to ask for your support in helping us spread the word about the upcoming Australian BioCommons 'Long read sequencing for bacterial genomics' workshop. If you’re able to share, you’ll find suggested promotional text and links below in this email to make this easy. Thank you so much in advance, Cheers, Giorgia ------- TEXT AND LINKS FOR SHARING ------ Australian BioCommons Workshop: Long read sequencing for bacterial genomics Short reads leaving gaps in your bacterial genome assemblies? Short read sequencing has long been the default for genomics, but restricted read lengths (150–300 bp) make it difficult to resolve large repetitive elements and separate mobile plasmids from main chromosomes. Long read sequencing addresses these challenges, but working with multi-kilobase data comes with its own unique analytical workflow requirements. Dr Magdalena Antczak (QCIF) and Dr Michael Geaghan (Sydney Informatics Hub, University of Sydney) will join Australian BioCommons to guide you through the fundamentals of long read sequencing, perform quality control, construct de novo bacterial genome assemblies from ONT data, and annotate genomes to identify antimicrobial resistance genes. This workshop is free but you must apply to join. 7-8 October 2026 (applications close Tuesday 29 September 2026) More information and applications: https://www.biocommons.org.au/events/long-reads-2026<https://url.au.m.mimecastprotect.com/s/xOZ7Cr8DKNfr3R5oyI7f66i4x8m3?domain=…> Share the event on LinkedIn<https://url.au.m.mimecastprotect.com/s/SzWpCvl0O7SE0nDKJfXhlliQNNEw?domain=…>! -------------- -- Giorgia Mori, PhD (she/her) BioCloud Training & Communication Officer Australian BioCommons The University of Melbourne M: +61 (0) 466344648 W: biocommons.org.au<https://url.au.m.mimecastprotect.com/s/b3sPCwVLP8HvZED95f9iGGiJ3FXt?domain=…> My position is funded by Bioplatforms Australia and hosted by The University of Melbourne. I acknowledge the Traditional Owners of the lands upon which I work and pay my respects to their Elders, both past and present. I work flexibly so this email may arrive out of hours - please respond at a time that suits you. [https://lh7-qw.googleusercontent.com/docsz/AD_4nXcs3_U3fiAeBJbLcwk6ZuXeePon…] To unsubscribe from this group and stop receiving emails from it, send an email to cooperative+unsubscribe(a)biocommons.org.au<mailto:cooperative+unsubscribe@biocommons.org.au>. This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Phylomania 2026 -- Save the Date!
by Michael Charleston 30 Jul '26

30 Jul '26

Dear Phylomaniacs, We are delighted to announce that Phylomania 2026 - the 18th Annual Theoretical Phylogenetics Conference at the University of Tasmania - will be going ahead again this year. Dates are set for the 25th – 27th of November. The conference will be in hybrid mode: attend in person in Hobart if you can, but we’re happy for (some) online talks, and we will attempt to schedule sessions at times that are somewhat less obnoxious for folks in different time-zones. We will have the registration page up and running soon! As usual, although the conference title is phylo-centric, we welcome talks on any mathematical, theoretical or applied aspects of evolutionary biology. We hope to see you in November! Please feel free to share this announcement with your friends & colleagues 🙂 Best wishes, Michael Charleston [cid:c2b10fe2-ac2a-4152-94f4-7d015df63876] Phylomania #18 Mathematical Biology Group Professor in Bioinformatics Coordinator, Dean's Summer Research Programme School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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FW: Request for help with Cutadapt
by Rebecca Jones 26 Mar '26

26 Mar '26

Hi George, Somebody on this bioinformatics list might be able to help you? Cheers Beck From: George Hamaty <george.hamaty(a)utas.edu.au> Sent: Wednesday, 25 March 2026 4:47 PM To: Floriaan Devloo-delva <floriaan.devloodelva(a)utas.edu.au>; Jim Weller <jim.weller(a)utas.edu.au>; Rebecca Jones <rebecca.jones(a)utas.edu.au>; Christopher Burridge <chris.burridge(a)utas.edu.au>; Narissa Bax <narissa.bax(a)utas.edu.au> Subject: Request for help with Cutadapt Hello all, My name is George Hamaty and I'm a student doing a Research Project in the unit KAA308. My project involves processing raw sequence data from eDNA samples collected in the Gascoyne Region in WA, and my supervisor, Dr Cindy Bessey, is based in Perth at CSIRO. I have emailed to ask for assistance with the nf.core/ampliseq pipeline. Some problems have occurred while trying to run Cutadapt on single-end reads, and I've unfortunately become quite stuck. Please let me know if this would be possible, or if you have any recommendations about who to speak to for help. Cheers, George Hamaty 596077 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Fw: Job opportunity for sharing - AI in Research Training Lead
by Michael Charleston 15 Oct '25

15 Oct '25

Dear all, Please find below an opportunity to work with a really wonderful group of people! I've worked with them from here at UTAS for many years and I have always found Australian BioCommons full of passionate, smart, awesome folk. Also it sounds like a really interesting challenge. 😄 Michael Charleston [cid:cbae9b96-957e-4860-8702-3d0db5b359db] Funded PhD project available in machine learning<https://www.utas.edu.au/research/degrees/available-projects/projects/mathem…> Phylomania #17: November 19-21, 2025<http://www.maths.utas.edu.au/phylomania/phylomania2025.html> Specialty Chief Editor in Frontiers in Ecology and Evolution - Coevolution Mathematical Biology Group Professor in Bioinformatics Coordinator, Dean's Summer Research Programme School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 ________________________________ From: Melissa Burke <melissa(a)biocommons.org.au> Sent: Wednesday, 15 October 2025 3:24 PM To: rachel.mckay(a)qcif.edu.au <rachel.mckay(a)qcif.edu.au>; Abdullah Shaikh <Abdullah.Shaikh(a)anu.edu.au>; Danny Meloncelli <danny.meloncelli(a)qcif.edu.au>; Selene Fernandez <s.fernandez_valverde(a)unsw.edu.au>; Laura Perlaza-Jimenez <laura.perlaza-jimenez(a)monash.edu>; Mariana Barnes <mariana.barnes(a)menzies.edu.au>; Capelli, Ludovic (Pawsey, Kensington WA) <Ludovic.Capelli(a)csiro.au>; Christina Hall <christina(a)biocommons.org.au>; Sarah Beecroft <sarah.beecroft(a)pawsey.org.au>; Michael Charleston <michael.charleston(a)utas.edu.au>; Jade Clarke <j44.clarke(a)hdr.qut.edu.au>; Emmal Gail <emma.gail(a)unimelb.edu.au>; Joel Bathe <joel.bathe(a)sahmri.com>; Georgina Samaha <georgina.samaha(a)sydney.edu.au>; Beecroft, Sarah (Pawsey, Kensington WA) <Sarah.Beecroft(a)csiro.au>; Melissa Burke <melissa(a)biocommons.org.au>; Giorgia Mori <giorgia(a)biocommons.org.au>; Sara King <Sara.King(a)aarnet.edu.au>; Kathryn Unsworth <kathryn.unsworth(a)ardc.edu.au>; Liz Stokes <liz.stokes(a)ardc.edu.au>; Ellen Lyrtzis <ellen.lyrtzis(a)ardc.edu.au>; Katherine Champ <k.champ(a)garvan.org.au>; Darya Vanichkina <darya.vanichkina(a)sydney.edu.au>; Amy Nisselle <amy.nisselle(a)mcri.edu.au> Subject: Job opportunity for sharing - AI in Research Training Lead Good afternoon training community, Australian BioCommons and the Sydney Informatics Hub, University of Sydney have just opened a new role for an AI in Research Training Lead. This role will collaboratively design and deliver a national training program to equip life science researchers with practical knowledge and hands-on skills on AI methods for text and code generation, data analysis, and literature synthesis and more. As people with a passion for training we'd love your help spreading the word about this. Could you please: * Reshare this LinkedIn post<https://url.au.m.mimecastprotect.com/s/tHqtC4QZgDUJOgvOECOfxu4gVqZ?domain=l…> * Post about it in your local Slack groups etc (suggested text below). Please feel free to reach out to me or Georgie Samaha (CC'd here) if you need more context or have questions. Thank you! Melissa Text for Slack etc Join Australian BioCommons and the Sydney Informatics Hub, University of Sydney as the AI in Research Training Lead! This collaborative role will equip life science researchers with practical knowledge and hands-on skills on AI methods for text and code generation, data analysis, and literature synthesis and more. * Work at the intersection of AI, training pedagogy, and life science research * Collaboratively design and deliver a national program on the effective and responsible use of AI tools * Salary: HEO8 $126,065 p.a. + 17% super ⭐Apply here before 26 Oct<https://url.au.m.mimecastprotect.com/s/0A3KC5QZjEU07ED73sOhOukOQ69?domain=u…>⭐ --- Melissa Burke, PhD (she/her) Training Manager Australian BioCommons The University of Queensland M: +61 (0)460 641 328 W: biocommons.org.au<https://url.au.m.mimecastprotect.com/s/1lxnC6X1k7CovzBv7Smi4u5nE19?domain=b…> My position is funded by Bioplatforms Australia and hosted at QCIF and RCC at The University of Queensland I acknowledge the Traditional Owners of the lands upon which I work and pay my respects to their Elders, both past and present. I work flexibly so this email may arrive out of hours - please respond at a time that suits you. [https://ci3.googleusercontent.com/mail-sig/AIorK4wXnPQsWbzYy4ZWIaMp3rIAQhvK…] This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Phylomania #17
by Michael Charleston 11 Mar '25

11 Mar '25

Dear previous attendees, friends of Phylomania etc., We are tentatively putting November 19th - 21st in our diaries for Phylomania 2025. Please do let us know if there's some big clash that we haven't thought of, so we can firm up the date and get ready (ahead of time!). And let us know if you'd love to come but that date is dreadful because of X. AND let us know if you'd like to come along and the date is good! Best wishes, Michael, Jeremy, Barbara and Peter Michael Charleston [cid:e66ba413-19c0-4daf-a4c5-7e9fca3d4a5e] Funded PhD project available in machine learning<https://www.utas.edu.au/research/degrees/available-projects/projects/mathem…> Tentative date for Phylomania #17: November 19-21, 2025 Specialty Chief Editor in Frontiers in Ecology and Evolution - Coevolution Mathematical Biology Group Professor in Bioinformatics School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Postdoc position in WA
by Nicholas Blackburn 13 Jan '25

13 Jan '25

Hi all, Just sharing information from a colleague about a potential bioinformatics postdoc 1 year opportunity. Info below. Regards, Nick Postdoctoral Research Associate – Bioinformatics (Evolutionary/Conservation) Employer: University of Western Australia Duration: 1yr Brief Position Description: We are looking at the evolutionary genomics of fragmented populations of lizards in relation to phenotype, habitat change and population structure. We have whole genome sequences for ~300 lizards across a spread of discrete populations and we are looking for a bioinformatician with skill strengths in estimating mutation load (SnpEff). The successful candidate will work under the supervision of Dr Natasha LeBas, Prof Leigh Simmons (Centre for Evolutionary Biology) and Professor Dave Edwards (Applied Bioinformatics Group). Remote working may be considered. We are keen to fill and commence soon, please contact for further information. Bioinformaticians working in other disciplines welcome to apply. Key Responsibilities: Estimate genomic parameters of interest (mutation load, GWAS, GEA) from whole genome sequences and prepare data for analysis, analyse data and contribute to manuscript preparation. Contact name: Natasha LeBas Contact email: natasha.lebas(a)uwa.edu.au<mailto:natasha.lebas@uwa.edu.au> This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Phylomania 2024 - last chance!
by Michael Charleston 15 Nov '24

15 Nov '24

Please ignore this message if you're not coming - but if you have been putting off registering for Phylomania #16, please go to the registration page asap! To prove you are a human, you have to solve the puzzle of locating where in this email is the relevant link 😉 Best wishes, MC Michael Charleston [cid:070bd014-fdc8-4570-93c6-77ae68c464d8] Phylomania 2024: November 27-29<http://www.maths.utas.edu.au/phylomania/phylomania2024.html> Funded PhD project available in machine learning<https://www.utas.edu.au/research/degrees/available-projects/projects/mathem…> Specialty Chief Editor in Frontiers in Ecology and Evolution - Coevolution Mathematical Biology Group Professor in Bioinformatics School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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