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... and if you thought sequencing was all nice and accurate
by Michael Charleston 11 May '17

11 May '17

https://www.wired.com/2017/04/geneticists-fear-illuminas-sequencers-may-dis… Michael Charleston Associate Professor in Bioinformatics Co-director of Data, Knowledge and Decisions Research Theme Head of UTAS node of EMBL-ABR 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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Genome Annotation and Open Science workshop: Final Dates June 29 & 30.
by Michael Charleston 27 Apr '17

27 Apr '17

Dear all, We are a GO* on the Genome Annotation and Open Science workshop, to be run by Dr Monica Munoz-Torres. We have had to change the date though: the workshops will now be on the 29th and 30th of June at UTAS on the Sandy Bay campus. The Genome Annotation workshop is a one-day affair and will be on the Thursday. I will send around details as to what you should do / prepare for (and I believe it’s quite minimal) when I have them. The Open Science workshop takes half a day and will be on the Friday morning. Dr Munoz-Torres will also be around that afternoon for more discussion. Please confirm now that you’re able to come – the more people who sign up, the cheaper it will be (and it will I expect be <$100). The very low cost is a direct consequence of the fantastic organisational skills of EMBL-ABR staff (some are cc’d above), who have enabled this roadshow-like tour to happen across Australia. Dr Munoz-Torres is visiting Melbourne, Hobart, Townsville, Sydney, Brisbane and Perth before returning to Prague. Let’s make her stay in Hobart the best one :) Here’s what I sent around last time, for a bit of a reminder: Bioinformatics users and researchers in Tasmania have a great opportunity to welcome an expert in genome annotation and bio-curation in the form of Dr Monica (Moni) Munoz-Torres from the Lawrence Berkeley National Laboratory in California. Dr Munoz-Torres’ home page: http://www.berkeleybop.org/people/monica-munoz-torres/ Google Scholar page: https://scholar.google.com.au/citations?hl=en&user=GaQVcBAAAAAJ&view_op=lis… and linkedin: https://www.linkedin.com/in/monimunozto/ And here’s a bit more information in the form of some questions, with answers from Monica: “Primer on Genome Annotation” workshop Is this a hands-on workshop with attendees bringing laptops? There will be a 'lecture' component and a hands-on component. The hands-on part will be conducting manual curation exercises using Apollo. Attendees must bring their own computer, and it must be able to wirelessly connect to the internet, must have an up-to-date version of a web browser (please advise them to use Chrome, Firefox, or Safari), and must be able to open PDF files. No additional software installations are necessary. Some people find using Apollo with the aid of a mouse much easier than with a trackpad, so please advise potential participants to bring a mouse if they think it would suit them better. Also note: we have a computer lab booked: the machines do indeed connect to the internet. Is there a maximum or recommended number of participants? I prefer to teach groups of max. 25 people. I have also taught classes for up to 40 people without teaching assistants (TAs) - it can become a bit of a 3-ring circus at times, but it is doable. How long does it take to run this workshop? Should we say 9am-5pm? This usually includes 5 hours of teaching material + practical exercises. It is correct to assume we can reserve time slots of 9AM to 5PM, factor in breaks and meals - and likely we should be done by or shortly before 5PM. “Open Science” workshop What would be the structure, format and duration of such a workshop? Going by my conversations with Vicky, we thought the "Open Science" portion would be a combination of talks and a discussion panel - to make a case for open science, opening the conversation to more than one 'speaker' will also be a great start. As far as duration, I don't see this as taking an entire day, but rather a morning session or afternoon session. It depends on how much more structure you wish to give it... we can evolve the concept into something larger, of course. There will be a registration page set up soon: stay tuned, and mark the dates! Best wishes Mike Michael Charleston Associate Professor in Bioinformatics Co-director of Data, Knowledge and Decisions Research Theme Head of UTAS node of EMBL-ABR School of Physical Sciences University of Tasmania AUSTRALIA phone: +61 3 6226 2444 *no, not gene ontology, a go like going 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: [EMBL-ABR Heads of Nodes] ANDS Medical webinar series: focus on Health and Medical data
by Michael Charleston 20 Apr '17

20 Apr '17

For all our interest! Michael Charleston Associate Professor in Bioinformatics Co-director of Data, Knowledge and Decisions Research Theme Head of UTAS node of EMBL-ABR School of Physical Sciences University of Tasmania AUSTRALIA phone: +61 3 6226 2444 Begin forwarded message: From: Fiona Louise Kerr <fiona.kerr(a)unimelb.edu.au<mailto:fiona.kerr@unimelb.edu.au>> Subject: [EMBL-ABR Heads of Nodes] ANDS Medical webinar series: focus on Health and Medical data Date: 20 April 2017 at 10:55:21 AM AEST To: "embl-abr-headsofnodes(a)lists.embl-abr.org.au<mailto:embl-abr-headsofnodes@lists.embl-abr.org.au>" <embl-abr-headsofnodes(a)lists.embl-abr.org.au<mailto:embl-abr-headsofnodes@lists.embl-abr.org.au>> From: Helen Gardiner <helen.gardiner(a)unimelb.edu.au<mailto:helen.gardiner@unimelb.edu.au>> Date: Thursday, 20 April 2017 at 10:36 am To: Fiona Kerr <fiona.kerr(a)unimelb.edu.au<mailto:fiona.kerr@unimelb.edu.au>> Subject: ANDS Medical webinar series: focus on Health and Medical data To all Node heads We recommend this series to all students and researchers working with health and medical data. Please advertise through your networks. Convenor, Kate LeMay, Senior Research Data Specialist (health and medical data) at ANDS, was interviewed late in 2016 for the EMBL Australia Bioinformatics Resource. We asked her about bioinformatics in general and the data life-cycle in particular. Her message was clear: using a framework like the data life cycle ensures that Australian bioinformaticians and life scientists will keep up with best practice standards being used and developed internationally. Full interview.<http://www.embl-abr.org.au/kate-lemay-interview/> Kind regards, Helen Helen Gardiner | Communications Manager | Melbourne Bioinformatics & EMBL Australia Bioinformatics Resource | University of Melbourne, Victoria 3010, Australia | t: +61 (3) 8344 2055 | m: +61 (0) 448 920 235 | @MelBioInf | @EMBL_ABR | w: http://www.melbournebioinformatics.org.au<https://www.melbournebioinformatics.org.au/> | www.embl-abr.org.au<https://www.embl-abr.org.au/><http://www.braembl.org.au/> | ______________________________ The Australian National Data Service (ANDS<http://www.ands.org.au/>) invite you to join our series of three short 30 minute lunchtime webinars which aim to support better management and publication of Health and Medical data. ANDS is an NCRIS facility whose core purpose is to make Australia’s research data assets more valuable for researchers, research institutions and the nation. These webinars are free and all ANDS materials are licensed Creative Commons CC-BY to enable easy reuse and re-purposing. Who would benefit from attending? * Researchers * Medical Research Institutes * Universities * Clinician researchers at hospitals * Research students (honours, Masters, PhD) * Medical librarians and data managers who deal with sensitive data Speaker list and full webinar details<http://www.ands.org.au/news-and-events/presentations/2017/webinars-heath-an…> These webinars will be recorded. If you can’t attend please register and we will send you the recording and handout links. Webinar summaries The webinars will address commonly held concerns from within the health and medical research field around data publication: 1. Funders and Publishers: What is being asked of researchers? Tues 9 May, 12:30pm-1pm AEST Register <https://attendee.gotowebinar.com/register/63834727562904322> 2. Storing and Publishing Health and Medical Data: Where can I store my data during and after my research project? Tues 16 May, 12:30pm-1pm AEST Register <https://attendee.gotowebinar.com/register/1287487815189085953> 3. Ethics, Legal issues and data sharing: How can I obtain informed consent for sharing my data? What do I need to consider around storage, access, de-identification and plans for sharing? What laws impact upon the collection, handling and sharing of health and medical research data? Tues 23 May, 12:30pm-1pm AEST Register<https://attendee.gotowebinar.com/register/5100061976688695043> Contact kate.lemay(a)ands.org.au<mailto:kate.lemay@ands.org.au>for more information. Kate LeMay Senior Research Data Specialist | Australian National Data Service T: +61 2 6125 8538 | E: kate.lemay(a)ands.org.au<mailto:kate.lemay@ands.org.au> | W: ands.org.au<http://ands.org.au/> Twitter: @katelemayands ORCiD: orcid.org/0000-0002-2405-7365<http://orcid.org/0000-0002-2405-7365> I work Monday-Thursday 9am-2:30pm Physical address: 9 Liversidge Street, Australian National University, Acton, ACT 2601 Postal address: 101 Liversidge Street, Australian National University, Acton, ACT 2601 Please consider the environment before printing this e-mail. _______________________________________________ EMBL-ABR-HeadsofNodes mailing list EMBL-ABR-HeadsofNodes(a)lists.embl-abr.org.au<mailto:EMBL-ABR-HeadsofNodes@lists.embl-abr.org.au> https://lists.embl-abr.org.au/cgi-bin/mailman/listinfo/embl-abr-headsofnodes 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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Re: bioinformatics-list Digest, Vol 19, Issue 3
by vikrant singh 20 Mar '17

20 Mar '17

Dear Dr Jac Charlesworth, I am Interested in to help with a genomics conference. Regards, Vikrant On Mon, Mar 20, 2017 at 2:23 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. Looking for PhD students to help with a genomics conference > in Hobart late Oct (Jac Charlesworth) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 20 Mar 2017 03:23:56 +0000 > From: Jac Charlesworth <jac.charlesworth(a)utas.edu.au> > Subject: Looking for PhD students to help with a genomics conference > in Hobart late Oct > To: "bioinformatics-list(a)utas.edu.au" > <bioinformatics-list(a)utas.edu.au> > Message-ID: <f0f6a6d950fb4ca189b74a3b46ad53ab(a)MBX12.utas.ad.internal> > Content-Type: text/plain; charset="us-ascii" > > Hi all, > > I'm looking for 2 local PhD students with an interest in genomics to > organise the student function as part of the Australasian Genomic > Technologies Association conference that will be in Hobart Oct 29th to Nov > 1st (http://agtaconference.org/) > > AGTA is an excellent interdisciplinary genomics conference. We have a > great line up of international speakers, with nationals soon to be > announced. > > The student function will have some budget for a venue and evening even > planned by PhD students and ECRs for their peers. We've previously seen > quiz nights, career mentoring sessions and 'science at the pub' type > speaking/socialising events. The students would work with the AGTA17 > organising committee in terms of organising the social event, but we're > hoping they will lead it. > > We'll provide conference registration as a thank you. > > Of you know someone who might be a good pick for this role please let me > know. It's good CV material and shouldn't be too onerous. > > Thanks in advance- > > Jac (convenor AGTA17) > > 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/> > [cid:image001.png@01D2A185.368A20B0]<http://agtaconference.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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Looking for PhD students to help with a genomics conference in Hobart late Oct
by Jac Charlesworth 20 Mar '17

20 Mar '17

Hi all, I'm looking for 2 local PhD students with an interest in genomics to organise the student function as part of the Australasian Genomic Technologies Association conference that will be in Hobart Oct 29th to Nov 1st (http://agtaconference.org/) AGTA is an excellent interdisciplinary genomics conference. We have a great line up of international speakers, with nationals soon to be announced. The student function will have some budget for a venue and evening even planned by PhD students and ECRs for their peers. We've previously seen quiz nights, career mentoring sessions and 'science at the pub' type speaking/socialising events. The students would work with the AGTA17 organising committee in terms of organising the social event, but we're hoping they will lead it. We'll provide conference registration as a thank you. Of you know someone who might be a good pick for this role please let me know. It's good CV material and shouldn't be too onerous. Thanks in advance- Jac (convenor AGTA17) 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/> [cid:image001.png@01D2A185.368A20B0]<http://agtaconference.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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Opportunity to learn about genome annotation and bio-curation
by Michael Charleston 10 Mar '17

10 Mar '17

Dear all, Bioinformatics users and researchers in Tasmania have a great opportunity to welcome an expert in genome annotation and bio-curation in the form of Dr Monica (Moni) Munoz-Torres from the Lawrence Berkeley National Laboratory in California. Dr Munoz-Torres’ home page: http://www.berkeleybop.org/people/monica-munoz-torres/ Google Scholar page: https://scholar.google.com.au/citations?hl=en&user=GaQVcBAAAAAJ&view_op=lis… and linkedin: https://www.linkedin.com/in/monimunozto/ Dr Munoz-Torres is able to travel to Hobart to deliver two workshops on 10th/11th of July this year (a Monday and Tuesday) on Genome Annotation and Open Science Bio/curation. EMBL-ABR(whose Deputy Director, Vicky Schneider, is cc’d) is coordinating an Australian tour by Dr Munoz-Torres, which will cut costs considerably, but in order for us to afford to bring her here we will to raise some funds! Please can I get a very quick show of hands, of people who would with high probability (at least 80%) pay up to $100 for a two-day workshop? The more we can get, the lower will be the total cost. I estimate we need to raise around $1650 which means at least 16.5 people :) I need to know as soon as possible so we can grab this opportunity – do let me know if you’re seriously interested! Best wishes Mike Michael Charleston Associate Professor in Bioinformatics Co-director of Data, Knowledge and Decisions Research Theme 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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KMA712 Introduction to Bioinformatics
by Michael Charleston 02 Feb '17

02 Feb '17

Don’t forget to enrol in Introduction to Bioinformatics this semester! * Learn how to use current bioinformatics software! * Learn how to do sequence alignment, phylogenetic analysis, RNA-Seq analysis, and next-generation sequencing analyses like mapping and de novo assembly! * Use the command-line like a boss! * Understand how bioinformatics algorithms work! * Cake! Big Data! Contact me directly if you have questions. Go on, you know you want to. 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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Doodle poll weirdness
by Michael Charleston 10 Jan '17

10 Jan '17

Hi all, Looks like if you're using Windows and Chrome then the poll is very unhelpful: no times or days are visible! Barbara Holland kindly discovered this strange behaviour which doesn't affect my Ubuntu + Firefox combination, and is also gone if she uses Firefox on her Windows machine; hence I advise that if it looks really broken, try a different browser. Cheers Mike -- Michael Charleston Associate Professor in Bioinformatics Co-director of Research Theme in Data, Knowledge and Decisions 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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Happy New Year!
by Michael Charleston 09 Jan '17

09 Jan '17

Welcome to 2017, a number with numerous numerical niceties: * it's prime ☺ * the binary expansion is 1111110001 which is rather pretty (I guess 11111100000 was too) * it's 7e1 in hexadecimal * CRISPR<http://www.vox.com/science-and-health/2017/1/3/14093794/crispr-gene-editing…> -- ok so that's nothing to do with the number 2017. * More bioinformatics! -- again, nothing to do with the actual value 2017, but don't hold that against me. This year we promise more workshops, more seminars, more activities! What's on, I hear you ask (in my head)? * Fortnightly meetings with guest seminars! (Dob someone in now!) * Workshops on demand (just start demanding them) * DaSH's Research Bazaar<https://2017.resbaz.com/> * GAMe 2017: Galaxy Australasia Meeting, 3rd-9th February in Melbourne 3rd-9th February (link here<https://www.embl-abr.org.au/game2017/>) * Lorne Genome conference, 12-14 February in Lorne, Victoria (probably too late to get to these two but you never know) * If you can't get to these this year maybe put them in your diaries for *next* year. * COMBINE and ABACBS, 13-15 November in Adelaide (link here<http://www.abacbs.org/conference/>) * Australasian Evolution Society Annual Meeting * Phylomania #9 * These last two are to be coordinated; dates to be determined but late November / early December looking likely It's also a good time to work out when are good meeting times. We had alternate Thursdays 4-5pm, but perhaps that isn't a great time. So there's a Doodle Poll to help us decide.. Cheers, Mike -- Michael Charleston Associate Professor in Bioinformatics Co-director of Research Theme in Data, Knowledge and Decisions 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: FW: Reminder Special Seminar 10am this morning Andrew Dobson Princeton Evolutionary Dynamics of an Emerging Pathogen]
by Michael Charleston 09 Dec '16

09 Dec '16

Late notice but definitely of interest to me! Seminar 1pm in Biological Sciences. > ##SELECTION_END## > Special seminar: > > Professor Andrew Dobson > Ecology and Evolutionary Biology, Princeton University > > "The Eye of the Finch: Evolutionary Dynamics of an Emerging Pathogen" > > Date and time: Thursday 8th December, 1-2pm > Venue: Life Sciences Lecture Theatre 1 > > Andy is pre-eminent in the field of the population and community ecology of infectious diseases. > He works in a variety of ecosystems across the globe. Please visit his website. > https://www.princeton.edu/~dobber/ > > Regards, > > Menna > > > ======================================= > Assoc Prof Menna Jones | ARC Future Fellow > School of Biological Sciences > University of Tasmania > Private Bag 55, Hobart, Tasmania 7001, Australia > > Email: Menna.Jones(a)utas.edu.au > Ph: +61 407 815606 | Fax: +61 3 62262745 > Web: http://fcms.its.utas.edu.au/scieng/zoo/pagedetails.asp?lpersonId=1321 > ======================================= > > > > 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. -- Michael Charleston Associate Professor in Bioinformatics Co-director of Research Theme in Data, Knowledge and Decisions School of Physical Sciences University of Tasmania AUSTRALIA phone: +61 3 6226 2444

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