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Phylomania 2023: Like and subscribe!!
by Michael Charleston 13 Oct '23

13 Oct '23

Dear all, The registration page, payment page and a cheeky announcement about a (free!) Cogent3 workshop are all live on the Phylomania 2023 web page! Here it is in case Google can't find it for you: http://www.maths.utas.edu.au/phylomania/phylomania2023.html Can't wait to see you all! Michael Charleston [cid:b3651a8f-8aa0-4f81-8f66-598bae99e09e] Phylomania 2023: November 22-24 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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Fw: Cogent3 workshop at Phylomania announcement
by Michael Charleston 03 Oct '23

03 Oct '23

From: Gavin A Huttley <Gavin.Huttley(a)anu.edu.au> Sent: Tuesday, 3 October 2023 2:54 PM To: Michael Charleston <michael.charleston(a)utas.edu.au> Subject: Cogent3 workshop at Phylomania announcement Hi 👋! The development team of cogent3<https://protect-au.mimecast.com/s/RVN3C3Q870UpzOogZigneHc?domain=cogent3.org> will run a half-day Data Wrangling with Cogent3 Workshop on the afternoon of 21st November 2023. This is before the start of Phylomania, and it's free 🎉! You can register here<https://protect-au.mimecast.com/s/IM2TC4QZgDUBKqE2rUxaS9_?domain=forms.gle>. Read on past the signature to see workshop details. We hope you can join us! On behalf of the cogent3 developer team, Gavin Huttley ________________________________ Data Wrangling with Cogent3 The workshop is geared towards developers who specialize in phylogenetic methods. Acquiring empirical data for evaluating the performance of a new method is challenging. Your choice of data has important ramifications for your evaluation of the performance of your method. While the standard strategy of recycling published data sets is convenient, this risks perpetuating biases embedded in those data sets. We will show how cogent3<https://protect-au.mimecast.com/s/RVN3C3Q870UpzOogZigneHc?domain=cogent3.org> and associated tools can greatly simplify getting public data for analyses, serving the needs of phylogenetic method developers. As there is an overlap with standard phylogenetic data pre-processing workflows, users of phylogenetic (or molecular evolutionary) methods can also benefit from attending this workshop. Workshop Content The topics we will cover are: * Factors for method developers to consider when designing experiments. * How to extract specific types of sequences (e.g. by homology type, sequence class, or level of divergence) from biological databases like Genbank and Ensembl. * Handling inconsistencies in biological data resources. * Multiple sequence alignment and subsequent quality control. Prerequisites All you need for this workshop is a laptop and some familiarity with command-line applications. Ideally, you should be able to install software on your machine (see Computer Setup<https://protect-au.mimecast.com/s/UJQ0C5QZjEUZL23PAcywB7p?domain=github.com> on the wiki). More workshop information Details regarding physical location and setting up your computer before the workshop will be posted to the Cogent3 Workshop Wiki<https://protect-au.mimecast.com/s/Wuq5C6X1k7CrYq76Xf51HA3?domain=github.com>. We look forward to seeing you there! 👾 cogent3's development team. ________________________________ Professor Gavin Huttley, Research School of Biology, ANU College of Science, RN Robertson Building, 46 Sullivans Creek Road, The Australian National University Canberra ACT 2600 Australia +61 2 6125 5308 https://biology.anu.edu.au/research/groups/huttley-group-bioinformatics-mol…<https://protect-au.mimecast.com/s/5QBFC71Zl7fA1w2XLcqzgE7?domain=biology.an…> CRICOS #00120C ________________________________ 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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ABACBS 2023, Brisbane, Dec 4-8
by Michael Charleston 19 Sep '23

19 Sep '23

Dear colleagues, On behalf of the organising committee, we would like to let you know that early bird registration has now opened for the 2023 Annual Australian Bioinformatics and Computational Biology Society (ABACBS) Conference, to be held in Brisbane on 4-8 Dec (https://2023.abacbs.org/<https://protect-au.mimecast.com/s/s1WrCyoNROTrVx5zzcZn8xU?domain=2023.abacb…>). ABACBS is Australia’s largest bioinformatics conference and represents a community of over 1100 members across the country. To maximise global outreach of Australian science to an international audience, for the first time in ABACBS history, the Brisbane 2023 edition will be held in collaboration with the International Society of Computational Biology (ISCB), the world's leading professional society in the discipline. In addition to the discounts we are offering through early bird registration rates, everyone who registers for ABACBS can also sign up for discounted ISCB membership! ABACBS 2023 will facilitate multidisciplinary crosstalk among researchers, academics, and professionals from Australia and abroad who are involved in both the generation and analysis of molecular data from a broad spectrum of life sciences research. As per tradition, our week starts with the student-led COMBINE symposium (4 Dec), followed by the annual conference (5-6 Dec), and concludes with two days of satellite events (workshops, symposia, etc.; 7-8 Dec). Our session themes include: 1. Machine Learning for Discovery 2. Epigenomics and Long Read Sequencing 3. Phylogenetics & Evolution 4. Agricultural and Environmental Omics 5. Human Health and Translation 6. Cutting Edge Omics Technologies and Analysis 7. Big data infrastructure If you’re interested in organising a workshop or symposia, please see the website for more info. Our call for abstracts is currently open and will close on 25 Sep. Early bird registration will close on 16 Oct so please register as soon as you can to avoid missing out! Best wishes, CX and Jess Co-Convenor, ABACBS 2023 ----------------------------------------------------- Cheong Xin (CX) Chan, Ph.D. (Queensland) Senior Research Fellow & Senior Lecturer, School of Chemistry and Molecular Biosciences Group Leader, Australian Centre for Ecogenomics Affiliate Research Fellow, Institute for Molecular Bioscience Co-Convenor, ABACBS 2023<https://protect-au.mimecast.com/s/s1WrCyoNROTrVx5zzcZn8xU?domain=2023.abacb…> The University of Queensland St Lucia, Brisbane, QLD 4072 Australia P: +61-7-33653829 F: +61-7-33654511 M: +61-416-310786 E: c.chan1(a)uq.edu.au W: https://cxchan.com/<https://protect-au.mimecast.com/s/f3LTCzvO0NfMV5oppsXaOgt?domain=cxchan.com/> (Forwarded with best wishes by...:) Michael Charleston [cid:4bd115cb-9e87-42f7-88d1-0d98bf0e1ab0] Phylomania 2023: November 22-24 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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Fw: EXTERNAL: Position advertised - Data systems scientist 12 months
by Michael Charleston 15 Sep '23

15 Sep '23

Forwarding this advertisement to the bioinformatics list: anyone want some good work up in Darwin? From: Caroline Chong <Caroline.Chong(a)nt.gov.au<mailto:Caroline.Chong@nt.gov.au>> Sent: Thursday, 14 September 2023 5:51 PM To: DEPWS FloraFauna ALL <DEPWSFloraFaunaALL(a)nt.gov.au<mailto:DEPWSFloraFaunaALL@nt.gov.au>> Subject: EXTERNAL: Position advertised - Data systems scientist 12 months Good afternoon, We are seeking to recruit to our Data Systems Scientist 12 month position in Darwin. This is an excellent opportunity to apply your expertise and join our team. Closing date is 26 September 2023 - apply online at https://jobs.nt.gov.au/<https://protect-au.mimecast.com/s/LzLyCK1qMkf2pNWMpTMQFvG?domain=jobs.nt.go…>. Please distribute to your relevant networks and potential candidates. Thanks, Caroline. Dr Caroline Chong A/Director – Species Management Flora and Fauna Division Department of Environment, Parks and Water Security Northern Territory Government CSIRO Complex, 564 Vanderlin Drive, Berrimah PO Box 496, Palmerston, NT 0831 P: +61 8 8999 4592 E: caroline.chong(a)nt.gov.au<mailto:caroline.chong@nt.gov.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 2023!
by Michael Charleston 17 Aug '23

17 Aug '23

Dear Phylomaniacs, We are delighted to announce that Phylomania 2023 - the 15th Annual Theoretical Phylogenetics at the University of Tasmania - will be going ahead again this year. Dates are set for the 22nd – 24th of November. Venue: Sandy Bay Campus of University of Tasmania (Hobart). The conference will be in hybrid mode again: online registration will be free, and we are working out the costing for attendance in person. We welcome abstract submissions from people wanting to present in person in Hobart as well as those who would prefer to present online. As per usual, although the conference title is phylocentric, we welcome talks on any mathematical, theoretical or applied aspects of evolutionary biology. The deadline for abstract submission is October 27th. Please see the conference website http://www.maths.utas.edu.au/phylomania/phylomania2023.html for more information! We hope to see you in Hobart in November! Stay tuned! Best wishes Mike, Barbara, Jeremy Michael Charleston [cid:da3731bc-18c2-42f0-bcef-ac31a3fd2075] Phylomania 2023: November 22-24 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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Fw: COMBINE survey 2023
by Michael Charleston 28 Mar '23

28 Mar '23

Hello Bioinformaticians! Here is a survey from COMBINE, the amazing student-run bioinformatics organization in Australia. They'd LOVE it if you would fill in this survey to help them plan events this year and next. Please can you help them out? Dear Bioinformatics community, Only 3 users have taken the below COMBINE survey! If you would like training workshops for bioinformatics / computational biology in Tasmania now is your opportunity to show the need! You do not need to be a COMBINE member to take the survey. Survey closes 31st March 2023 Supervisors – please encourage your students to complete this! You can complete it too. Regards, Nick [cid:b56fd09a-f6ae-4bc4-9398-190f6c1cf0a0] Hello, Bioinformatics community! We are planning bioinformatics events for 2023, and we want your input. Please take this survey to tell us about your needs. Take the survey now<https://docs.google.com/forms/d/e/1FAIpQLSdvlPu-jauTiMOxkrYf_hnkxPTrhTEiY39…>! [https://lh6.googleusercontent.com/USpUEyyTZ2R6yMsurZjVLu0Doaq2kB93El9pVjPWG…]<https://docs.google.com/forms/d/e/1FAIpQLSdvlPu-jauTiMOxkrYf_hnkxPTrhTEiY39…> COMBINE Survey 2023<https://docs.google.com/forms/d/e/1FAIpQLSdvlPu-jauTiMOxkrYf_hnkxPTrhTEiY39…> docs.google.com To value your time and to appreciate your contribution, we will be giving out a $25 Prezze gift voucher to two randomly chosen participants. Please add your email when prompted if you wish to enter the draw. Have you heard about COMBINE? COMBINE is a student-run Australian organisation for students in computational biology, bioinformatics, and related fields. COMBINE is the student subcommittee of The Australian Bioinformatics And Computational Biology Society (ABACBS). We aim to bring together students and early-career researchers from the computational and life sciences for networking, collaboration, and professional development. Australia has many research institutes, each with their own cohorts of students. Aside from conferences, there are few opportunities that bring these students together, allowing them to discover the different kinds of research going on at other institutes. COMBINE aims to bridge this institutional divide by organising seminars, workshops and social events, also as the yearly COMBINE Student Symposium. Together, these events allow students to connect with each other and build a network in a casual environment. Are you not a COMBINE member yet? Please join now<https://www.combine.org.au/>! Kind regards, Gayathry Krishnamurthy COMBINE Training and Events Officer (TAS) PhD Candidate (Medical Studies) Menzies Institute for Medical Research University of Tasmania menzies.utas.edu.au<https://menzies.utas.edu.au/> 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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PhD scholarship to use machine learning to develop wildlife health intelligence system
by Andy Flies 16 Feb '23

16 Feb '23

Hello everyone, We are looking for a PhD student to help develop a wildlife health intelligence system! This machine learning project but will include regular interactions with Tasmanian devils in captivity and some fieldwork. Contact me at andy.flies(a)utas.edu.au<mailto:andy.flies@utas.edu.au> for more info. Please share this message with any people or lists that might be interested https://www.utas.edu.au/research/degrees/available-projects/projects/menzie… Selection criteria Basic to advanced computer programming skills Prior experience in machine learning algorithms Ability to work with a diverse academic and industry team Interested people can see a bit more about our research program on this recent ABC 7:30 program video. https://www.abc.net.au/news/2023-01-16/hopes-for-new-vaccine-for-tasmanian-… Kind regards, Andy -- Andrew S. Flies, PhD Senior Research Fellow Chair - UTAS Institutional Biosafety Committee Menzies Institute for Medical Research University of Tasmania t: +61 3 6226 4614 | e: Andy.Flies(a)utas.edu.au<mailto:Andy.Flies@utas.edu.au> Website: WildImmunity.com<https://wildimmunity.com/> | Facebook: WildImmunity<https://www.facebook.com/WildImmunity/> Twitter: @WildImmunity<https://twitter.com/WildImmunity> | Youtube: @WildImmunity<https://www.youtube.com/@WildImmunity> | Instagram: WildImmunity<https://www.instagram.com/wildimmunity/> Wild and Comparative Immunology Consortium<https://www.wacimmuno.com/> Recent publication: Class II transactivator induces expression of MHC-I and MHC-II in transmissible Tasmanian devil facial tumours<https://doi.org/10.1098/rsob.220208> (Open Biology) Recent publication: A human adenovirus encoding IFN-γ can transduce Tasmanian devil facial tumour cells and upregulate MHC-I<https://doi.org/JGV-D-22-00136> (Journal of General Virology) Recent publication: Fluorescent Adaptable Simple Theranostic (FAST) proteins for single-step testing of recombinant proteins<https://doi.org/10.1126/sciadv.aba5031> (Science Advances) menzies.utas.edu.au<https://menzies.utas.edu.au/> [cid:image001.png@01D9421C.4F50C070] 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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Save the Date for ASPS2023 Plant Science Conference
by Frances Sussmilch 13 Jan '23

13 Jan '23

Hi All, We are organising a national plant science conference for the Australian Society of Plant Scientists (ASPS2023) to be held in Hobart later this year. If you are interested in attending and/or assisting with conference organisation, please fill out the short expression of interest form linked below and circulate with your students and colleagues. Apologies for any cross-posting. Cheers, Frances ________________________ Dr Frances Sussmilch Biological Sciences School of Natural Sciences University of Tasmania Private bag 55, Hobart 7001 Tasmania, Australia [https://www.asps.org.au/wp-content/uploads/aspsbanner.jpg] Save the Date for ASPS2023! We are planning an in-person plant science conference in Hobart from 28 Nov - 1 Dec 2023. Please add yourself to our mailing list and help us during the planning stages by filling out our EOI form: https://forms.gle/osUAvNEyn9jcwtw78<https://protect-au.mimecast.com/s/611EC81Zm7f67ZVyyInei27?domain=asps.org.au> We welcome you to circulate this widely among your networks. Looking forward to seeing you there, The ASPS 2023 Organising Committee [cid:image001.png@01D91609.21932B30] Copyright © Australian Society of Plant Scientists 2023 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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COMBINE!
by Michael Charleston 18 Nov '22

18 Nov '22

COMBINE is a wonderful student-run society of bioinformaticians in Australia. They have asked me to forward this advert along, so here it is! Are you a current student studying computational biology or bioinformatics? Are you interested in being part of a community that supports students by planning events, encouraging social interactions and promoting technical skills — then come and join the COMBINE committee! Applications will be open until 12th December 2022 and new committee members will be contacted in early January 2023. Detailed position descriptions are listed here<https://protect-au.mimecast.com/s/9-0uCq7BJXt8WjqyLfZBsXz?domain=combine.us…>. Nominate yourself or someone else to join via the Nomination Form<https://protect-au.mimecast.com/s/qvmBCr8DKNf89lgRwfzkJCJ?domain=combine.us…>. For more information please contact combine(a)combine.org.au<mailto:combine@combine.org.au> Michael Charleston [cid:dd7d9f31-2dff-47a9-bd90-20318825f55c] Phylomania 2022 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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FW: Contract computation work ...
by Barbara Holland 11 Nov '22

11 Nov '22

fyi From: Alex Hewitt <alex.hewitt(a)utas.edu.au> Sent: Wednesday, 9 November 2022 8:01 PM To: Barbara Holland <barbara.holland(a)utas.edu.au> Subject: Contract computation work ... Hi Barbara, You wouldn't happen to know any local students/graduates who may be interested in some contract bioinformatics work? We have some NGS data which relate to viral quasispecies and we are keen to churn through some analyses etc. It would be good if they knew python and R ... Best wishes, Alex Hewitt m. 0407359824 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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