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173 discussions

Command-line workshop – a few notes
by Michael Charleston 28 Aug '16

28 Aug '16

Hi folks, If you’re coming along to the command-line workshop / drop-in tomorrow in the Maths & Physics building, I’ve prepared a few thoughts on the original wordpress site (which I think has more followers still), here<https://bioinformaticstasmania.wordpress.com/2016/08/28/command-line-fu/>. Enjoy! Michael Charleston A/Prof in Bioinformatics School of Physical Sciences University of Tasmania phone: +61 3 6226 2444; ext 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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AB^3ACBS 2016 – Conference announcement!
by Michael Charleston 26 Aug '16

26 Aug '16

Check out the conference below! (And the command-line workshop is on THIS MONDAY, the 29th!) 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 on Monday!
by Michael Charleston 26 Aug '16

26 Aug '16

If you’re interested in coming to learn a bit of command-line-fu in a very informal environment, please come along to the Maths & Physics building, room 335 any from from 9am. If you have a computer of your own, do bring it – if you don’t have a University (UTAS) log-in you’ll need your own anyway! If you’re running Windows, and want to do that on the day, you’ll have to have Cygwin<https://www.cygwin.com/> installed. I’ll run through some basics and there will be worksheets to go through; I’ll also attempt to upload some exercises to the blog over the weekend. I’ll try to show you how to copy files around, to find out what’s in files without using a GUI, and we might even have a crack at some scripting, to turn tedious jobs into repeatable workflows.. Don’t worry if you haven’t already let me know you’d like to come: just drop by. 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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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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