July 2016 - bioinformatics-list - lists2.utas.edu.au

RNA-Seq Workshop
by Michael Charleston 01 Aug '16

01 Aug '16

Dear all, I’m happy to let you know that we’re now (with COMBINE<https://combine.org.au/>) investigating the feasibility of an RNA-Seq workshop to run here on Sandy Bay campus, in late November. If anyone knows of any major clashes around that time please let me know, so we can try to avoid them. I’m aware of (because I’m running) Phylomania 2016<http://www.maths.utas.edu.au/phylomania/phylomania2016.htm>, which goes 16-18 November; the RNA-Seq workshop would be after that. Best wishes Mike Michael Charleston Associate Professor in Bioinformatics School of Physical 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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Graphics
by Michael Charleston 01 Aug '16

01 Aug '16

Dear bioinformaticians et al., I’m collating graphics for the new website that will be at http://www.utas.edu.au/bioinformatics (or something close), and would love some more beautiful pictures! If you have some of your own images – photos, figures, diagrams, etc. – that you’d be happy to have on such a site, then please can you let me know? If they’re too big to email then we can use other means, no problem. The added benefit to you would be that all such images can be linked back to you. (There: enlightened self interest can be leveraged..) Best wishes Mike Michael Charleston Associate Professor in Bioinformatics School of Physical 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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Fwd: DaSH: Software Carpentry Workshops, August-September
by Michael Charleston 29 Jul '16

29 Jul '16

Now, I’ve sent out a link to the DaSH-run Software Carpentry Workshop already; those who are interested in learning some coding (both R and python will be taught) should consider coming along! Also, if there are any of you out there with Friday mornings free, or at least available for the next couple of months, who could help out with the training, you are wonderful and invaluable people and you should definitely feel free to volunteer some of your expertise. The more one-on-one help available, the better. Let me know if you’d like to offer some help for some of the sessions. Also, places are filling up fast. They’re already half-full… Best wishes, Michael Charleston Associate Professor in Bioinformatics School of Physical Sciences University of Tasmania AUSTRALIA phone: +61 3 6226 2444 Begin forwarded message: From: Michael Sumner <mdsumner(a)gmail.com<mailto:mdsumner@gmail.com>> Subject: DaSH: Software Carpentry Workshops, August-September Date: 29 July 2016 at 9:41:27 AM AEST To: <michael.charleston(a)utas.edu.au<mailto:michael.charleston@utas.edu.au>> Reply-To: Michael Sumner <reply-19ea1=b688fc55-c8fb-47b4-96b2-5ad3c5683bb4(a)tinyletter.com<mailto:reply-19ea1=b688fc55-c8fb-47b4-96b2-5ad3c5683bb4@tinyletter.com>> Hi DaSHers, Following on from last year's workshops, Data Science Hobart will run its second Software Carpentry Workshop on Friday mornings in August and September 2016. Please see the schedule, and register here to attend: https://datasciencehobart.github.io/2016-08-05-hobart/ The sessions start on 5 August at the IMAS waterfront building, please see the site above for all details. Happy DaSHing! Data Science Hobart <http://tinyletter.com/datasciencehobart> by Michael Sumner IMAS Waterfront Building, Castray Esplanade Hobart, Tasmania 7004 Australia Sent to michael.charleston(a)utas.edu.au <x-msg://41/#> — Unsubscribe <http://tinyletter.com/datasciencehobart/unsub?c=b688fc55-c8fb-47b4-96b2-5ad…> Delivered by [TinyLetter]<http://www.tinyletter.com/> 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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Bioinformatics Club: today's meeting is cancelled
by Michael Charleston 28 Jul '16

28 Jul '16

...But stay tuned for next week: Andrew Phipps has kindly offered to present a workflow (actually he said pipeline but you know I have issues with that term!) on ChIP-Seq analysis or something similar. Best wishes Mike Michael Charleston Associate Professor in Bioinformatics School of Physical 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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Bioinformatics club: Today's meeting
by Michael Charleston 28 Jul '16

28 Jul '16

Dear all, Last chance: if you have something (anything!) to present, please let me know; or we will cancel today’s meeting. Please can someone present a paper or do a seminar in a fortnight? Best wishes Mike Michael Charleston Associate Professor in Bioinformatics School of Physical 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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DataScience Hobart is hosting a Software Carpentry Workshop
by Michael Charleston 26 Jul '16

26 Jul '16

https://datasciencehobart.github.io/2016-08-05-hobart/ Michael Charleston Associate Professor in Bioinformatics School of Physical 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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Bioinformatics @ UTAS
by Michael Charleston 21 Jul '16

21 Jul '16

Dear all, As I’ve mentioned before there is to be a web space for bioinformatics, at http://www.utas.edu.au/bioinformatics. It’s now being created for us (it fell through the cracks once it was approved, but they're back on track now). Can anyone help me out with the following? * I need some funky bioinformatics-y graphics. I have some of my own but the more the better. If you have some great high-quality graphics relating to your bioinformatics work, or organisms you are studying, and you’re willing to have them go on the UTAS “face of bioinformatics” page, please let me know! There are some fine examples of what can be done here<http://www.utas.edu.au/research/research-rankings-and-performance> and here<http://www.utas.edu.au/land-food>, and don’t forget the sage advice on what to include, here<https://xkcd.com/773/>. * I will add my name, and Jac Charlesworth’s as “People mainly associated with bioinformatics here at UTAS”. If you’d like your home page or lab page or contact details findable on this site, please let me know and I will send the information on to the web services team. I’m not assuming you want to spend heaps of time on it, but if you want to take a more admin/leading role let me know that too! (I’m ok if you don’t; just don’t want to leave people out..) * At present the idea is to have a fairly standard format: Home / Research / News / People / Contact / Resources menus, and a link to the blog, which will be at https://blogs.utas.edu.au/bioinformatics/ and which have all the content imported from our current unofficial blog. But maybe I’m missing something! Is there something in particular that you feel we should urgently have? I’ll be able to make edits on the site so it won’t be set in stone, but it would be good to have it more-or-less right when it goes live. Perhaps a “find an expert” page, or a “career advice” or “my data are awful what do I do?” page. Speak now, or, well, later! Right that’s enough for now: I have programming to do. Michael Charleston Associate Professor in Bioinformatics School of Physical 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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Next week's Bioinformatics Club
by Michael Charleston 21 Jul '16

21 Jul '16

Hello folks, It’s about time we had a presentation from someone other than me – does anyone have a paper they’d like to present, or a seminar they’ve prepared for something else? If not then I *can* do one on cophylogenetic analysis or network alignment, but then I’ll have nothing up my sleeve…. Oh, and if you would like to get COMBINE to do a workshop in RNASeq analysis<http://combine-australia.github.io/2016-05-11-RNAseq/> please let me know. If there isn’t interest we’ll do something else.. Cheers Mike p.s. What about using the “off” weeks for more social, less formal ad-hoc get-togethers? Michael Charleston Associate Professor in Bioinformatics School of Physical 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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2016 EMBL Australia *Postgraduate* Symposium
by Jac Charlesworth 20 Jul '16

20 Jul '16

Hi again, This one is for all the postgrads or supervisors with relevant postgrads. The EMBL Australia Postgraduate Symposium - run by students for students - is coming up. I highly recommend you get your students to attend, it is brilliant. Last message from me today ;) Thanks, Jac EMBL Australia 2016 Postgraduate Symposium Early bird registration now open - 2016 EMBL Australia Postgraduate Symposium The EMBL Australia 2016 Postgraduate Symposium Committee would like to invite all research students to attend the 2016 EMBL Australia Postgraduate Symposium. Symposium Date: Wednesday 16th November - Friday 18th November 2016 Venue: South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA Speakers: We have an excellent line-up of both national and international speakers including Prof John Quackenbush and Prof Nadia Rosenthal, among many others Registration and abstract submission are now open! Click here<https://eaps2016.eventbrite.com.au/> to register and secure your place. End of early bird registration: 26th August 2016 Due date for abstracts: 2nd September 2016 The symposium brings together students from a broad range of disciplines around Australia and is a great opportunity to showcase your work in an open and friendly environment. We welcome all levels of research students; Honours, Masters and PhD. To make the symposium more accessible to interstate students we are subsidising the cost of accommodation at YHA Adelaide; only a short walk from SAHMRI. Availability is limited so be sure to register early to avoid disappointment. We will also be hosting a significantly subsidised conference dinner at the Adelaide Pavilion. If you are one of the first 25 early bird tickets to register, you will get a free conference dinner! For more information, please see the attached flyer or visit our website http://eaps.org.au/. We look forwards to seeing you in November! Kind regards, The 2016 EMBL Postgraduate Symposium Organising Committee. Email: committee.phdsymposium(a)emblaustralia.org<mailto:committee.phdsymposium@emblaustralia.org> Facebook: https://www.facebook.com/EMBLAphdsymposium/ Twitter: https://twitter.com/emblausymposium -- Jane McCausland Student Programs Coordinator EMBL Australia Australian Regenerative Medicine Institute Level 1, 15 Innovation Walk (Building 75) Monash University ph: (03) 990 29607 email: jane.mccausland(a)monash.edu<mailto:jane.mccausland@monash.edu> 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: Early Bird & Call for Abstracts closing at the end of this month
by Jac Charlesworth 20 Jul '16

20 Jul '16

Hi folks, The Australasian Genomic Technologies Association (AGTA) conference is being held in Auckland in October this year. It's a great, interdisciplinary and bioinformatics-heavy conference. Details below. Dr Jac Charlesworth Senior Research Fellow - Computational Genomics Menzies Institute for Medical Research University of Tasmania p 6226 4607 | m 0424 709 440 | f 6226 7704 17 Liverpool St (Private Bag 23) Hobart TAS 7001 | www.menzies.utas.edu.au<http://www.menzies.utas.edu.au/> 2016 AGTA/NZ NGS Conference Early Bird Registration & Call for Abstracts closing at the end of the month View this email in your browser<http://www.agtaconference.org/wp-content/uploads/2016/07/AGTA-E-blast-July-…> [https://gallery.mailchimp.com/01aee0597c0bbdea3855bcddc/images/f42f36e7-9f3…]<http://www.agtaconference.org/> EARLY BIRD REGISTRATION & CALL FOR ABSTRACTS CLOSING AT THE END OF THIS MONTH Closing 5pm on 29 July CLICK HERE TO VIEW THE FULL PROGRAM<http://www.agtaconference.org/program/> Register before the close of Early Bird to enter the competition to win a free analysis of your sample using MinION technology Do you have a favourite DNA sample (non-human in origin) that you would like to be sequenced using the long-read MinION technology? If so, register for the 2016 AGTA/NZ NGS Conference before the close of Early Bird (29 July) and enter the competition to win a free analysis of your sample. Click here<http://www.agtaconference.org/minion-technology-competition/> for more information. Thanks to Oxford Nanopore Technologies and Genesearch NZ for providing support for this project. For more details about MinION sequencing technology visit https://www.nanoporetech.com/products-services/minion-mki. REGISTER NOW<http://www.agtaconference.org/registration/> SUBMIT AN ABSTRACT<http://www.agtaconference.org/abstract-submissions/> PRE-CONFERENCE WORKSHOPS Two Pre-Conference Workshops have now been confirmed, to be held on Sunday 9 October from 10am - 4.30pm at the Old Government House. Cost is $55 per person, which includes lunch, morning and afternoon refreshments. Delegates are invited to attend one of the following workshops. Click here<http://www.agtaconference.org/pre-conference-workshops/> for more information on each. 1. Bisulfite Sequencing: Genomewide Methylation Sequencing 2. Metagenomics: Understanding microbial communities with next-generation sequencing [https://gallery.mailchimp.com/01aee0597c0bbdea3855bcddc/images/90a669a3-4d7…]<http://www.agtaconference.org/getting-there/> AIR NEW ZEALAND DISCOUNT CODE A promotional code will be available for delegates registered for the 2016 AGTA/NZ NGS Conference to receive a 10% discount on return airfares from Australia to New Zealand for travel between 5 October and 16 October. The code has been emailed to registered delegates and will be emailed to any new registrants via their confirmation email. View our website<http://www.agtaconference.org/getting-there/> for more information and terms and conditions. THANK YOU TO OUR SPONSORS [https://gallery.mailchimp.com/01aee0597c0bbdea3855bcddc/images/b0149ff7-be1…]<http://www.agtaconference.org/sponsors/> Have a question? Contact us! Annika Hofsink Conference Coordinator Leishman Associates annika(a)leishman-associates.com.au<mailto:annika@leishman-associates.com.au?subject=AGTA%2FNGS%202016%20Enquiry> 03 6234 7844 <http://www.leishman-associates.com.au/>[https://gallery.mailchimp.com/01aee0597c0bbdea3855bcddc/images/a9fc15f7-136…]<http://www.leishman-associates.com.au/><http://www.leishman-associates.com.au/> [https://cdn-images.mailchimp.com/icons/social-block-v2/outline-dark-faceboo…]<http://leishman-associates.us12.list-manage2.com/track/click?u=01aee0597c0b…> Share<http://leishman-associates.us12.list-manage2.com/track/click?u=01aee0597c0b…> [https://cdn-images.mailchimp.com/icons/social-block-v2/outline-dark-twitter…]<http://leishman-associates.us12.list-manage1.com/track/click?u=01aee0597c0b…> Tweet<http://leishman-associates.us12.list-manage1.com/track/click?u=01aee0597c0b…> [https://cdn-images.mailchimp.com/icons/social-block-v2/outline-dark-linkedi…]<http://leishman-associates.us12.list-manage1.com/track/click?u=01aee0597c0b…> Share<http://leishman-associates.us12.list-manage1.com/track/click?u=01aee0597c0b…> This email was sent by Leishman Associates, Conference & Event Management, 113 Harrington Street Hobart, TAS, 7000 on behalf of the organisers of the above mentioned conference. As the recipient you have received this notice as a past delegate or potential delegate of the above mentioned conference. Unsubscribe<https://leishman.eventsair.com/Unsubscribe/17e7bbde-3552-4d21-9f5a-d32f042b…> 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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bioinformatics-list July 2016