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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/

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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/

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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/

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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/

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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/

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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/

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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/

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Re: [gxy-train] [BBC] Online Galaxy training material hackathon
by Dave Clements 06 Oct '16

06 Oct '16

Hi All, In case you haven't seen this through other channels this starts on Thursday morning, wherever you are. Thanks, Dave C On Tue, Oct 4, 2016 at 4:03 AM, Frederik Coppens <frcop(a)psb.vib-ugent.be> wrote: > Hi all > > I would like to bring this hackathon to your attention: > https://www.elixir-europe.org/events/galaxy-training-material-hackathon It’s > an online contribution fest organized by the Galaxy Training Network, > October 6-7. > > This stems from an idea at GCC2016 to centralize Galaxy training material > on github. Bjoern Gruening already collected a lot of material (checkout > https://github.com/bgruening/training-material) and we’d like to further > grow this resource and make it more uniform. > > You can (optionally) indicate your interest here: https://github.com/ > bgruening/training-material/issues/58 > > You can find a list of topics here: https://github.com/ > bgruening/training-material/issues > > Everybody’s welcome to join, you really don’t need programming skills to > contribute. If the hackathon doesn’t fit your schedule (it’s a bit short > notice, I realise), you can always contribute at a later point, as > everything is available on github. > > cheers > > Frederik > > ================================================================== > Frederik Coppens, Ph.D. > Project Leader Applied Bioinformatics & Biostatistics > IT manager > > Tel: 32 (0)9 3313812 Fax:32 (0)9 3313809 > VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent > Technologiepark 927, 9052 Gent, BELGIUM > > frcop(a)psb.ugent.be http://www.psb.ugent.be/abb > ================================================================== > > > _______________________________________________ > BBClist mailing list > BBClist(a)psb.ugent.be > https://maillist.psb.ugent.be/mailman/listinfo/bbclist > > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Fwd: September Carpentries Newsletter
by Dave Clements 29 Sep '16

29 Sep '16

Hello all, The Software and Data Carpentry communities have a new low-volume mailing list <http://software-carpentry.us14.list-manage.com/subscribe?u=46d7513c798c6bd4…> for announcements and news. See below for the first edition. Thanks, Dave C ---------- Forwarded message ---------- From: Software and Data Carpentry <jduckles(a)software-carpentry.org> Date: Wed, Sep 28, 2016 at 6:50 AM Subject: September Carpentries Newsletter To: clements(a)galaxyproject.org Welcome to the inaugural Software and Data Carpentry newsletter. We are launching this newsletter to keep you well informed around all of the various activities and opportunities in the community. View this email in your browser <http://us14.campaign-archive2.com/?u=46d7513c798c6bd41e5f58f4a&id=13b596f2d…> *September 2016 Carpentries Community Newsletter* *From the Software and Data Carpentry Community Calendar* *October Community Call* - October 20th, 2016 - Come join us <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> for the community call on Thursday October 20th. We will be talking about improving assessment and other community happenings. Have a look at last month’s notes <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> if you missed the call. *Discussion Sessions* - Discussion session times have changed to better accommodate our global community. Two sessions are held every Tuesday alternating between 7:00, 20:00 UTC and 15:00, 23:00 UTC. They’re a great way to prepare for upcoming workshops, debrief on past ones and learn from others in the community. Information about upcoming sessions can be found on the discussion etherpad <http://software-carpentry.us14.list-manage2.com/track/click?u=46d7513c798c6…>, sign up for one if you’ve recently taught or want to reconnect with Software and Data Carpentriy instructors. If you are an experienced instructor, having taught 3 or more times, please consider signing up to lead a session <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…>. Want to learn more, get on the mentoring email list <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> or join a mentoring meeting <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…>. Details are on the community calendar. ------------------------------ *Community Calendar* - with so many activities and subcommittee meetings, we’ve begun to keep a community calendar <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…>. Consider subscribing to the calendar so you can participate in the activities and events that interest you. ------------------------------ *Community News* *New Announcements List - *We’ve created an announcements list <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> to better communicate with community members. You can expect a monthly newsletter and periodic and timely community announcements on this list. It is meant to be the canonical source for information from both Data and Software Carpentry. Feel free to share the signup link <http://software-carpentry.us14.list-manage2.com/track/click?u=46d7513c798c6…> with interested parties. *Nominations for Community Service Award - *We are now accepting nominations <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> for a community service award. Please contribute your nominations so that we can recognize the community members who have made this organization a better place for all of us. *Special Election on Software Carpentry Steering Committee rules -* See the following blog post on rules for SWC Steering Committee <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> voting. This minor tweak serves to ensure that the Software Carpentry Steering Committee continuity is preserved in cases where a large number (or all) Steering Committee members change in an election. *2017 Software Carpentry Steering Committee Election -* It is time to start thinking about the Steering Committee Election coming up in early 2017. If you’re interested in serving on the steering committee, start thinking about a blog post to share your vision for the future of Software Carpentry. We’ll have an official call for blog posts in December and the deadline for them will be in early January. The election will follow 30-days after blog posts from candidates are submitted. *There were or will be talks pertaining to Software and Data Carpentry at - *SciDataCon <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> Denver, Colorado, USA / International Congress of Entomology <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> in Orlando, FL, USA / NETTAB <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> Rome, Italy / US White House Open Data Innovation Summit <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…>, Washington, DC, USA *Please welcome our new instructor trainers* to the instructor training community. Neal Davis (U. Illinois, USA), Karin Lagesen (U. Oslo, Norway), and Anelda van der Walt (Talarify, South Africa). This brings our total number of instructor trainers to 11 globally. If you’re a senior instructor interested in takings steps to become an Instructor Trainer in the future, please contact Greg Wilson <gvwilson(a)software-carpentry.org>. *Sloan Foundation grant to NumFOCUS - *Our fiscal sponsor NumFOCUS received a grant <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> from the Alfred P. Sloan Foundation entitled "Building Capacity for NumFOCUS Open Source Projects to Develop and Sustain Industry Relationships" <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…>. This grant will help all NumFOCUS projects receive training and mentorship related to sustaining Open Source activities that are important to the scientific software community. ------------------------------ *Papers & manuscripts from the community* Our community participated in the creation of the following manuscripts and papers. Please contribute comments to the manuscripts and read/share the papers with your community. *Manuscript* - Ten Simple Rules for Making Research Software More Robust <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…>, please contribute comments here <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> *Manuscript* - Good Enough Practices for Scientific Computing <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…>, please contribute comments here <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> *Pre-print* - A vision for collaborative training infrastructure for bioinformatics <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> (Free pre-print <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> ) Please make suggestions for the Software Carpentry website section on reading material <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> relevant to our community. Pull requests on GitHub are welcome to this file <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> . ------------------------------ *What you may have missed on the blogs and mailing lists* *Teaching with Git and GitHub Desktop <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> *- Discuss thread *Python as a second language <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…>* - Discuss thread *What are the most popular languages by research discipline? <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…>* - Discuss thread *I think I can. Self-efficacy and the Carpentry learner <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…>* - DC Blog Post ------------------------------ *Job postings* Postdoc at rOpenSci <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> - University of California Berkeley Data Science Coordinator <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> - University of California Davis Transparency and Openness Training Coordinator <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> - Center for Open Science Postdoctoral Researcher <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> - The Jackson Laboratory Research Data Manager <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> - Brown University ------------------------------ *Other places to connect* If you can't get enough Software and Data Carpentry. Here are a few other places to connect with our community. *Going to a workshop* or conference, add the details to our events etherpad <http://software-carpentry.us14.list-manage2.com/track/click?u=46d7513c798c6…> and meet other carpenters. *Twitter* - Software Carpentry <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> / Data Carpentry <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> *GitHub* - Software Carpentry <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> / Data Carpentry <http://software-carpentry.us14.list-manage2.com/track/click?u=46d7513c798c6…> Slack <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> / LinkedIn <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> / Facebook <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> Mailing lists <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> Have something you’d like to have included in the next newsltter, please send it to newsletter(a)software-carpentry.org <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> DC <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> DC <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> <http://software-carpentry.us14.list-manage2.com/track/click?u=46d7513c798c6…> DC <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> SWC <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> <http://software-carpentry.us14.list-manage1.com/track/click?u=46d7513c798c6…> SWC <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> <http://software-carpentry.us14.list-manage2.com/track/click?u=46d7513c798c6…> SWC <http://software-carpentry.us14.list-manage.com/track/click?u=46d7513c798c6b…> *Copyright © 2016 The Carpentries, All rights reserved.* You are receiving this email because you signed up to get announcements from the Software and Data Carpentry community. *Our mailing address is:* The Carpentries P.O. Box 90596 Austin, TX 78709 Add us to your address book <http://software-carpentry.us14.list-manage.com/vcard?u=46d7513c798c6bd41e5f…> Want to change how you receive these emails? You can update your preferences <http://software-carpentry.us14.list-manage2.com/profile?u=46d7513c798c6bd41…> or unsubscribe from this list <http://software-carpentry.us14.list-manage.com/unsubscribe?u=46d7513c798c6b…> [image: Email Marketing Powered by MailChimp] <http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletter&utm…> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Announcement - new shared training material and technologies for training!
by Björn Grüning 09 Sep '16

09 Sep '16

Dear training enthusiast, We have started to work on an unification of the Galaxy training material as discussed during the GCC 2016. As a first example we have chosen our Exome-Seq tutorial and have ported it over to give a real world example of how we imagine the next generation of Galaxy training looks like. Look by yourself: https://github.com/bgruening/training-material/tree/master/Exome-Seq A few highlights: * Slides are written in reveal.js With this we can create slides in Markdown, which is convenient to write and to share/improve with GitHub. PDFs can be automatically generated and we plan to do this automatically via Travis CI. Moreover these slides can be viewed with every Web browser, so you can watch them while you are exploring our training material, without downloading anything. An example can be found here: http://bgruening.github.io/training-material/Exome-Seq/slides/index.html A reveal.js template is available (http://bgruening.github.io/training-material/shared/slide_template/index.ht…) to get started, with on the first slide the GTN logo and some instructions how to use the presentation. * Docker container for the training We want to make Galaxy training scale. This means every trainer should be able to get a training instance with all tools, reference datasets, example input datasets up and running in minutes. For this, every training will have a versioned Docker container which can be easily deployed on clusters, clouds or laptops. Naturally, these training instances are available for everyone at any time, so they can used by the trained people to redo the workshop and then consolidate the learned techniques. * Galaxy tours! Every training should offer an interactive Galaxy tour. This is especially useful if someone wants to train herself. The interactive Galaxy tour will be in the Docker container. Hence someone using the Docker container can start the interactive tour and follows interactively the instructions. * Persistence and citability of the training data All the training data on which your training is based should be persistent and citable. For this we recommend to upload the datasets on Zenodo (in Galaxy training network community). A DOI associated to these datasets will be generated. The datasets can then be downloaded into the Docker container and reused everywhere. * Landing page An initial landing page is generated automatically from the general README file: http://bgruening.github.io/training-material Some broader plans we have and we need your comments and help! * We would like (and we started) to migrate the other training material in a similar fashion than the Exom-Seq. To get an idea of the current and needed work, check the open PRs on https://github.com/bgruening/training-material/ * We are planning a contribution-fest to consolidate our training material and improve the overall training experience in Galaxy on the 6.-7th October 2016! We will send an invitation to GOBELT and see if someone from them are also interested. * We would like to have the material for RNA-Seq, ChIP-Seq, MethylC-Seq and Genome Annotation updated by the end of this year. * We would like to write about this effort a small manuscript to attract more people and to announce the new capabilities of Galaxy training (tours, self-containing training with Docker …). We will keep a ToDo and discussion list on GitHub under the following URL: https://github.com/bgruening/training-material/issues Please contribute to these discussions and help make Galaxy training outstanding in Bioinformatics! Please let us know what you think! Bérénice and Bjoern P.S. If you want to share this news, please take this link: https://gist.github.com/bgruening/a54a8600c5cddca82424ad13569708c3

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