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167 discussions

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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