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166 discussions

command-line day
by Michael Charleston 12 Aug '16

12 Aug '16

Dear all, The Mid Semester Break is soon to be upon us (August 29 - September 2). As I’ve mentioned before, I’d be happy to run a workshop in using the command-line; with that in mind, I’d like to get a sense of which day would suit people the best, from Monday, Tuesday, Thursday or Friday that week (I’m getting Older on Wednesday so the trauma might be too much). If you’ve missed out on the DaSH Software Carpentry course, or even if you didn’t, you might like to drop in to a completely unstructured day in which you can, with luck & perseverance, become more comfortable using the command-line and Unix. If there are any of you out there who’d like to drop in to help too, that would be great. (Hint, hint.) Here’s<http://doodle.com/poll/t76nwg6addv5tcab> the Doodle Poll. 30 people max: that’s doubling up on 11 of the computers which will probably be good to do. Cheers 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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RNA-Seq workshop
by Michael Charleston 11 Aug '16

11 Aug '16

Hello hello, Great news – COMBINE<https://combine.org.au/> has found people willing and able to run a workshop in late November on RNA-Seq expression data analysis. Andrew Phipps and I are coordinating with the lovely folk in COMBINE to bring you the absolute best in how to Do That Thing, in a TWO DAY WORKSHOP here in UTAS. There will be a small cost! It will be to cover catering (and because people are often willing to skip free events; some interesting related reading here<http://rady.ucsd.edu/faculty/directory/gneezy/pub/docs/fine.pdf>). Who’s in? Don’t forget, Andrew is also presenting some of his thoughts on CHiP-Seq this afternoon, 4pm. See you then! Pub afterwards is also an option of course. Cheers 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 next meeting
by Michael Charleston 04 Aug '16

04 Aug '16

… of course *next meeting* is the one NEXT WEEK, which is August 11th. No meeting today, in case I inadvertently confused you! 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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Variant call tools
by Sanjay Gautam 01 Aug '16

01 Aug '16

Hi, I am currently working on next generation sequencing platform. I will be pleased to hear if someone in the group could help me get into variant call methods (particularly SNPeff, SAMtools and bcftools platform). Thank you ? Sanjay Gautam, B.Sc. MLT, M.Sc. Med. Microbiology PhD Student/School of Medicine/ Breathe Well Center University of Tasmania, 17 Liverpool Street, Hobart TAS 7000,Australia M +61416181795<tel:%2B61416181795> / E.mail: Sanjay.Gautam(a)utas.edu.au<mailto:Sanjay.Gautam@utas.edu.au> 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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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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