bioinformatics-list April 2017

bioinformatics-list@list.utas.edu.au

1 participants
3 discussions

... 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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bioinformatics-list April 2017