- bioinformatics-list - lists2.utas.edu.au

FW: ANZIAM local seminar - Joshua Stevenson
by Jeremy Sumner 12 May '22

12 May '22

Please see below for details on phylogenetics talk by Joshua Stevenson (maths Phd candidate) occurring next week on zoom. Cheers Jeremy -----Original Appointment----- From: Courtney Quinn <courtney.quinn(a)utas.edu.au> Sent: Thursday, 12 May 2022 11:52 AM To: Courtney Quinn Cc: SNS-Maths-Academic; SNS-Maths-Postgrad; SNS-Physics-Academic; SNS-Physics-Postgrad Subject: ANZIAM local seminar - Joshua Stevenson When: Thursday, 19 May 2022 3:00 PM-4:00 PM (UTC+10:00) Hobart. Where: https://utas.zoom.us/j/88961934178 Hello everyone, Our second talk of the ANZIAM* local seminar series will be held via Zoom on Thursday 19 May at 3:00pm. Joshua Stevenson, PhD student of Jeremy Sumner and Venta Terauds, is an invited speaker to the 2022 Student Symposium in Combinatorics and has kindly offered to present his talk to us. His title and abstract can be found below. Title: Algebraic Models of Circular Genome Rearrangement Abstract: Phylogenetics is the study of evolutionary relationships between present-day organisms. Evolution can occur via a number of mechanisms, and one such mechanism is the application of large-scale genome rearrangement events, in which sections of the genome are broken apart and reattached in a different order or orientation. By considering the possible combinations of rearrangements that could convert one genome into another, we can identify how closely related the organisms are. I will give an overview of genome rearrangement modelling as an applied combinatorial problem, and then present our algebraic framework for modelling genomes. I will discuss some of my recent work in characterising `biologically reasonable' rearrangements and determining how many of these there are for a given number of regions. *ANZIAM (Australia and New Zealand Industrial and Applied Mathematics) is a division of the Australian Mathematical Society As usual, please get in touch if you would like to present in our seminar series. Kind regards, Courtney Courtney Quinn is inviting you to a scheduled Zoom meeting. Join Zoom Meeting<https://utas.zoom.us/j/88961934178> Meeting URL: https://utas.zoom.us/j/88961934178 Meeting ID: 889 6193 4178 Join by Telephone For higher quality, dial a number based on your current location. Dial: Australia: +61 3 7018 2005 H.323/SIP: 88961934178(a)zoom.aarnet.edu.au<mailto:88961934178@zoom.aarnet.edu.au> [https://zoom.us/account/branding/p/858d91c4-ab9b-4bae-b88b-3c72cf4ae2a3.png]<https://utas.zoom.us/j/88961934178> 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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Introduction to BIoinformatics: KMA712
by Michael Charleston 03 Feb '22

03 Feb '22

Dear all, I'm pleased to say that this year the (Introduction to) Bioinformatics unit, KMA712, will be running again after a hiatus last year. It is a full semester unit that will have four hours face to face (ideally) or zoom classes (if necessary) each week in Semester 1. If you, or someone you know, might be interested in learning about * how to use the command-line effectively, * how to use remote computing, * molecular sequence analysis (alignment, motif-finding, BLAST) * phylogenetics, * genomics, * genome assembly, * RNA expression analysis, * and a range of algorithms and statistics used in bioinformatics please check out https://www.utas.edu.au/courses/cse/units/kma712-bioinformatics for more information. Best wishes Mike Michael Charleston [cid:7cad241b-a496-4914-aa8b-df96269d3c85] 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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AusBioCommons Workshop
by Michael Charleston 27 Jan '22

27 Jan '22

Dear all, Australian BioCommons is running the following online workshop: please register at the link below if you are interested, and let me know if you do, or if have any queries. Qiime (pronounced "chime") is a standard tool for analysis of microbiome data so this could be very handy! Cheers Mike WORKSHOP: Introduction to Metabarcoding using Qiime2 Tuesday, 22 February 2022,12:00 - 5:00 pm AEDT Qiime2 is a popular tool used to perform powerful microbiome analysis that can transform your raw data into publication quality visuals and statistics. In this interactive online workshop you will learn how to use this pipeline to run essential steps in microbial analysis. Applications close 8 Feb 2022. Registrations are free but limited: https://www.biocommons.org.au/events<https://protect-au.mimecast.com/s/T5_jCROAWrhvRwgyYt9x0l1?domain=biocommons…> Michael Charleston [cid:54c3e72c-24bb-489f-b2b5-3b2a999d7d50] 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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Bioinformatics Training Survey
by Michael Charleston 25 Jan '22

25 Jan '22

Hi all, Here's a link to a bioinformatics training needs survey, put out by Australian BioCommons (which used to be EMBL-ABR) -- if you have a moment, could you please look at it? We do have some responses from Tasmania but I would love to be able to get more! Best wishes Mike Michael Charleston [cid:eb79dc0c-6973-4f55-a990-21942212af7e] 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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Opportunity for paid work.
by Adam Smolenski 14 Dec '21

14 Dec '21

Hi all, There is a 5 week position available involving the extraction of DNA from 120 endangered sea stars and screening those individuals with seven microsatellite loci as well as Sanger sequencing two mtDNA regions. All work will be carried out in the CSL molecular genetics laboratories and I will be on hand to assist with the running of samples on the sequencer. A/Prof Chris Burridge is a co- chief investigator. The samples will be supplied by Ecomarine Consulting and the project is funded by Pitt & Sherry. The successful applicant will need to have a solid background in population genetics and will be required to produce a detailed report for the funding body. The position is funded at HEO6 level. Please get in touch with me if you are interested or know of someone who might be and I can provide you with further details. Thanks. Regards, Adam. Adam Smolenski Senior Scientist Molecular Genetics Central Science Laboratory Private Bag 55 Hobart Tasmania, 7001 Tel. Int+613 6226 1833 Fax Int+613 6226 2745 Email Adam.Smolenski(a)utas.edu.au<mailto:Adam.Smolenski@utas.edu.au> http://www.utas.edu.au/research/central-science-laboratory/home [UTAS_colour_CMYK-domestic_SM] 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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What are your bioinformatics training needs?
by Michael Charleston 13 Dec '21

13 Dec '21

We're part of the National Bioinformatics Training Cooperative who offers national training to uplift the skills of Australian biologists and bioinformaticians. We collaborate to ensure we can offer the best training opportunities in areas that are relevant. It is important for us to hear what training you need so that we can best support your research. We'd love to know what bioinformatics training you wish you could attend. The survey should take less than 10 minutes to complete. Please, would you complete the Bioinformatics Training Needs survey: https://tinyurl.com/bioinf-training-needs<https://protect-au.mimecast.com/s/s3QOCD1jB7f5JrpMEhZc0_r?domain=tinyurl.com> ? Thanks so much! Michael Charleston [cid:4b344f64-46b6-4ef0-96f4-a51f09afac19] 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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Faprotax
by Shane Powell 01 Dec '21

01 Dec '21

Hi everyone, Has anyone used to FAPROTAX tool / database for microbial community analysis? We'd like to try it out but have run into some problems. Thanks, Shane ************************************************ Dr Shane Powell Senior Lecturer Program Lead, Learning & Teaching Tasmanian Institute of Agriculture University of Tasmania Private Bag 98, Hobart TAS 7001 shane.powell(a)utas.edu.au<mailto:shane.powell@utas.edu.au> +61 3 6226 6286 CRICOS 00586B 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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Don't forget to register!
by Michael Charleston 01 Oct '21

01 Oct '21

Hello on a rainy Friday in Hobart! Don't forget that registration is closing soon for Phylomania, ABACBS and COMBINE! If you haven't yet registered and want to come along, please go to https://www.abacbs.org/conference2021 and Do That Thing you Know You Want To 🙂 Best wishes Mike (goes and registers now..) Michael Charleston [cid:b11921cc-8b73-4089-a3b7-737a7758d888] 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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Registration Extended: COMBINE, ABACBS and Phylomania 2021
by Michael Charleston 20 Sep '21

20 Sep '21

Hello again, If you have struggled with the excruciating pressure of the much earlier-than-usual deadline for Phylomania this year (because we're teaming up with the bigger ABACBS and COMBINE conference), fear not, for the good news of today is that the deadline has been extended by two more weeks: The main conference website is at https://www.abacbs.org/conference2021/, but go to https://www.abacbs.org/conference2021/important-dates and you shall see this welcome text: Submission due date: 20th September (Monday) 4th October (Monday) Go on, you know you want to . Best wishes Mike Michael Charleston [cid:e9d8e4fe-9896-42cc-a855-2f1b2d5ef894] 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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AGTA Live - Future of Conservation Genomics: Preserving biodiversity of our planet (12 August)
by Jac Charlesworth 21 Jul '21

21 Jul '21

And one more then I promise to stop spamming you! The next AGTA Live free event on The Future of Conservation Genomics will be held on August 12. Details and registration are available on the AGTA website: https://agtagenomics.org.au/agta-live/ [cid:image001.png@01D77E40.16918040]<https://agtagenomics.org.au/agta-live/> 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: 2021 eResearch Australasia Conference - Submit an Abstract
by Jac Charlesworth 21 Jul '21

21 Jul '21

Hi folks, Anyone who has an interest in eResearch/Digital Research or big data should check out the eResearch Australasia conference – details below. Abstracts still open, it’s online with a local social event and it has a pretty broad remit. Best wishes, Jac View this email in your browser<https://protect-au.mimecast.com/s/jAfZCjZryVCnn5ZZvIW6wQd?domain=mailchi.mp> conference.eresearch.edu.au<https://protect-au.mimecast.com/s/3U4QCp8AG6fnnMppBI7X_XN?domain=conference…> [https://mcusercontent.com/bb7cb2d3340b796d722112cc1/images/3bbadfcd-89c4-4b…]<https://protect-au.mimecast.com/s/BEVICq7BJXt880JJoHvv9kk?domain=conference…> Submit an Abstract The 2021 eResearch Australasia Conference will be held from 11 – 15 October and will include a variety of in-person and online options. Brisbane will operate as the eResearch Conference hub with node locations in major cities. In-person events will follow a “hub and node” model, with all registrations including access to an event in your nearest location. The conference will offer delegates the opportunity to engage, connect, and share their ideas and exemplars concerning new eResearch capabilities, and how information and communication technologies help researchers to collaborate, collect, manage, share, process, analyse, store, find, understand and re-use data and information. Submissions are invited for the following presentation types which will be delivered as part of the online conference program. Oral Presentations BoFs Lightning Talks Posters The call for submissions will close at 17:00 AEST on Friday 30 July. We look forward to receiving your submission and seeing you at the conference! Loretta Davis, Alex Reid Co-Chairs, 2021 eResearch Australasia Conference Program Committee SUBMIT AN ABSTRACT HERE<https://protect-au.mimecast.com/s/g-6uCr8DKNf88V44GHLGp5z?domain=conference…> The 2021 eResearch Australasia Conference is hosted by [https://gallery.mailchimp.com/bb7cb2d3340b796d722112cc1/images/c7287ab8-9d1…]<https://protect-au.mimecast.com/s/jn5mCvl0O7S77Nrr3IEcScj?domain=conference…> Platinum Sponsor [https://mcusercontent.com/bb7cb2d3340b796d722112cc1/images/ef664c94-e4aa-0e…] Copyright © 2021 Conference Design Pty Ltd, All rights reserved. You are receiving this email because you have previously attended or expressed interest in an eResearch conference. We apologise if you are receiving this email in error. Our mailing address is: Conference Design Pty Ltd 228 Liverpool Street Hobart, TAS 7000 Australia Unsubscribe<https://protect-au.mimecast.com/s/tRQaCoVzE9Hrrq660ComTMr?domain=conference…> [https://mcusercontent.com/bb7cb2d3340b796d722112cc1/images/0c010b8c-5057-7f…] 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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DADA2
by Shane Powell 22 Jan '21

22 Jan '21

Hi everyone, Is anyone using the DADA2 script for processing MiSeq data? I have a student who is running into problems and having someone else who has used it and has another perspective on it to talk to would be very helpful. I am also new to DADA... Please let me know if you have time to chat to Bri and I'll ask her to contact you directly. Thanks, Shane University of Tasmania Electronic Communications Policy (December, 2014). 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: Postdoc opening! Bayesian evolutionary algorithms for the analysis of B cell receptor (i.e. antibody) sequence lineages
by Jeremy Sumner 21 Jan '21

21 Jan '21

Dear all, See below for a post-doc opportunity with Erick Matsen’s group. Cheers Jeremy From: Erick Matsen <ematsen(a)gmail.com> Sent: Wednesday, 20 January 2021 8:35 AM To: Erick Matsen <ematsen(a)gmail.com> Subject: Postdoc opening! Bayesian evolutionary algorithms for the analysis of B cell receptor (i.e. antibody) sequence lineages Dear Colleague-- I hope you are doing as well as could be hoped for given the circumstances, and I apologize for the mass email. We have a postdoc opening! Here's the headline: The goal of our project is to develop, implement, and apply Bayesian evolutionary algorithms for the analysis of B cell receptor sequence lineages. These lineages are important for understanding the events leading to the development of high-affinity antibodies. We are motivated to: * use a Bayesian approach to appropriately account for uncertainty in phylogenetic inferences (which is considerable in this case) * fit and use complex models of somatic hypermutation and selection that violate the commonly-applied IID assumption in phylogenetics * develop efficient, elegant, and robust implementations of the newly developed methodology and make them available in open-source software for the community. Here's the full description: https://matsen.fredhutch.org/general/2021/01/15/bcell-postdoc.html<https://protect-au.mimecast.com/s/GOAmCjZryVCq99xoCWC4yf?domain=matsen.fred…> If you know any trainees who might be interested in working in this area, please let me know! I also note that we may have a slot to work on variational Bayes approaches to phylogenetics, but that will be dependent on funding. Nevertheless, if you know someone who would be interested in helping build fundamentally new approaches to Bayesian phylogenetics, I'd be happy to get to know them! Members of underrepresented groups are especially encouraged to apply. Thank you, Erick -- Frederick "Erick" Matsen (he/him) Professor, Fred Hutchinson Cancer Research Center http://matsen.fredhutch.org/<https://protect-au.mimecast.com/s/Z-9UCk8vzVfQNNJ2tVM9zk?domain=matsen.fred…> University of Tasmania Electronic Communications Policy (December, 2014). 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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Data scientist job at TIA
by Beth Penrose 21 Jan '21

21 Jan '21

Hi everyone, The Tasmanian Institute of Agriculture (TIA) are looking for a data scientist. If you know anyone who would be interested in this role, please pass this email on. Details of the job can be found here: https://www.seek.com.au/job/51353988?type=standout#searchRequestToken=d452e… Thanks Beth Dr. Beth Penrose Lecturer in Pasture Science Honours coordinator Tasmanian Institute of Agriculture Academic co-Lead, UTAS - Data, Knowledge, Decisions University of Tasmania, Sandy Bay Campus Private Bag 98, Hobart TAS 7001 T: +61 3 6226 5569 M:+61 4 18 895 382 utas.edu.au/tia<http://www.utas.edu.au/tia/home> [cid:image001.jpg@01D6EFEC.90F2A630] TIA is a joint venture of the University of Tasmania and the Tasmanian Government CRICOS 00586B University of Tasmania Electronic Communications Policy (December, 2014). 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: Postdoc/ Research Fellow in biological data science
by Michael Charleston 07 Jan '21

07 Jan '21

An opportunity to move to another safe island just now... Dunedin is a lovely city! Michael Charleston [cid:49bc7fa5-a30a-4f7e-b019-2a1fa3333807] Mathematical Biology Group Professor in Bioinformatics Associate Head of School (Learning and Teaching) Academic co-Lead, UTAS - Data, Knowledge, Decisions School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 Zoom ID: https://utas.zoom.us/j/2948029484 ________________________________ From: Alex Gavryushkin <alex(a)biods.org> Sent: Monday, 4 January 2021 12:09 PM Subject: Postdoc/ Research Fellow in biological data science Dear colleagues, We are looking for a postdoc/ research fellow to work on computational cancer evolution. I would be very grateful if you could share the following links with your networks. https://otago.taleo.net/careersection/2/jobdetail.ftl?job=2002201<https://protect-au.mimecast.com/s/MzAbCANZy7iW37kruGYjUQ?domain=otago.taleo…> https://www.linkedin.com/posts/alex-gavryushkin_working-at-otago-your-caree…<https://protect-au.mimecast.com/s/cqJuCBNZz7i49EYPS6R5xg?domain=linkedin.com> Best wishes, Alex University of Tasmania Electronic Communications Policy (December, 2014). 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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Wild and Comparative Immunology 2020
by Andy Flies 03 Dec '20

03 Dec '20

Hello all, In 2019 we held the inaugural Wild and Comparative Immunology (WACI) workshop in Hobart. Our in person workshop discussions led to a 'Rewilding immunology<https://science.sciencemag.org/content/369/6499/37>' Perspective article in Science from our WACI consortium. This year we are totally online and have 33 speakers and over 135 people registered from 12 countries (https://www.wacimmuno.com/program/). There are still two days left to register for the 2020 Wild and Comparative Immunology workshop (https://www.wacimmuno.com/registration-2020/) and there is no fee this year. In 2021 we hope to get back to in person workshops, and will be supported as an Australian and New Zealand Society for Immunology (ASI) special interest group. Best, Andy - - Andy Flies, PhD Recent publication: A novel system to map protein interactions reveals evolutionarily conserved immune evasion pathways on transmissible cancers<https://advances.sciencemag.org/content/6/27/eaba5031> (Science Advances) Recent publication: Rewilding immunology<https://science.sciencemag.org/content/369/6499/37> (Science) Recent publication: Tasmanian devil CD28 and CTLA4 capture CD80 and CD86 from adjacent cells<https://doi.org/10.1016/j.dci.2020.103882> (Dev. & Comp. Immunology) Senior Research Fellow and ARC Discovery Early Career Researcher<http://www.utas.edu.au/profiles/staff/menzies/andrew-flies> Menzies Institute for Medical Research | College of Health and Medicine University of Tasmania Private Bag 23, Hobart TAS 7000 t: +61 3 6226 4614 | e: Andy.Flies(a)utas.edu.au<mailto:Andy.Flies@utas.edu.au> @WildImmunity<https://twitter.com/WildImmunity> | WildImmunity.com<https://wildimmunity.com/> Wild and Comparative Immunology Consortium<https://www.wacimmuno.com/> Science in the Pub Tasmania<http://scienceinthepubtasmania.org.au/> [Electronic Signature] CRICOS 00586B University of Tasmania Electronic Communications Policy (December, 2014). 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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Epigenetics 2021 to circulate to AEpiA committee
by Michael Charleston 03 Dec '20

03 Dec '20

A conference that has come to my attention this morning: just in the nick of time for early bird registration (which appears to cover a coffee cart surprise in the mail, and a dinner if at all possible). Good morning everyone, Our flagship Australian Epigenetics Alliance conference will be held in February next year, all online and with a fantastic speaker list! Please see below for further information. Early bird registration closes on 4th December 2020, along with abstract submission for oral presentations. I hope to see you online! Cheers, Pip A message from the Australian Epigenetics Alliance (AEpiA): [cid:image001.png@01D6C890.BCC262B0]<https://protect-au.mimecast.com/s/sZR3C81Zm7fK6kY5cnHkOM?domain=ausepi21.ep…> Dear friends & colleagues, Our flagship scientific meeting, Epigenetics 2021<https://protect-au.mimecast.com/s/TdRUC91Zn7fpkO2WcE4LBo?domain=ausepi21.ep…>, will be online next 17- 19th February 2021. This meeting will bring together Australian and international researchers from across epigenetics-related fields, connecting senior, emerging and early-career scientists. Register by Friday 4th December for early bird rates <https://protect-au.mimecast.com/s/XF_uC0YZ4yFLGymXs2rxPN?domain=ausepi21.ep…> Early bird rates: Regular: $150 / Student: $100 Abstract Submission Deadline: Friday 4th December 2020<https://protect-au.mimecast.com/s/P_QsCgZovVC7ABG1s3itWA?domain=ausepi21.ep…> We invite abstracts for both oral and poster presentation. We will have awards for Best Talks & Best Student Talks, and poster prizes too. Program & Speakers: Epigenetics 2021 will be a fully immersive virtual event using the Attendify and Gather platforms. We've been planning a fantastic program<https://protect-au.mimecast.com/s/SD19CjZryVCvnOR4S14afD?domain=ausepi21.ep…>, with session topics including: Single-cell epigenetics, Epigenetics and stem cells Epigenetics in immunity Environmental epigenetics Transgenerational epigenetics and DOHAD Integrative OMICs (including epigenetics) Epigenetic aging Translational and clinical epigenetics We have a wonderful line-up of invited speakers<https://protect-au.mimecast.com/s/8VlyCk8vzVfpOw5yc8ha1S?domain=ausepi21.ep…>, including keynote international speakers Steve Horvath (UCLA, USA), Liran Carmel (Hebrew University of Jerusalem, Israel) and Wolf Reik (Babraham Institute, UK). We also have many national speakers, invited from all over Australia. Coffee & Dinner: Everyone who registers before the end of December can also chose to receive a coffee cart surprise in the post! We're also hoping to be able to hold satellite conference dinners in each state, which will be included in your registration fee. Fingers crossed that continued easing of covid-19 restrictions will allow these to go ahead. Keep an eye out for further updates on ausepi21.epialliance.org.au<https://protect-au.mimecast.com/s/TdRUC91Zn7fpkO2WcE4LBo?domain=ausepi21.ep…> or on Twitter at #AusEpi21<https://protect-au.mimecast.com/s/G6pwCmOxBVhrjMWof312fz?domain=twitter.com>. Sponsors: We are very grateful to our generous sponsors, without whom this meeting could not occur. Thanks to Abcam, Qiagen, Decode Science, Illumina, Custom Science, New England Biolabs, BMG Labtech and MDPI Epigenomes Journal. We look forward to seeing you at Epigenetics 2021! Best wishes from the Epigenetics 2021 Local Organising Committee and all the AEpiA Management Committee. [cid:image002.png@01D6C950.7A53B080] ausepi21.epialliance.org.au<https://protect-au.mimecast.com/s/G8s3CnxyDVHY7WmZIvAcbq?domain=ausepi21.ep…> | epialliance.org.au<https://protect-au.mimecast.com/s/HmSvCp8AG6fBnwA0FVvTUD?domain=epialliance…> | Contact AEpiA<mailto:contact@epialliance.org.au> | Follow us on Twitter<https://protect-au.mimecast.com/s/y3WzCq7BJXto82Xyso7aft?domain=twitter.com> University of Tasmania Electronic Communications Policy (December, 2014). 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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PhD Scholarship at UTAS - Molecular Basis for Plant Humidity Responses
by Frances Sussmilch 05 Nov '20

05 Nov '20

Hi All, I have a PhD scholarship (AUD$28,092/year full time for 3.5 years) available for a project co-supervised by Mike Charleston and Tim Brodribb focussing on how plants regulate their own water loss. We are looking for a student who has completed Honours in molecular biology, bioinformatics, plant physiology or genetics who is currently in Australia/NZ. A plant science background is not essential. If you know of any current or previous students who may be interested or other relevant networks where this could be shared, please let me know or feel welcome to forward these details on directly. Full details here: https://www.utas.edu.au/research/degrees/available-phd-projects/phd-project… Many thanks, Frances ________________________ Dr Frances Sussmilch Biological Sciences School of Natural Sciences University of Tasmania Private bag 55, Hobart 7001 Tasmania, Australia Ph: (+61) 03 6226 7583 Fax: (+61) 03 6226 2698 University of Tasmania Electronic Communications Policy (December, 2014). 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 available: genomic transitions between modes of sex-determination
by Christopher Burridge 18 Sep '20

18 Sep '20

Postdoc position: Genomic transitions between modes of sex-determination Fixed term, full-time, 3 years Based at the University of Tasmania, Hobart PROJECT THEME Sex-determination controls the most significant variation within animals—the division into males and females. While the different systems of sex-determination involving genetic or environmental control are relatively well understood, transitions between these systems remain enigmatic in evolutionary biology. This project aims to address this gap by revealing the genomic changes required to transition between modes, using one of only two known lizard species exhibiting both genetic and temperature control of sex. This knowledge will have important implications for species conservation, facilitating predictions of highly biased sex ratios under climate change, plus potential commercial applications for species where the production of one sex is favoured. A Postdoc position is available to contribute to this research. The postdoc will perform advanced genomic and transcriptomic sequencing of species of Australian lizards to identify the genomic changes accompanying transitions between genetic and temperature-dependent sex determination. This collaborative research project is funded by an Australian Research Council Discovery Project grant awarded to the University of Tasmania (Assoc Profs Erik Wapstra and Chris Burridge), the University of Canberra (Prof Tariq Ezaz), and the University of Vienna (Prof. Oleg Simakov). This Postdoc will be based at the University of Tasmania, but will also work closely with Prof Simakov at the University of Vienna and a PhD student conducting related cytogenetic studies at the University of Canberra. THE IDEAL CANDIDATE The ideal candidate is expected to have knowledge in relevant aspects of genomics (e.g. NGS genome and transcriptome sequencing, mapping, screening for orthologs and homologs, assembly, annotation). Knowledge of sex determination is also desirable. The candidate will be self-motivated and well-organised, with a demonstrated capacity to learn and apply the broad skill set necessary for the successful completion of a research project. The successful candidate will be able to work alongside a wide variety of people in multi-function and multicultural laboratories. The successful candidate will also have a strong commitment and demonstrated excellence in research and research communication. SELECTION CRITERIA Essential A PhD, and experience in a relevant research area Knowledge and demonstrated expertise in areas such as NGS genome and transcriptome sequencing, mapping, screening for orthologs and homologs, and genome assembly and annotation. A demonstrated record of publication of scientific research in high-ranking international peer-review journals Desirable Knowledge of sex determination systems Knowledge and demonstrated expertise in phylogenetics, trait mapping, and ancestral state reconstruction The position is open to all nationalities. There is the potential to start this project remotely (i.e., outside Australia), given the nature of the project, desired start time (late 2020, early 2021) and the current challenges of international travel to Australia. HOW TO APPLY Interested applicants should submit a cover letter, CV, responses to the selection criteria listed above, and contact details of 2 potential referees to: chris.burridge(a)utas.edu.au<mailto:chris.burridge@utas.edu.au> Applications will close Oct 16, 2020 FURTHER INFORMATION For further information about the position please contact chris.burridge(a)utas.edu.au<mailto:chris.burridge@utas.edu.au> Chris Burridge | Associate Professor, Molecular Ecology & Evolution School of Natural Sciences | University of Tasmania | Private Bag 55 | Hobart | Tasmania 7001 | Australia Room 320a Life Sciences Building | Ph +61 3 6226 7653 | Fax +61 3 6226 2698 | https://rmdb.research.utas.edu.au/public/rmdb/q/indiv_detail_warp_trans/397… http://scholar.google.com.au/citations?user=4cYH8ZYAAAAJ&hl=en evogentas.org<http://evogentas.org/> University of Tasmania Electronic Communications Policy (December, 2014). 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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2020 IGV SCIENTIFIC MEETING
by Michael Charleston 04 Sep '20

04 Sep '20

Hi folks, Here's an interesting looking conference: (Forwarding this message:) The Immunology Victoria meeting is coming up. This is a meeting (virtual this year) specifically designed to promote speaking opportunities for Victorian and Tasmanian students and early-career postdocs. Would you mind forwarding around to the division? October 23rd is the date. It is free for ASI members, and $20 for non-members. https://www.immunology.org.au/events/2020-IgV-Scientific-Meeting/ [cid:bdd7e594-fbab-4530-8650-da1597b57e76] University of Tasmania Electronic Communications Policy (December, 2014). 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: Software developer to support dartR (software package in wildlife genomics)
by Michael Charleston 02 Sep '20

02 Sep '20

An opportunity for 2-year part-time work. From: Bernd.Gruber <Bernd.Gruber(a)canberra.edu.au> Sent: Tuesday, 1 September 2020 1:23 PM Subject: Software developer to support dartR (software package in wildlife genomics) Dear Colleagues, Can you please circulate the link to an offering for a software developer in the area of wildlife genomics to support the development of our R package (dartR) to potentially interested candidates. It is a two years, 0.5 FTE position. More information can be found here: * UC website – https://uctalent.canberra.edu.au/cw/en/job/494678/software-developer<https://protect-au.mimecast.com/s/xLyMCP7yRpt2BQXZuzJcoL?domain=uctalent.ca…> Thanks, take care and kind regards, Bernd ============================================================================== Dr Bernd Gruber Tel: (02) 6206 3804 Fax: (02) 6201 2328 Professor Institute for Applied Ecology Faculty of Applied Science University of Canberra ACT 2601 AUSTRALIA Email: bernd.gruber(a)canberra.edu.au<mailto:bernd.gruber@canberra.edu.au> WWW: http://www.canberra.edu.au/faculties/science/staff/profiles/dr-bernd-gruber<https://protect-au.mimecast.com/s/roygCQnzVqtKn7P9HPx-25?domain=canberra.ed…> Australian Government Higher Education Provider Number CRICOS:#00212K NOTICE & DISCLAIMER: This email and any files transmitted with it may contain confidential or copyright material and are for the attention of the addressee only. If you have received this email in error please notify us by email reply and delete it from your system. The University of Canberra accepts no liability for any damage caused by any virus transmitted by this email. ============================================================================== [UC Logo]<https://protect-au.mimecast.com/s/Oql4CROAWrhpwNWQsPR2KK?domain=canberra.ed…> [#1 in the ACT for three years running Full-time employment and graduate starting salaries Good Universities Guide 2021]<https://protect-au.mimecast.com/s/0zfBCVAG1yhEVMyXUJX9A0?domain=canberra.ed…> [UC Facebook]<https://protect-au.mimecast.com/s/EF2oCWLJ2zfQ10qxtm8BN6?domain=facebook.com>[UC Twitter]<https://protect-au.mimecast.com/s/SXFfCXLK3AfglmKGi9pJNX?domain=twitter.com>[UC Instagram]<https://protect-au.mimecast.com/s/2fU3CYWL4BsvK5lgu3CwoM?domain=instagram.c…>[UC Linkedin]<https://protect-au.mimecast.com/s/NoZ3CZYM5DFw1zgxUN9Upf?domain=au.linkedin…>[UC Youtube]<https://protect-au.mimecast.com/s/km-FC1WZ5zs0r8GOUminVt?domain=youtube.com> [University of Canberra]<https://protect-au.mimecast.com/s/Oql4CROAWrhpwNWQsPR2KK?domain=canberra.ed…> Australian Government Higher Education Registered Provider (CRICOS) #00212K The University of Canberra acknowledges the Ngunnawal people, traditional custodians of the lands where Bruce Campus is situated. We wish to acknowledge and respect their continuing culture and the contribution they make to the life of Canberra and the region. We also acknowledge all other First Nations Peoples on whose lands we gather. NOTICE AND DISCLAIMER: This email and any files transmitted with it may contain confidential or copyright materials and are for the attention of the addressee only. If you have received this email in error please notify us by email reply and delete it from your system. The University of Canberra accepts no liability for any damage caused by any virus transmitted by this email. University of Tasmania Electronic Communications Policy (December, 2014). 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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IHP program: Quantitative evolution, phylogeny and ecology, Jan 11 to Feb 19, 2021, Paris (France)
by Peter Jarvis 13 Jun '20

13 Jun '20

FYI Peter _________________________________________________________________________________________________ IHP program: Quantitative evolution, phylogeny and ecology, Jan 11 to Feb 19, 2021, Paris (France) More information at: https://indico.math.cnrs.fr/category/389/<https://protect-au.mimecast.com/s/HmU-C3Q870UzPBEYHgibUM?domain=indico.math…> Please pre-register at: https://indico.math.cnrs.fr/event/5760/registrations/432/<https://protect-au.mimecast.com/s/RjC2C4QZgDUKnovAuxxTPb?domain=indico.math…> preferably by June 15. Registrations are and will remain free of charge. We are aware of the uncertainties regarding travel in the next months. Pre-registrations are non-binding, but necessary for organizational reasons. From: Anne-Florence Bitbol <anne-florence.bitbol(a)epfl.ch<mailto:anne-florence.bitbol@epfl.ch>> University of Tasmania Electronic Communications Policy (December, 2014). 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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Webinars on using Containers in bioinformatics
by Michael Charleston 05 Jun '20

05 Jun '20

Hi all! Long time no hear. There are a series of bioinformatics webinars being run soon by Australian BioCommons, on the use of Containers. Here's the link: https://www.biocommons.org.au/events/containers-intro [http://static1.squarespace.com/static/5d3a4213cf4f5b00014ea1db/5d3a5c1b6311…]<https://www.biocommons.org.au/events/containers-intro> WEBINAR SERIES: Using Containers in Bioinformatics — Australian BioCommons<https://www.biocommons.org.au/events/containers-intro> Using containers in bioinformatics can bring benefits like software portability, data reproducibility and improved collaboration. Are containers the right fit for your research? This three-part series takes you from the absolute basics of containers through to demonstrating how to use containers in www.biocommons.org.au What's a container? It's a way of packaging up analyses with correct versions of software and data to make analyses highly reproducible, which as we know is incredibly important and often rather lacking in published work. There's a really nice blog entry here on why containers, in particular one system called Docker, is handy. Very accessible read: link below. If you're interested in "attending" the webinars then you can register to do so, and I think they'll be recorded. After the webinars there will be some online workshops learning how to use containers; you don't have to worry about registering for them now but I'd like to get a sense if anyone was interested in *maybe* doing one of those. I get the impression they will use command-line tools but don't know yet. Anyway, have a read over the long weekend: https://www.molecularecologist.com/2016/05/docker-making-our-bioinformatics… Cheers for now, Michael Charleston [cid:5060fe50-be4c-4a29-8610-59a03a6b9461] Mathematical Biology Group Associate Professor in Bioinformatics Associate Head of School (Learning and Teaching) Academic co-Lead, UTAS - Data, Knowledge, Decisions School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 Zoom ID: https://utas.zoom.us/j/2948029484 University of Tasmania Electronic Communications Policy (December, 2014). 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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A little more information on the next AusBiocommons workshop on information visualisation
by Michael Charleston 28 Jan '20

28 Jan '20

This extra wording is now on the Eventbrite page for the event: ___ LEARNING OUTCOMES By completing this workshop you will learn to generate a multi-track Circos image and use rules to format the image dynamically based on data values and positions. INTENDEND AUDIENCE This workshop is aimed at biologists and bioinformaticians with no previous Circos knowledge. A familiarity with the Galaxy environment is assumed. Please bring along: * your Galaxy Australia login credentials * a WIFI enabled laptop You can apply for a free Galaxy Australia account using an Australian university email address here: https://usegalaxy.org.au<https://protect-au.mimecast.com/s/8qzcCOMxQoFLyAKrFEHuJB?domain=usegalaxy.o…>. You can watch a quick introduction to using Galaxy Australia on the Australian BioCommons youtube channel<https://protect-au.mimecast.com/s/uSZ9CP7yRpt1k4xAT0xFIV?domain=youtu.be>. If you need to brush up on your Galaxy knowledge, you can find great background information that's easy to follow here: https://training.galaxyproject.org/training-material/topics/visualisation/t…<https://protect-au.mimecast.com/s/TFsRCQnzVqt1y6W4TMWsik?domain=training.ga…> University of Tasmania Electronic Communications Policy (December, 2014). 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: Register now: Using Circos in Galaxy Australia webinar & workshop
by Michael Charleston 24 Jan '20

24 Jan '20

Hi folks, I nice opportunity to learn some data visualisation as it pertains to bioinformatics! Please register if you are interested. I'll be facilitating the event here in Sandy Bay if you would like to come along. The room holds about 15 (though if there's a sudden flurry of interest I'll try to find somewhere bigger!). Cheers Mike Michael Charleston [cid:05ba583b-d22b-45f0-8805-4354810c1269] Mathematical Biology Group Organiser of Phylomania<http://www.maths.utas.edu.au/phylomania/phylomania2018.htm> conference 2019 November 20-22 Associate Professor in Bioinformatics Associate Head of School (Learning and Teaching) Academic co-Lead, UTAS - Data, Knowledge, Decisions School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 ________________________________ From: Christina Hall <christina(a)biocommons.org.au> Sent: Thursday, 23 January 2020 11:37 PM To: Christina Hall <christina(a)biocommons.org.au> Subject: Register now: Using Circos in Galaxy Australia webinar & workshop Dear colleague, We are excited to share the details of two upcoming Australian BioCommons / Galaxy Australia training events. Lucky for us, Martin Krzywinksi from Canada's BC Cancer Genome Sciences Center is visiting Melbourne and he has agreed to take part in a couple of national training activities on Monday 3 February, 2020. Martin Krzywinski works in bioinformatics, data visualization, science communication and the interface of science and art. He applies design, both data and artistic, to assist discovery, explanation and engagement with scientific data and concepts. Martin is the creator of Circos and hive plots and his information graphics have appeared in the New York Times, Wired, Scientific American and covers of numerous books and scientific journals such as Nature and Genome Research. He is a co-author of the Nature Methods Points of View and Points of Significance columns. WEBINAR: The essence of data visualization in bioinformatics Mon 3 Feb, 12:00-13:00 AEDT / 11:00-12:00 AEST / 9:00-10:00 AWST WORKSHOP: Using Circos in Galaxy Australia Mon 3 Feb, 14:00-17:00 AEDT / 13:00-16:00 AEST / 11:00-14:00 AWST Further information and registration details are available here: https://www.biocommons.org.au/events<https://protect-au.mimecast.com/s/idNAC81Zm7f5A815Tn_Ywx?domain=biocommons.…> Martin has put together a couple of posters to advertise the events (attached). Please distribute widely and we look forward to seeing you and your colleagues on the day. Kind regards, Christina. -- Christina Hall, PhD Training and Communications Manager Australian BioCommons Melbourne Bioinformatics, University of Melbourne M: +61 (0) 402 973 338 W: biocommons.org.au<https://protect-au.mimecast.com/s/QHqiC0YZ4yFX90VXT2eEkR?domain=protect-au.…> This position is funded by Bioplatforms Australia and hosted at Melbourne Bioinformatics, University of Melbourne I acknowledge the Traditional Owners of the land on which I work, and pay my respects to the Elders, past, present and emerging [https://docs.google.com/uc?export=download&id=1sSOPhFHGho1UC8FJte2UAPCHvX8B…] University of Tasmania Electronic Communications Policy (December, 2014). 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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