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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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Phylomania2019
by Michael Charleston 05 Nov '19

05 Nov '19

Hi there! If you haven't registered for Phylomania 2019 (It Goes To Eleven) then there's still time. It runs from 20th to 22nd November, here in Sandy Bay. While we are now in the throes of putting the schedule together we do have some room for a few more presentations, so head over to http://www.maths.utas.edu.au/phylomania/phylomania2019.htm and register! This is *the* phylogenetics conference in Australia, even if we do say so ourselves: it's friendly, it's leading edge stuff, it's varied, and we have good food, and fantastic t-shirts.. Cheers, Mike Michael Charleston [cid:fc08c31d-1c9b-493b-9670-f4b20456aa65] 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 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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You may have missed an announcement for a beginner's guide to phylogenetic analysis that will be run on Friday 8th November
by Michael Charleston 05 Nov '19

05 Nov '19

In case this is true, check out https://www.biocommons.org.au/events where you can register for a free, easy afternoon of an introduction to phylogenetic estimation, guided by me and with the expert help of Dr Bennet McComish. The venue is in the Maths and Physics building and it will run from 1-4pm. This workshop is the first of two planned; the second will be a follow-up where you bring your own problematic data for discussion or help. It will be run nationally via videoconfering technology, thanks to the amazing people at the Australian Biocommons, which used to be EMBL-ABR. Let me know if you're interested, and go register! (Did I mention it's free?) Michael Charleston [cid:9d36606b-6dc7-49e6-896e-ea2656ed16a4] 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 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: Five permanent positions in bioinformatics/biostatistics (M/F) at the Institut Pasteur (Paris)
by Michael Charleston 20 Aug '19

20 Aug '19

From: Olivier GASCUEL <olivier.gascuel(a)pasteur.fr> Sent: Tuesday, 20 August 2019 2:32 AM To: Olivier GASCUEL <olivier.gascuel(a)pasteur.fr> Subject: Five permanent positions in bioinformatics/biostatistics (M/F) at the Institut Pasteur (Paris) Dear Colleagues and Friends, Please forward this job announcement (and sorry for the spam). Don’t hesitate if you need further information. Best regards, Olivier Gascuel ::::::::::::::::::::::::::::::: Five permanent positions in bioinformatics/biostatistics (M/F) at the Institut Pasteur (Paris) The Hub of Bioinformatics and Biostatistics, created in 2015 to provide support in these domains to the Units and Platforms of the Institut Pasteur, is recruiting five bioinformaticians to continue the support activities and taking over the increasing requests for the analysis of biological data. The recruited engineers will be allocated for part of their time to Research Units and/or Technology Platforms. Teaching missions (academic and/or professional education, possibly internationally) may also be requested. Tasks and responsibilities: The main mission is to provide support to Research Units and Platforms for the bioinformatics and/or biostatistics analysis of their data. This support includes : - advising and guiding the implementation of methods and tools for the analysis of biological data, - maintaining an active bibliographic survey and evaluating published tools and methods, - developing, when necessary, new analytical methods and tools, - analyzing data in collaboration with the Units and Platforms, - participating in the development of national and international collaborative projects, - ensuring the transfer of tools and expertise to the Units and Platforms, - delivering training courses in bioinformatics and biostatistics, - maintaining the methods and tools developed by the Units, and ensuring their integration into core software solutions like Galaxy or Snakemake, - interacting with the Institut Pasteur International Network (IPIN, 33 institutes around the world), in particular for trainings and data analysis, - participating in the writing of scientific articles. Job profiles: Several needs have been identified and the following profiles are expected: - Analysis of standard HTS data (variant calling, genome assembly, differential expression, ...), - Metagenomics, metatranscriptomics, - Single-cell analysis , - Analysis of metabolomic data, - Epigenomics and epitranscriptomics - Flux cytometry data analysis - Biological databases - Proteomics (main affiliation to the UTechS Mass Spectrometry for Biology) - Omics data analysis and integration (affiliation to the Hearing Institut) Candidate profiles and conditions: It is necessary to satisfy one of the two following profiles: - Bac+5 level (Master, engineer or equivalent) in bioinformatics, statistics, applied mathematics, or a related field, followed by a professional experience of at least 3 years in research or support for research in bioinformatics, biostatistics, or biological data analysis, - PhD in bioinformatics, statistics, applied mathematics or a related field, followed by at least 2 years of professional experience in research or research support in bioinformatics, biostatistics, or biological data analysis. Teaching experience in bioinformatics/biostatistics will be appreciated. The Hub and Institut Pasteur are committed to foster gender equality, so female candidates are encouraged to apply. To apply: Applications (cover letter, detailed CV, and reference contact) should be submitted online via the following URL: https://c3bi.pasteur.fr/jobs/hub-2019-available-positions/hub-2019-job-appl…<https://protect-au.mimecast.com/s/DXEpCNLwPnf2DYE6smkifB?domain=c3bi.pasteu…> The deadline for applying is September 8 of 2019. Candidate pre-selection will be on October 1st . Successful candidates will be received for interviews between October 8 to 10 of 2019 (please, make sure to be available for these dates). Hiring date is planned between December 2019 and March 2020. 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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