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We are hiring! Don't forget to apply!
by Michael Charleston 20 Jun '22

20 Jun '22

Dear bioinformatics folk, If anyone out there is interested in a challenging, exciting and all-over wonderful three-year full-time research position developing new bioinformatics tools to tackle some cool problems, please look at the link below! https://careers.utas.edu.au/en/job/497476/postdoctoral-research-fellow The position is funded by the ARC Center of Excellence for Plant Success in Nature and Agriculture. It will be based in Hobart, Tasmania. The successful applicant should have a PhD in bioinformatics, computational biology, biostatistics or similar. We want to find someone who will be able to think outside the box and create new approaches that, with the expertise in plant science in the Centre, will enable researchers to uncover novel, complex molecular interactions from multiple -omics data. Programming and mathematical skills are more important than biological background. Feel free to contact me, Jazmine Humphreys (jazmine.humphreys(a)utas.edu.au) or Steve Smith (steven.smith(a)utas.edu.au) for more details, but applications must be made via the link above: don't send them straight to me! If you are unsure whether you have all the boxes ticked, please do get in touch. We are particularly keen to have a diverse range of backgrounds and experience talk to us. Applications close on 29th June - you have a bit over a week! (Blurb from the ad below:) We are seeking to appoint a Postdoctoral Research Fellow in the field of bioinformatics, School of Natural Sciences (https://www.utas.edu.au/natural-sciences), part of the College of Sciences and Engineering (https://universitytasmania.sharepoint.com/sites/CoSE). This position will be located within the School of Natural Sciences. The Postdoctoral Research Fellow will undertake research as part of a project funded by the Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, at the University of Tasmania node. The candidate will contribute to a key project within the Centre led by Chief Investigator Prof. Steven Smith and Prof. Michael Charleston entitled ‘Integrating multi-omics data to reveal gene expression networks in plants.’ The project will involve collaboration with other nodes of the Centre of Excellence. The Postdoctoral Research Fellow will develop new computational tools to gain greater insight into gene regulation by integrating different -omics datasets and interrogating them in ways that will reveal previously inaccessible information and understanding. This will require extending existing software packages while laying the groundwork to develop new analysis pipelines and programs. The researcher should have recognised expertise in biostatistics / bioinformatics, and programming, e.g., using R, python or C++. The researcher will be actively engaged with experimental biologists from the outset to ensure synergy between experimental and computational biology. In addition, they will contribute substantially to interaction with collaborators, project integration and reporting, and the supervision of research students. The appointee will be expected to operate with a degree of independence following general direction from the project leaders, and to interact positively and productively with other researchers participating in the project. Michael Charleston [cid:9e911cb1-c07d-40c9-a5ef-2f508c3b06e4][cid:a80a6fbd-e9dd-4c10-aa30-b218620ba092] 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: Seminar today 3pm - Joshua Stevenson
by Jeremy Sumner 19 May '22

19 May '22

Dear all, Just a friendly reminder that we have an ANZIAM* seminar this afternoon given by Joshua Stevenson via ZOOM at 3pm. Please see details below. Meeting URL: https://utas.zoom.us/j/88961934178 Meeting ID: 889 6193 4178 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 Dr Courtney Quinn Lecturer (Mathematics) School of Natural Sciences College of Sciences and Engineering University of Tasmania E: courtney.quinn(a)utas.edu.au<mailto:courtney.quinn@utas.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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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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