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

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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Galaxy Admin Training: November 7-11, Salt Lake City, Utah.
by Dave Clements 06 Sep '16

06 Sep '16

Hello all, This is a request to please help get the word out about the upcoming Galaxy Admin Training event in Salt Lake. Please consider forwarding this announcement to any individuals or groups that might be interested. Thanks, Dave C. The Galaxy Admin Training workshop <https://wiki.galaxyproject.org/Events/AdminTraining2016> will be held November 7-11 in Salt Lake City, Utah, the week before Supercomputing’16 <http://sc16.supercomputing.org/> also meets in Salt Lake. The workshop offers Basic <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession> and Advanced <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession> sessions. Galaxy <https://galaxyproject.org/> is an open web based platform for biomedical data integration and analysis. It is deployed at large and small organizations around the world and used in a broad range of biomedical research domains, and across the tree of life. Galaxy enables life science researchers to perform their own data analysis without having to learn command line interfaces or Linux package management. Galaxy transparently records all analysis steps and eases workflow reuse and sharing. If your organization is looking for how to empower your researchers, then please consider attending one or both sessions. Participants will learn how to install, configure, customize, and extend their own Galaxy servers. Topics include tool configuration, authentication and user management, using heterogeneous storage and compute services, and many other topics that will enable you to get your own Galaxy server up and running, performing well, and used by your community. Registration <https://wiki.galaxyproject.org/Events/AdminTraining2016/Registration> is now open, but space is limited. *Early registration ends September 19*. Participants can register for one or both sessions. Please review each session’s prerequisites before registering. Galaxy Admin Training 2016 is hosted by the University of Utah Center for High Performance Computing (CHPC) <http://www.chpc.utah.edu/>, the Department of Biomedical Informatics <http://medicine.utah.edu/dbmi/> and the Clinical & Translational Science Biomedical Informatics Core (CCTS BMIC) <http://medicine.utah.edu/ccts/bmic/> at the University of Utah <http://utah.edu/>. We hope to see you in Salt Lake! The Galaxy Team PS: Please share this flier <https://wiki.galaxyproject.org/Events/AdminTraining2016/Publicity> with any individuals or groups who might be interested in this event. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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