November 2016 - Galaxy-training - lists.galaxyproject.org

Fwd: Joint Data Carpentry / Jupyter Notebook curriculum development hackathon, January 9-11 in Berkeley, CA
by Dave Clements 30 Nov '16

30 Nov '16

Hi All, There is no direct tie-in to Galaxy here, but the event is about reproducibility, Jupyter, and curriculum development. If that combination is relevant to you, and you can make it to Berkeley in January, I encourage you to apply by next Monday. Cheers, Dave C ---------- Forwarded message ---------- From: Hilmar Lapp <hilmar.lapp(a)duke.edu> Date: Mon, Nov 21, 2016 at 9:17 AM Subject: Joint Data Carpentry / Jupyter Notebook curriculum development hackathon, January 9-11 in Berkeley, CA To: "<repr-sci-curriculum(a)googlegroups.com>" < repr-sci-curriculum(a)googlegroups.com> Hi all, The RRhack, Data Carpentry, and Jupyter Notebook projects are jointly organizing a curriculum development hackathon on Reproducible Research using Jupyter Notebooks. The event will take place Jan 9-11 at BIDS in Berkeley, CA. A brief summary of the event and how to apply for participation is enclosed below. The full Call for Participation is here: https://git.io/vXAaa I hope in particular those of you who have been interested in porting the RR curriculum to Python are interested in participating, and will apply! Please also redistribute freely to interested people and/or communities as you see fit. -hilmar Reproducible Research using Jupyter Notebooks: Curriculum Development Hackathon Goal: Develop the content of a two-day Data Carpentry workshop teaching how to conduct research reproducibly using the Jupyter notebook Location: Berkeley Institute for Data Science (BIDS), Berkeley, CA Dates and times: January 9 - 11, 2017; 9 am - 5 pm each day To apply: https://goo.gl/aPO71f; deadline December 5, 2016. Successful applicants will be notified by December 12. Synopsis Making science more reproducible has enormous potential to accelerate research advances, including for practicing individuals. Despite this, the tools and approaches that are already available are rarely taught. To address this, we are organizing a 3-day hands-on workshop aimed at developing, and later teaching, a short-course curriculum on using Jupyter notebooks for reproducible research practices. The event will be held January 9 - 11, 2016, in Berkeley, CA, at the Berkeley Institute for Data Science (BIDS). We aim to assemble a diverse and interdisciplinary group of participants, and invite those interested to apply by December 5, 2016, at https://goo.gl/aPO71f. Full details at the Call for Participation: https://git.io/vXAaa -- Hilmar Lapp -:- genome.duke.edu -:- lappland.io -- You received this message because you are subscribed to the Google Groups "Curriculum for reproducible science" group. To unsubscribe from this group and stop receiving emails from it, send an email to repr-sci-curriculum+unsubscribe(a)googlegroups.com. To post to this group, send email to repr-sci-curriculum(a)googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/ msgid/repr-sci-curriculum/70A5900E-D792-47D2-87BF-978A68821318%40duke.edu <https://groups.google.com/d/msgid/repr-sci-curriculum/70A5900E-D792-47D2-87…> . For more options, visit https://groups.google.com/d/optout. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0

Fwd: GOBLET AGM - some outcomes
by Dave Clements 14 Nov '16

14 Nov '16

Hello all, And here's the summary of the GOBLET meeting in Brisbane. Cheers, Dave C ---------- Forwarded message ---------- From: Teresa Attwood <teresa.k.attwood(a)manchester.ac.uk> Date: Thu, Nov 10, 2016 at 5:21 PM Subject: GOBLET AGM - some outcomes To: "gobletvotes(a)mygoblet.org" <gobletvotes(a)mygoblet.org> Cc: Teresa Attwood <teresa.k.attwood(a)manchester.ac.uk> Dear All, First of all, thanks to everyone for their massive contributions to the AGM - it was great to see new (and young!) faces, and to feel the energy in the room! One of the things we discussed was the mission and vision of GOBLET. Together, we arrived at new drafts, which we hope better reflect GOBLET's raison d'être: Vision To unite, inspire and equip bioinformatics trainers worldwide Mission To cultivate the global bioinformatics trainer community, set standards and provide high-quality resources to support learning, education and training We distilled the objectives (very roughly) as follows: 1. Portal - to become a pull mechanism and repository 2. Develop branded materials - e.g., Train the Trainer/Teacher packages, etc. 3. Training of a) trainers/teachers and b) users 4. Develop standards 5. Provide resources - surveys, best practice guidelines, icebreakers, technologies for classrooms 6. Fund our objectives 7. Offer network/community forum (e.g., biostars, ISCB connect) 8. Later priority: Trainer recognition – depends on evolution of GOBLET brand We proposed to retain the GOBLET tag line: Empowering people, harnessing communities, networking networks We welcome your thoughts on the new mission and vision, and on the objectives. Best wishes, and thanks again for all your valuable input, Terri On behalf of the new executive board Terri, Michelle, Celia, Annette -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0

Fwd: white paper "Defining a lingua franca for the ELIXIR/GOBLET e-learning ecosystem"
by Dave Clements 14 Nov '16

14 Nov '16

Hello all, The latest from GOBLET. Dave C ---------- Forwarded message ---------- From: Patricia Palagi <Patricia.Palagi(a)sib.swiss> Date: Sun, Nov 13, 2016 at 12:34 PM Subject: white paper "Defining a lingua franca for the ELIXIR/GOBLET e-learning ecosystem" To: "gobletvotes(a)mygoblet.org" <gobletvotes(a)mygoblet.org> Dear Gobleteers, the white paper "Defining a lingua franca for the ELIXIR/GOBLET e-learning ecosystem" is finally online at Zenodo: https://zenodo.org/record/166378#.WCi6EHeZMW0 Thank you all for your contributions. In particular, a big and warm thanks to Terri who did 99.99% of the work. Enjoy! All the best, Patricia -- *Patricia Palagi, PhD* Head of Training *SIB | Swiss Institute of Bioinformatics* CMU - 1 Michel Servet - CH 1211 Geneva 4 - Switzerland - Mon, Wed - t +41 22 379 5831 Quartier Sorge, Genopode - CH 1015 Lausanne - Switzerland - Tue, Thu - t +41 21 692 4078 Patricia.Palagi(a)sib.swiss - www.sib.swiss/training *New email address: Patricia.Palagi(a)sib.swiss <Patricia.Palagi(a)sib.swiss>* -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0

GTN at 2016 GOBLET meeting
by Dave Clements 10 Nov '16

10 Nov '16

Hi All, Maria Doyle will be officially representing GTN at the GOBLET AGM <http://www.abacbs.org/goblet_agm/> in Brisbane, early next month. Maria works at PeterMac in Melbourne and is a Galaxy veteran. Two other Galaxy veterans, Annette McGrath of CSIRO and Igor Makunin of U Queensland, will also be there to present Galaxy savvy points of view. I'd like to come up with a list of agenda items for Maria to present on behalf of GTN. Last year's list: Last year we discussed what our priorities for the GOBLET meeting <http://galaxy-training-mailing-list-archive.35427.n7.nabble.com/GTN-issues-…> should be. and came up with this list <http://galaxy-training-mailing-list-archive.35427.n7.nabble.com/Galaxy-Trai…>. Here's what I think happened with those 5 items: *1. Enable/Host online discussion about bioinformatics training.* As far as I can tell no action has been taken. *2. Either start sending a regular newsletter, or stop saying we have one.* This has been started. *3. Should GOBLET offer a bioinformatics trainer certification?* I have no emails since the last meeting with the words GOBLET and certify/certification in them. So, no progress. And from Peter VH during last year's meeting: There is not really a concept of Goblet Certified Trainer being thrown > around but there has been a discussion on what a "Goblet branded" set of > training materials or course would involve. The idea is that certain > requirements have to be met to get this "Goblet branded" badge. *4. Make it easier to publish, share, and refine training material.* I should have titled this "Embrace the Carpentry model for training materials." The *Galaxy Community* has actually made a lot of progress on this independent of GOBLET. There was a two day training material hackathon this month. See here <https://wiki.galaxyproject.org/GalaxyUpdates/2016_10#Galaxy_training_contri…>. (I'm hoping to have a summary in the November newsletter as well.) As far as I can tell, GOBLET has not done anything with this. There is an item on this year's agenda about GOBLET's relationship with Software Carpentry, not about training materials per se. *5. Shared Training Datasets are Precious!* No progress from GOBLET here either. However, Björn and Bérenice made progress on this for Galaxy during the October hackathon. This year's list: What should be on this year's list? What are our priorities for the coming year? How can GOBLET help us? How can we help GOBLET? I encourage you to post your ideas to this list. I'll send my suggestions in a separate email as well. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

6 10

Fwd: Join the GOBLET AGM via Zoom
by Dave Clements 03 Nov '16

03 Nov '16

And, if you want to listen to this year's meeting online, you can. Dave C ---------- Forwarded message ---------- From: <Annette.Mcgrath(a)data61.csiro.au> Date: Wed, Nov 2, 2016 at 8:43 PM Subject: Join the GOBLET AGM via Zoom To: gobletvotes(a)mygoblet.org Hi everyone For those who are unable to travel to Brisbane to attend the GOBLET AGM in person, you can still join in the GOBLET AGM via Zoom. *Date:* Mon Nov 7th 2016 *Time:* 9am to 4pm (AEST). AEST is GMT + 10 hours. The agenda can be found here: http://www.abacbs.org/gobletagenda/ The Zoom details are below and we look forward to seeing you on Sunday/Monday. Best wishes Annette Meeting ID: 507 665 5382 Join from a PC, Mac, iOS or Android: https://qut.zoom.us/j/5076655382 Or iPhone one-tap (Australia Toll): +61280152088,5076655382# Or Telephone: Dial: +61 2 8015 2088 Meeting ID: 507 665 5382 International numbers available: https://qut.zoom.us/zoomconference?m= rM67KvIZNY7qhoqBxP1tdTpTbfybJTkd Or a H.323/SIP room system: Dial: +61 2 6222 7588 or SIP:7588@aarnet.edu.au or H323:5076655382@182.255.112.21 (From Cisco) or H323:182.255.112.21##5076655382 (From Huawei, LifeSize, Polycom) or 162.255.37.11 or 162.255.36.11 (U.S.) Meeting ID: 5076655382 *Annette McGrath * Principal Research Scientist | Team Leader, Life Science Informatics *DATA61 | CSIRO* *E* annette.mcgrath(a)csiro.au *T* +61 2 6216 7251 *M* 0467 744 551 GPO Box 664, Canberra, ACT 2601 www.data61.csiro.au CSIRO’s Digital Productivity business unit and NICTA have joined forces to create digital powerhouse Data61 *PLEASE NOTE* The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. *Please consider the environment before printing this email.* -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0

Fwd: GOBLET AGM Meeting Minutes from 2015 - for review and approval
by Dave Clements 03 Nov '16

03 Nov '16

Hi All, Here's the minutes from last year's GOBLET meeting. I haven't reviewed them yet, but will get to them when I start working on slides. Thanks, Dave C ---------- Forwarded message ---------- From: Michelle Brazas <Michelle.Brazas(a)oicr.on.ca> Date: Wed, Nov 2, 2016 at 8:38 PM Subject: GOBLET AGM Meeting Minutes from 2015 - for review and approval To: "gobletvotes(a)mygoblet.org" <gobletvotes(a)mygoblet.org> All, A reminder that we will need to approve the meeting minutes from GOBLET's 2015 AGM in Cape Town. The meeting minutes were posted online at the end of the page here: http://mygoblet.org/about-us/goblet-events/goblet-agm-2015-cape-town Please take a moment to review them before Monday. Michelle -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0

Fwd: GOBLET Newsletter September 2016
by Dave Clements 01 Nov '16

01 Nov '16

Hi All, I just noticed that I did not forward this to the list when it arrived a month ago. Look for another email shortly. Dave C ---------- Forwarded message ---------- From: erikbong <erikbong(a)mac.com> Date: Tue, Sep 27, 2016 at 7:22 AM Subject: GOBLET Newsletter September 2016 To: all(a)mygoblet.org Dear All, Attached the second GOBLET Newsletter for 2016, full of information from past and coming events where GOBLET members participate. Happy reading! On behalf of the Outreach & PR Committee Erik PS. Please distribute on your own distribution channels. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0