April 2016 - bioinformatics-list

Thursday forum
by Sharee McCammon 28 Apr '16

28 Apr '16

Hi all If you missed last weeks Bioinformatics Forum, you missed a great opportunity to learn a lot about bioinformatics in a relaxed, knowledgable group. Bioinformatics is becoming increasingly important in all areas of molecular biology. Whether it frightens you or not, you need to know more about bioinformatics. It is much less daunting to learn about it with others in the Bioinformatics Forum, so don't waste the opportunity to come along every 2nd Thurs. What you can get out of these meetings...... * Access to bioinformatics experts * Answers to your bioinformatics questions - yep, even the dumb questions that aren't as dumb as you think * Info on software available * An understanding of new concepts * Networking with others working on similar data The next meeting will be Thurs 5th May 4-5pm, Lecture Theatre 2, Maths & Physics building. At this meeting we hope to have an open discussion around your bioinformatics questions. So please let Michael Charleston or me know if you have questions to bring along. See you there Cheers Sharee? Sharee McCammon Molecular Analyst Molecular Genetics Lab Central Science Laboratory University of Tasmania c\- Private Bag 54 Hobart, TAS 7001. Ph: (03) 6226 8553 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 Discussion : Just in case
by Michael Charleston 28 Apr '16

28 Apr '16

If you missed the memo, there’s nothing scheduled for bioinformatics discussion today – but if you want to come along for a chat I’m here :) 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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Journal club: paper suggestions for next Thursday (May 5th)
by Michael Charleston 27 Apr '16

27 Apr '16

Dear all, Does anyone have any papers they’d like to go through next Thursday? Voting is open! 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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Protein-ligand docking
by vikrant singh 15 Apr '16

15 Apr '16

Hi Sam, There are few softwares which you can use, including online server too. 1) Swiss dock (online sever for docking ) - http://www.swissdock.ch 2) AutoDock - http://autodock.scripps.edu (Open source) I have attached AutoDock Manual with this mail. Please find the attachment. Cheers, Vikrant On Fri, Apr 15, 2016 at 12:00 PM, < bioinformatics-list-request(a)list.utas.edu.au> wrote: > Send bioinformatics-list mailing list submissions to > bioinformatics-list(a)list.utas.edu.au > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.utas.edu.au/mailman/listinfo/bioinformatics-list > or, via email, send a message with subject or body 'help' to > bioinformatics-list-request(a)list.utas.edu.au > > You can reach the person managing the list at > bioinformatics-list-owner(a)list.utas.edu.au > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of bioinformatics-list digest..." > > > Today's Topics: > > 1. Protein-ligand docking (Sam Cook) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 14 Apr 2016 04:53:24 +0000 > From: Sam Cook <sam.cook(a)utas.edu.au> > Subject: Protein-ligand docking > To: "bioinformatics-list(a)utas.edu.au" > <bioinformatics-list(a)utas.edu.au> > Message-ID: <D3355F63.5828%sam.cook(a)utas.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > Hi bioinformatics subscribers. > > My name is Sam Cook and I'm looking for some help with modelling > protein-ligand docking as a potential aspect of my PhD. > I know that this isn't exactly bioinformatics but, if you or someone you > know is familiar with such software or has experience in this field, I > could really use a hand. > > If you can help please get in touch: Sam.Cook(a)utas.edu.au > > Thanks a bunch, > > Sam > > -- > Sam Cook > PhD Candidate|Student Representative > School of Biological Sciences > University of Tasmania > Private Bag 55 > Hobart > 7001 TAS > > Ph: +61 03 6226 8528 > Mob: +61 430 951 385 > > > 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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Protein-ligand docking
by Sam Cook 14 Apr '16

14 Apr '16

Hi bioinformatics subscribers. My name is Sam Cook and I'm looking for some help with modelling protein-ligand docking as a potential aspect of my PhD. I know that this isn't exactly bioinformatics but, if you or someone you know is familiar with such software or has experience in this field, I could really use a hand. If you can help please get in touch: Sam.Cook(a)utas.edu.au Thanks a bunch, Sam -- Sam Cook PhD Candidate|Student Representative School of Biological Sciences University of Tasmania Private Bag 55 Hobart 7001 TAS Ph: +61 03 6226 8528 Mob: +61 430 951 385 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 journal
by Michael Charleston 12 Apr '16

12 Apr '16

Dear all, As previously suggested, the first journal club will be on Thursday of next week, here in Maths & Physics building, Lecture Theatre 2, 4pm. This was the most popular time among the respondents. I’ve set up a web page on Wordpress for this group, which has a “follow” option. The site is https://bioinformaticstasmania.wordpress.com/. The site is in construction but I hope will be a good place for things to begin... Dr Valerie Hecht has found this paper to consider: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8 See (some of) you then! Best wishes, Mike A survey of best practices for RNA-seq data analysis * Ana ConesaEmail author<mailto:aconesa@ufl.edu>, * Pedro MadrigalEmail author<mailto:pm12@sanger.ac.uk>, * Sonia Tarazona, * David Gomez-Cabrero, * Alejandra Cervera, * Andrew McPherson, * Michał Wojciech Szcześniak, * Daniel J. Gaffney, * Laura L. Elo, * Xuegong Zhang and * Ali MortazaviEmail author<mailto:ali.mortazavi@uci.edu> Genome Biology201617:13 DOI: 10.1186/s13059-016-0881-8 © Conesa et al. 2016 Published: 26 January 2016 Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics. 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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Journal Club
by Michael Charleston 12 Apr '16

12 Apr '16

Dear all, I think it would be good to keep this ball rolling and start the journal club! Next week (an even week) is the first session if you’d like to come along. It will be in Lecture theatre 2, on Thursday, at 4pm, in the Maths and Physics building, Sandy Bay campus. I haven’t picked a paper to discuss yet so if you’d like to suggest one, please do before this week ends; otherwise I’ll choose something (fairly general / accessible) to get us started. Cheers Mike (P.S. If you want your Google Calendar to show week numbers, follow the instructions here<https://productforums.google.com/forum/#!topic/calendar/guNxk0AB8JU>.) 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: Preferences for Journal Club
by Michael Charleston 08 Apr '16

08 Apr '16

Dear all, There’s a slight overall preference for Thursdays, 4pm, for a (mostly?) regular meeting of bioinformatics-related things. With that in mind I’ve booked a room, Lecture Theatre 2 in the Maths & Physics building, Sandy Bay Campus, for each Thursday at 4-5pm. I’ve chosen a lecture theatre to make it possible for people to present stuff, but we can of course be as informal as we like. Last week during the visit of Vicky Schneider we discussed the potential for a forum in which people could ask questions locally, and at all levels, about bioinformatics-related things, and I’m investigating options for that; one possibility is using the open-source software that’s used to run BioStars itself (available from https://github.com/ialbert/biostar-central). It’s not clear how long it will take to do it, though, so in the meantime I’ll set up a blog site (wordpress) for the activities of the bioinformatics list. If you’d like to be involved in administration of the site, please let me know: it would be useful to have more than just one person doing it, to ensure quick responses and that the site is kept up to date. 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 Tasmania meetings
by Michael Charleston (via Doodle) 04 Apr '16

04 Apr '16

Hi there, Michael Charleston (michael.charleston(a)utas.edu.au) invites you to participate in the Doodle poll "Bioinformatics Tasmania meetings." Hi folks, This is a poll to get a handle on when to have these regular bioinformatics meetings. This will be regular and start once we have a good sense of when and where to have them! They won't be all theory, nor will they be solely about applications. The idea is that for the even-numbered weeks of the year we will have a journal club – one person present a paper that they find interesting (or confusing (or both)) and for the odd-numbered weeks we will get together more informally, to discuss challenges or have guest talks, or just brainstorm over beer. Please indicate any time you could make it – not just your favourite! We want to include as many people as possible. Thanks! Mike Participate now https://doodle.com/poll/6mwpkkwgwnescn74?tmail=poll_invitecontact_participa… What is Doodle? Doodle is a web service that helps Michael Charleston to find a suitable date for meeting with a group of people. Learn more about how Doodle works. (https://doodle.com/features?tlink=checkOutLink&tmail=poll_invitecontact_par…) ---------------------------------------------------------------------- You have received this e-mail because "Michael Charleston" has invited you to participate in the Doodle poll "Bioinformatics Tasmania meetings." ---- Doodle is also available for iOS and Android. ---- Doodle AG, Werdstrasse 21, 8021 Zürich

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RE: journal paper submission workshop
by Andrew Chan 03 Apr '16

03 Apr '16

Dear all, Would you be interested in meeting the two editors? Who in the school do you think would benefit from a journal paper submission workshop given by them? Thank you for your attention. Regards, Andrew Professor Andrew Chan Professor and Head School of Engineering and ICT Room Centenary 355 Private Bag 65 University of Tasmania Hobart 7000 Tel: +61 3 6226 2954 (Launceston Tel: +61 3 6324 3476) Mobile: +61 439 094 236 (China +86 15840884396) Email: Andrew.Chan(a)utas.edu.au<mailto:Andrew.Chan@utas.edu.au> Webpage: http://www.utas.edu.au/engineering/people/andrew-chan OrcID: http://orcid.org/0000-0003-0042-8448 [Small_esig] CRICOS 00586B 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. From: Henry Duh Sent: Friday, 1 April 2016 4:55 PM To: Andrew Chan Subject: Re: journal paper submission workshop Hi Andrews, The journal are IEEE Transaction on Fuzzy System IEEE Transaction on Evolutionary Computation I believe the journal scopes are widely enough to cover Engineering, Computing and some other disciplines. It does not just benefit to our school but also other science disciplines. Chin Teng just moved to Australia and good to work with him to apply for ARC grants. Kay Chan was the EiC of Computational Intelligence Magazine, AE of IEEE Transaction on Computational Intelligence and AI in game Cheers - Henry From: Andrew Chan <andrew.chan(a)utas.edu.au<mailto:andrew.chan@utas.edu.au>> Date: Friday, 1 April 2016 at 3:16 PM To: Henry Duh Per <Henry.Duh(a)utas.edu.au<mailto:Henry.Duh@utas.edu.au>> Subject: RE: journal paper submission workshop Dear Henry, Which of our people would be able to write papers in those areas? Thank you for your attention. Regards, Andrew Professor Andrew Chan Professor and Head School of Engineering and ICT Room Centenary 355 Private Bag 65 University of Tasmania Hobart 7000 Tel: +61 3 6226 2954 (Launceston Tel: +61 3 6324 3476) Mobile: +61 439 094 236 (China +86 15840884396) Email: Andrew.Chan(a)utas.edu.au<mailto:Andrew.Chan@utas.edu.au> Webpage: http://www.utas.edu.au/engineering/people/andrew-chan OrcID: http://orcid.org/0000-0003-0042-8448 [Small_esig] CRICOS 00586B 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. From: Henry Duh Sent: Friday, 1 April 2016 1:35 PM To: Andrew Chan Subject: journal paper submission workshop Hi Andres, I am thinking to use my fund inviting may be 2 IEEE Transaction chief editors here or someone in Australia got many ARC grants(I know them so that it is not hard to invite them over). Their area is in 0801 (artificial intelligence) but certainly across to engineering, data science and decision science. They can have a workshop here to share their perspectives and let our colleagues know the trend of publication etc. To encourage our colleagues to go for journal route, it is important for them to know the practice I guess. Any thoughts? - Henry 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 April 2016