bioinformatics-list

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167 discussions

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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It's Phylomania Month!
by Michael Charleston 01 Nov '24

01 Nov '24

Forget the US Election (unless you have to vote there and haven't) — November is all about Phylomania. This is our 16th Season! If you haven't yet registered<http://www.maths.utas.edu.au/phylomania/phylomania2024.html> for our world famous conference on theoretical phylogenetics, there's still time! Face to face attendance is great, but if you can only register for online attendance, that's free! — So if your university is typical just now and tightening belts, you can always rock up from the comfort of your own home/office via Zoom. Join us, won't you? Oh — here's the conference page: http://www.maths.utas.edu.au/phylomania/phylomania2024.html (Don't be alarmed that it's only http, not https — registration and payments are secure.) Michael Charleston [cid:047c6aeb-4f47-4fd4-a4d5-15e209b6e666] 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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Postdoc position at the Menzies
by Bennet McComish 31 Oct '24

31 Oct '24

Hi all, I'm looking to recruit a postdoc to investigate the evolution of multiple sclerosis risk. The Postdoctoral Research Fellow will be involved in NHMRC and MS Australia funded research. This work uses population genomics to identify functional variation under selection at loci associated with multiple sclerosis risk, improving our understanding of the mechanisms underlying the disease. You will apply statistical and genomics expertise to develop pipelines to detect balancing selection in the major histocompatibility (MHC) region of the genome using large population datasets. This position will offer the opportunity for you to further develop leadership skills through planning and leading statistical genomics research and support the training and development of junior research staff and students. What we're looking for: + A PhD or equivalent in statistical genetics, genetic epidemiology, or a related field. + Experience in the analysis of genomic data including practical experience with the use of high performance computing for the analysis of genome sequence data, and ideally with a focus on analysing immune system genes in the MHC region. + Demonstrated skills in bioinformatics relevant programming languages such as python, R, or perl. + A good record of, and continuing commitment to, research that has achieved national recognition and made worthwhile contributions to the field of statistical genetics, demonstrated by a record of quality publications, presentations at conferences and preferably success in securing external competitive and other funding relative to career stage and opportunity. + A record of contributing to building and maintaining effective and productive links locally and nationally with the discipline, profession, industry (where relevant) and wider community. + Demonstrated ability to work autonomously, as well as to collaborate successfully with other researchers/clinicians and be able to prioritise tasks and meet deadlines. This is a full time, 1 year Fixed-Term position based in Hobart, Tasmania, with part-time hours considered for the right candidate. Details at: https://careers.utas.edu.au/cw/en/job/500426/postdoctoral-research-fellow-s… Applications close Monday, 25 November 2024, 11.55pm AEDT Please share with any potential candidates, and contact me for further information. Regards, Bennet Dr Bennet McComish Senior Research Fellow - Bioinformatics and Human Genetics Menzies Institute for Medical Research | University of Tasmania Private Bag 23, Hobart TAS 7000 +61 3 6226 4285 | bennet.mccomish(a)utas.edu.au<mailto:Bennet.McComish@utas.edu.au> I acknowledge and pay respect to the Tasmanian Aboriginal community as the traditional and original owners and continuing custodians of the land on which I work. 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 is coming!
by Michael Charleston 18 Oct '24

18 Oct '24

Don't forget to register and come to the SIXTEENTH annual Phylogenetics meeting held here in beautiful Hobart! Please spread the word 😄 Conference information, registration and payment page from here: http://www.maths.utas.edu.au/phylomania/phylomania2024.html Michael Charleston [cid:2c2f5484-04ea-4581-96d8-2518c031c102] 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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Genetic outlier analysis workshop - Sydney edition 4-5 July
by Michael Charleston 24 May '24

24 May '24

The Genetic Outlier Analysis workshop<https://url.au.m.mimecastprotect.com/s/uVJOCq7BJXt8q5rwjiXJrOd?domain=bioco…> will run 4-5 July 2024 at the UNSW, Kensington Campus. It will introduce the basics of genetic selection analysis, and step through the process of identifying signals of selection using participants' own data (or an example genomic dataset) using the outlier analysis method. The two-day workshop will be led by Dr Katarina Stuart from the University of Auckland, thanks to a grant from the Genetics Society of AustralAsia. It is fully-subsidised for Australian researchers and/or members of the Genetics Society of AustralAsia (subject to selection). Apply now<https://url.au.m.mimecastprotect.com/s/uVJOCq7BJXt8q5rwjiXJrOd?domain=bioco…> or read what previous participants have said<https://url.au.m.mimecastprotect.com/s/pClnCr8DKNf8gvjJli4HKcU?domain=bioco…> about the workshop. -- [https://ci3.googleusercontent.com/mail-sig/AIorK4zRFxnSsH5ylYQ8Tz5e6EKV45kV…] 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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The first Australian BioCommons workshop of 2024!
by Michael Charleston 17 Jan '24

17 Jan '24

Hello and welcome to 2024. Australian BioCommons has a number of exciting workshops planned for the year, the first of which is on the identification of genetic outliers, spread over two linked 5-hour online sessions. Here's the main page, which will allow you to register: https://www.biocommons.org.au/events/genetic-outlier<https://protect-au.mimecast.com/s/9kMmCvl0O7S71AyqVhQx2gF?domain=biocommons…> ... and here are a couple of relevant social media posts: https://twitter.com/AusBiocommons/status/1747059289611780383<https://protect-au.mimecast.com/s/tW2TCxnMQNt18xQDNIYqfXN?domain=twitter.com> https://www.linkedin.com/feed/update/urn:li:activity:7142700103013707778<https://protect-au.mimecast.com/s/aJ5fCyoNROTrDLyKVuRlMUV?domain=linkedin.c…> Enjoy, and share! Best wishes, Michael Charleston [cid:e1aa5815-487b-48c8-bbcd-a7617249f44d] Phylomania 2023: November 22-24<http://www.maths.utas.edu.au/phylomania/phylomania2023.html> 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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