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

Meeting Thursday 4pm 25th August, Lecture Theatre 2, As Usual.
by Michael Charleston 24 Aug '16

24 Aug '16

Hi folks, Tomorrow’s meeting will be an opportunity for you all to help me out with the bioinformatics page! Oh, you go, what fun that sounds… but I do want to get your input on what content to put in it. I’m happy to fill it in, but it’s to be our public face and no doubt you have opinions of value. In case you can’t make it to the meeting, and to maybe get you thinking about it now, I’m just going to paste in some images from the current site, which is not live, to give you an idea of what it looks like so far: [cid:C302208D-0403-43F6-B79D-E319E6BA7E89@maths.utas.edu.au][cid:E16040A2-4F72-4D50-9DE2-CEBD11688C1B@maths.utas.edu.au][cid:36FB9CD3-5499-47B8-AFE3-1DF6746B4AA5@maths.utas.edu.au] and here’s some text: Research Because bioinformatics is so broad, research in it is very diverse. Here at UTAS we have a very strong group of researchers interested in a problem of particular interest called phylogenetics, which is how to most reliably estimate the evolutionary history of groups of species, given that we do not have a time machine. What we do have is usually in the form of molecular sequences – sequences of nucleotides that make up DNA, or amino acids that make up proteins, from which we have to try to work out what are the evolutionary relationships between the species. It's a biologically, statistically, and computational problem. Study If you're interested in learning about bioinformatics, there are several options open to you. One of the most obvious is the University unit, Introduction to Bioinformatics<http://www.utas.edu.au/courses/set/units/kma712-bioinformatics>. This 700-level unit introduces research students to some of the techniques and concepts that underpin usingbioinformatics in the Life Sciences. It helps you get to grips with using the command-line (or terminal) to run programs on remote machines, such as in the Cloud. It exposes you to some of the key challenges in bioinformatics, from the computational complexity of assembling a genome and the fastest ways to find matching DNA sequences in a database, to the statistical difficulty of dealing with many thousands of tests and accounting for thousands of potential false positives. There are also many potential research projects in, or using, bioinformatics – in understanding how gene activity varies with different conditions, or how bio-molecules evolve, or how much gene flow there is between different eucalypts. The best way to find out what projects we're currently pursuing is by contacting some of us – go to the Contacts page for details. It’s very much a draft as you can see, and I’d love some suggestions of what other kinds of things you’d like to see on the site. I’d like to add a page of external links and contacts we have for those who are connected in some way with UTAS bioinformatics – e.g., funding bodies – but not officially part of UTAS, and I’d like to include a list of PhD projects. Clearly also a link to this very mailing list would be useful. If all that takes only a short while then I’ll give a completely spontaneous talk on cophylogenetics. I have a suspicion I coined this term but you can google it if you don’t know.. Cheers, see you tomorrow! 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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command-line workshop
by Michael Charleston 15 Aug '16

15 Aug '16

Dear all, Thanks everyone who put down a preference for when they’d like to drop in on some command-line-fu. The slight majority have chosen Monday 29th August, All Day as their favourite option, so that is when it will be. Room 329 in the Maths & Physics building, Sandy Bay Campus. Do drop in any time from 9 to 5pm; I’ll be there almost all that time. If there are others who’d be willing to provide some expertise please let me know, I’d love to be able to plan on some helpers being there! 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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you'd think I'd know
by Michael Charleston 12 Aug '16

12 Aug '16

… *shakes head in disbelief* … ok my busy day is the Tuesday, not the Wednesday. My own fault. Ignore my dotardness… At any rate, given that the timing is clearly an issue, I’ll obviously be running another one a bit later :) 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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www.utas.edu.au/bioinformatics/
by Michael Charleston 12 Aug '16

12 Aug '16

Dear all, The website is coming along nicely, which is great! I asked at yesterday’s Bioinformatics meeting (before Andrew Phipps gave a great talk on bioinformatics in ChIP-Seq<https://bioinformaticstasmania.wordpress.com/2016/08/08/thursday-11th-augus…>) for some more graphics for the website. Currently we have two beautiful photos of eucalyptus kindly provided by Rebecca Jones, but it would be great, great great, to have some more. I’d most like to have * photos of organisms we work on; * pictures of us working (Sunday best, white lab-coat because we all wear lab coats, or fieldwork-camo); * microscope slides * really good diagrams! While Marketing prefers to work with photos and therefore high resolution TIFF and JPG images, a lot of what we do is producing great figures – so vector graphics of your beautiful gene regulatory network, or ecological model, or whatever, would be great too. Things I don’t want, and which you’d probably never want to provide anyway: * pictures of computers. At present I’m running the site, adding content as I can, but I welcome any thoughts and suggestions of what you’d like to see on it. At present it’s not open for general viewing but I’d like your opinion, so please let me know if you think there are major things that you’d like to see, or you’d like avoided, on the site. Alternatively, because I *do* have access, you can always drop in (I like visitors) and let me know to my actual face (erk, scary). Also, there’s a people page on the site. Currently there are three names on the page: mine, Jac Charlesworth (Menzies), and Chris Burridge (Biological Sciences). If you’re actually pretty into bioinformatics and you’d like your name to be on that page too, it can be set up, but due to our being in different Faculties, I cannot edit the People page directly: it has to be handled by the web services team centrally. Ergo, if you want your name on it, please let me know and I’ll request it of the web services team. Best wishes, sorry for all the emails, I promise it will settle down! 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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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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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. 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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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P.S.
by Michael Charleston 29 Jun '16

29 Jun '16

For trying out NeCTAR,bBring a laptop if you wish, and if you can access eduroam network. - Michael Charleston Associate Professor in Bioinformatics School of Physical Sciences University of Tasmania (Sent from my phone) 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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Risky but worth it
by Michael Charleston 29 Jun '16

29 Jun '16

Hi all, In attempt to help you all use the NeCTAR national computing (cloud-based) infrastructure, I'm going to break my usual rule (Never Do Live Demos) and take you through the why & how to set yourself up with a computer in the cloud. I'll choose a willing guinea pig (I have a volunteer already) and go through how to set up and then use a FREE, pretty powerful computer for your bioinformatics. Don't forget, Thursday 4pm in the maths & physics building -- come along! Best wishes Mike - Michael Charleston Associate Professor in Bioinformatics School of Physical Sciences University of Tasmania (Sent from my phone) 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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First announcement! Phylomania 2016
by Michael Charleston 27 Jun '16

27 Jun '16

Dear colleague, We’re delighted to announce the 8th annual theoretical phylogenetics meting, a.k.a. Phylomania 2016, to be held in Hobart from November 16th to 18th inclusive. We would love it if you would consider coming along! It’s a great, friendly, relaxed conference with a consistently high standard of presentations. And it’s in beautiful Hobart, which if you haven’t visited, you really should. Here’s the blurb, which I hope you’ll both read and circulate. This is the first call to register to attend Phylomania 2016 - The 8th Annual conference of the UTAS Theoretical Phylogenetics group, to be held 16th-18th November in Hobart, Tasmania. Phylomania will be held within the School of Physical Sciences at the University of Tasmania. The meeting will bring together mathematicians and biologists to discuss current research in phylogenetics. All the details and some pertinent local information can be found at the meeting website http://www.maths.utas.edu.au/phylomania/phylomania2016.htm General registration is expected to be $175, with reduced rates for students, to cover catering. To register your interest in attending please use the form on the website given above. The payment system is not yet set up but this gives you an idea of the cost. There’s also a place there for you to enter an abstract: if you do, use normal text, html, or LaTeX. If you only have a (rough!) title just now that’s fine, you can update us with more information closer to the conference. You can bring a talk, or a poster, or both! Please do feel free to forward this announcement to others who may be interested in attending — the more the merrier! Best wishes, Mike Charleston and the Theoretical Phylogenetics Group<http://www.maths.utas.edu.au/People/Holland/theoreticalPhylogenetics.htm> 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: workflows – please!
by Michael Charleston 15 Jun '16

15 Jun '16

Hi folks, There’s only a day to send in your workflows, else we’ll have to re-think our meeting topic for tomorrow. Does anyone have something for me? 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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Fwd: 2016 Winter School early bird rego closing tomorrow
by Michael Charleston 14 Jun '16

14 Jun '16

In case you didn’t already know about this… Begin forwarded message: From: Karen Bradford <karen.bradford(a)utas.edu.au<mailto:karen.bradford@utas.edu.au>> Subject: FW: 2016 Winter School early bird rego closing tomorrow Date: 14 June 2016 at 1:10:27 PM AEST To: Mathematics & Physics - All <SET-DL-Maths-And-Physics-All(a)utas.ad.internal<mailto:SET-DL-Maths-And-Physics-All@utas.ad.internal>> Winter School 2016: It's like an international conference on your doorstep, you'd be crazy to miss it! Early bird registration for Winter School closes tomorrow (15 June 2016). Registration includes tasty lunches and morning/afternoon teas! All for only $260 for students if you register now! ** 2016 Winter School in Mathematical & Computational Biology ** A premier annual bioinformatics training event in Australia for 13 years, the Winter School in Mathematical & Computational Biology will be held 4 to 8 July 2016 at the Institute for Molecular Science, The University of Queensland, St Lucia. Only $260 for the whole week for early bird students! The series of winter schools is designed to introduce bioinformatics, mathematical and computational biology to advanced undergraduate and postgraduate students, postdoctoral researchers and others working in the fields of biology, mathematics, statistics, computer science, information technology, complex systems analysis, and chemical and medical sciences and engineering. THEMES * Next generation sequencing & bioinformatics * Bioinformatics methods, models and applications to disease * Advanced bio-data visualisation * Ecogenomics FEATURED SPEAKERS -- Professor Burkhard Rost, Technische Universität München (TUM), Munich, Germany -- Professor Ed DeLong, University of Hawaii, USA -- Professor Howard Ochman, University of Texas, USA -- Dr Seán O'Donoghue, CSIRO -- Dr Kate Patterson, Garvin Institute of Medical Research -- Dr Mathieu Bourgey, Research and Development Canadian Centre for Computational Genomics (C3G), Canada Speakers at Winter School are chosen as great presenters and world leaders in their field. See website<http://bioinformatics.org.au/ws16> for the complete list of 30 or so speakers and presentation titles. WORKSHOP & BOOTCAMP A Genomics Virtual Laboratory training workshop (limited places) will be run during the Winter School on Wednesday 6th July. A Software Carpentry Bootcamp (11-12 July) is also being run in conjunction with the Winter School. Both events were fully subscribed in days last year, so register early to avoid disappointment. FEEDBACK FROM PREVIOUS WINTER SCHOOLS “I would strongly encourage all biologists even without any mathematical background to attend the Winter School.” “Fantastic speakers.” “Great networking opportunities.” “It takes special talent to pull off a conference people actually enjoy attending and it was thanks to some of the more charismatic orators, that I was able to enjoy the Winter School so much.” “Gave me the confidence I need to talk to other people and bioinformaticians about the analysis of my NGS data. Thanks." KEY DATES Online registration: Monday 20 April to 26 June 2016 - Early bird – 20 April to 15 June 2016 - Normal – 16 June to 26 June 2016 -- ----------------------------------------------------------------------- Dr Nicholas Hamilton, Institute BioMathematician Bio-Imaging, Modelling and Data Viz Institute for Molecular Bioscience Queensland Cyber Infrastructure Foundation (QCIF) Research Computing Centre (RCC) The University of Queensland. Ph:+61 7 3346 2033 | Fax: +61 7 3346 2101 2016 Winter School in Mathematical and Computational Biology http://bioinformatics.org.au/ws16/ Home Page http://www.imb.uq.edu.au/nick-hamilton Software http://icluster.imb.uq.edu.au<http://icluster.imb.uq.edu.au/> http://obcol.imb.uq.edu.au<http://obcol.imb.uq.edu.au/> http://domaindraw.imb.uq.edu.au<http://domaindraw.imb.uq.edu.au/> http://visiblecell.org<http://visiblecell.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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Fwd: Invitation to Royal Society Tas Winter Series July 2016
by Michael Charleston 10 Jun '16

10 Jun '16

Something for the diaries! This year the Royal Society Tas has a great program of Winter Lectures lined up, which I'm sure which will be of interest to a wide audience.The topic is 'Living in an uncertain world: data and decisions'. More information is available at: www.rst.org<http://www.rst.org><http://www.rst.org>. Many thanks and kind regards Mary Mary Koolhof Publicity Officer The Royal Society of Tasmania 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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Tomorrow's meeting
by Michael Charleston 01 Jun '16

01 Jun '16

Dear all, Don’t forget tomorrow’s Bioinformatics Club meeting: 4pm, Lecture Theatre 2 in the Maths & Physics building. The goal will be to create a graph that relates data, methods, and analyses. For more detail check out the blog note at https://bioinformaticstasmania.wordpress.com/2016/05/27/its-all-connected-m…. Bring your sketched workflows and ideas! We might need a really big piece of paper… 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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