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167 discussions

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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AMSI BioInfoSummer 2022, 21-24 November, The University of Melbourne - register now
by Michael Charleston 08 Aug '22

08 Aug '22

[ Or stay in Tasmania for Phylomania #14, November 23-25! (Official announcement and registration page soon) (yes, sorry they clash) ] Registrations are now open for AMSI BioInfoSummer 2022<https://protect-au.mimecast.com/s/OyLsCnxyDVH7yBJBzsrxumv?domain=bis.amsi.o…>. The four-day bioinformatics conference will be hosted by Melbourne Integrative Genomics at The University of Melbourne from 21-24 November. The program includes specialist lectures, hands-on workshops, an interactive careers advice session, a public lecture and networking events. Delegates are strongly encouraged to attend in person to maximise their conference experience however virtual participation is also available. Conference themes: * High-resolution biology * Genome architecture * Whole-cell modelling * Populations As usual, we need your help to promote this program please. How you can help: 1. Forward the BioInfoSummer 2022 event emails through your networks as your receive them (attached is the latest one sent yesterday) 2. Display the attached digital posters on your electronic signage boards around your departments/organisations (please advise if you require different sizing) 3. Ask lecturers and tutors to promote in classes by including the attached posters in their slide deck 4. Encourage your students, ECRs and colleagues to register 5. Make your students aware of any travel funding they can access from their home departments to support their attendance AMSI BioInfoSummer 2022 21-24 November | The University of Melbourne bis.amsi.org.au<https://protect-au.mimecast.com/s/OyLsCnxyDVH7yBJBzsrxumv?domain=bis.amsi.o…> Audience: 3rd year undergraduates through to early career researchers, academics and industry professionals Registration fees: Discounted AMSI member four-day conference registration $160 student / $320 standard (day registration and virtual participation also available). Travel grants: Students can apply for a travel grant sponsored by Australian BioCommons to support in-person participation in Melbourne. Applications close midnight Monday 17 October. We have a limited grant budget so ask all applicants to explore what funding is available to them at their home universities to supplement AMSI support. Poster abstract submissions close Monday 31 October. A great opportunity for delegates to share their research with the bioinformatics community. Up to $800 in prizes in prizes for the best poster and best fast forward talks Kind regards Angela Angela Coughlin Program Manager, Research and Higher Education [cid:image001.png@01D8A812.310FB3E0] Australian Mathematical Sciences Institute Building 161, Monash Rd, c/- The University of Melbourne, Victoria 3010 Australia P: 03 8344 2103 | E: angela.coughlin(a)amsi.org.au<mailto:angela.coughlin@amsi.org.au> | W: amsi.org.au<https://protect-au.mimecast.com/s/n5LBCoVzE9HroW7WMC0QxxO?domain=amsi.org.a…> [cid:image002.png@01D8A812.310FB3E0]<https://protect-au.mimecast.com/s/Yl65Cp8AG6fnl6j6Gc6qCG8?domain=facebook.c…> [cid:image003.png@01D8A812.310FB3E0] <https://protect-au.mimecast.com/s/la9OCq7BJXt84wpwDu9Z2Id?domain=twitter.com> [cid:image004.png@01D8A812.310FB3E0] <https://protect-au.mimecast.com/s/e-shCr8DKNf8NJ5JpuO9lqi?domain=au.linkedi…> [cid:image005.png@01D8A812.310FB3E0]<https://protect-au.mimecast.com/s/OyLsCnxyDVH7yBJBzsrxumv?domain=bis.amsi.o…> 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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BioHackathon 2022
by Michael Charleston 25 Jul '22

25 Jul '22

This just in! (ok while I was on leave)... Help make the BioHackathon global Are you interested in joining us for the Australian Outpost of the BioHackathon Europe? This is a unique opportunity to participate in a significant global event and network with your international peers while working locally on practical coding challenges. BioCommons will cover flights and accommodation for the duration of ELIXIR’s BioHackathon, 7-11 November 2022. Expressions of interest due 1 Aug 2022. Find your project and express your interest<https://protect-au.mimecast.com/s/8aQjC3Q870Up8WAXATgM6NB?domain=biocommons…> Thanks very much! Michael Charleston [cid:53684f1d-32d2-4dea-840e-27d07d4a5634] 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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PhD scholarship at UTAS - Genetics of flowering in chickpea
by Jakob Butler 01 Jul '22

01 Jul '22

Hey bioinformatics-inclined people, We're on the hunt for a PhD student to join a project supervised by Jim Weller examining the genetics of flowering time in chickpeas. The prospective candidate will be using GWAS, bi-parental genetics and transcriptomics to exploring the architecture of phenology traits across the chickpea genome, with the aim of informing breeder decisions into the climate-addled future we're looking at. This project is under the banner of the GRDC, and comes with a guaranteed 3.5 year scholarship. We're hoping for someone who has completed Honours in molecular biology, bioinformatics, plant physiology or genetics (or anything else tangentially related). A background in plant science is not essential, but the project will involve a fair chunk of plant husbandry, so be prepared! Applications close on the 18th July (so about two weeks). https://www.utas.edu.au/research/degrees/available-projects/projects/biolog… Cheers, Jak --------------------------------------------------------------- Dr Jakob Butler | Postdoctoral research fellow University of Tasmania (UTAS) | School of Natural Sciences Rm372d, Life Sciences Building, Churchill Avenue, Hobart, TAS 7005, Australia M: +61 439 323 751 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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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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