Galaxy-training

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87 discussions

GTN (online) CoFest and community call - 16th of May
by Bérénice Batut 16 Apr '19

16 Apr '19

Dear all, The Galaxy Training Network is organizing online CoFests (Collaboration/Contribution Fests) every 3 months for a day of the collaborative work on the training content. The next one will be on the 16th of May. Anyone who would like to contribute on any other topics is very welcome to join. We will coordinate via Hangout <https://hangouts.google.com/hangouts/_/calendar/Z2FsYXh5dW5pZnJlaWJ1cmdAZ21…> (drop-in channel we will keep open the whole day) and the GTN Gitter channel <https://gitter.im/Galaxy-Training-Network/Lobby>. During the day, we plan to have GTN community calls to discuss the recent changes and future directions. To accommodate different time zones and schedules, we will have 2 calls (with similar discussions) at 8am (UTC + 2) <http://arewemeetingyet.com/Berlin/2019-05-16/08:00/GTN%20meeting> and 4pm (UTC + 2) <http://arewemeetingyet.com/Berlin/2019-05-16/16:00/GTN%20meeting> via Hangout <https://hangouts.google.com/hangouts/_/calendar/Z2FsYXh5dW5pZnJlaWJ1cmdAZ21…>. More details about this day can be found on the Galaxy website (https://galaxyproject.org/events/2019-05-gtn/ <https://galaxyproject.org/events/2019-05-gtn/>) and the dedicated GitHub issue <https://github.com/galaxyproject/training-material/issues/1339>. Please forward this email to any potentially interested individuals and groups. We hope to see you there, Best, Bérénice Bérénice Batut ----------------------------------------------------------------------------------- PhD in Bioinformatics and Computational Biology Post-doc in Bioinformatics ----------------------------------------------------------------------------------- http://bebatut.fr

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[Galaxy Community Conference] Vote for Training
by Bérénice Batut 28 Jan '19

28 Jan '19

Hi all, We are proud to announce that the Galaxy Community Conference (GCC) <https://galaxyproject.org/events/gcc2019> 2019 will be held in Freiburg <https://www.freiburg.de/> (Germany) in the Konzerthaus <https://www.konzerthaus.freiburg.de/startseite/7/de/home.html> from 1.-6. July 2019. It will start with training but also continues with training throughout the conference. The community proposed some topics but as we try to reach this year a lot more users, we are really interested it what you would like to learn. Please take a few minutes to vote which training should be offered at GCC2019: https://goo.gl/forms/iaY5AezdFpyJ0ETh2 <https://galaxyproject.org/events/gcc2019/training/> Thank you very much :-) Best, Bérénice, in behalf of the GCC organization committee PS: Feel free to forward this email to anyone who may be interested. Thanks! Bérénice Batut ----------------------------------------------------------------------------------- PhD in Bioinformatics and Computational Biology Post-doc in Bioinformatics ----------------------------------------------------------------------------------- http://bebatut.fr

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GTN (online) CoFest and call on Galaxy Training Material - 21st February
by Bérénice Batut 21 Jan '19

21 Jan '19

Dear all, The Galaxy Training Network is organizing online CoFests (Collaboration/Contribution Fests) every 3 months for a day of the collaborative work on the training content. The next one will be on the 21st of February. Anyone who would like to contribute on any other topics is very welcome to join. We will coordinate via the GTN Gitter channel <https://gitter.im/Galaxy-Training-Network/Lobby> and Hangout During the day, we will also have GTN community calls to discuss the recent changes and future directions for the Galaxy Training Materials. To accommodate different time zones and schedules, we will have 2 calls (with similar discussions) at 8am (UTC + 1) <http://arewemeetingyet.com/Berlin/2019-02-21/08:00/GTN%20meeting> and 4pm (UTC + 1) <http://arewemeetingyet.com/Berlin/2019-02-21/16:00/GTN%20meeting> via Hangout <https://hangouts.google.com/hangouts/_/calendar/Z2FsYXh5dW5pZnJlaWJ1cmdAZ21…>. More details about this day can be found on the Galaxy website (https://galaxyproject.org/events/2019-02-gtn/ <https://galaxyproject.org/events/2018-11-gtn/>) and the dedicated GitHub issue <https://github.com/galaxyproject/training-material/issues/1152>. Feel free to forward this email to any potentially interested individuals and groups. We hope to see you there Best, Bérénice Batut ----------------------------------------------------------------------------------- PhD in Bioinformatics and Computational Biology Post-doc in Bioinformatics ----------------------------------------------------------------------------------- http://bebatut.fr

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End of 2018 Reminders: Admin Training, GCC2019 Training Topic Nominations, and GalaxyAdmins meetups topics
by Dave Clements 27 Dec '18

27 Dec '18

Happy Holidays all! A couple of reminders before 2019 arrives: - *Galaxy Admin Training <https://galaxyproject.org/events/2019-admin-training/>*, January 28-February 1. Learn best practices for installing and supporting your own Galaxy service. Split into a 2-day intro session, and a 3 day advanced session. *Advance registration ends December 31, and then rates go up by, um, a lot. Register by Monday.* - *GCC2019 Training Topic Nominations <https://galaxyproject.org/news/2018-12-gcc2019-training-nomination/> end 31 December! * Nominated topics will be voted on by the community in January. Topics nominated thus far are here <https://galaxyproject.org/events/gcc2019/training/#training-topic-nominatio…>. Please nominate new topics here <https://docs.google.com/forms/d/1fBPjEmw7Td52rhBnC0SvflnQCD7Ue5IMJ9RkM0SjnY…>, and if you want to expand on existing nominations <https://galaxyproject.org/events/gcc2019/training/#training-topic-nominatio…> you can edit the hub directly, or send the edits to me. (Note: I suspect, but don't know, that we'll extend this deadline into early January.) - *GalaxyAdmins meetups <https://galaxyproject.org/news/2018-12-galaxy-admins/>* will resume in 2019 <https://galaxyproject.org/news/2018-12-galaxy-admins/>. If you have ideas for meetup topics, please nominate them <https://docs.google.com/forms/d/e/1FAIpQLSfv257YcdQQO7gp3K4USoBzqkd-UDEblst…> . - We need your project ideas for *Google Summer of Code 2019* <https://docs.google.com/forms/d/e/1FAIpQLSfv257YcdQQO7gp3K4USoBzqkd-UDEblst…>*. *Please add your project ideas to the proposal, either directly on this page <http://gmod.org/wiki/GSOC_Project_Ideas_2019> (requires an account), of via this online form <http://bit.ly/gsoc-2019-ogi-propose>. Finally, for those of you not on Twitter, I can't resist sharing this post from Martin Čech <https://twitter.com/martenson?ref_src=twsrc%5Etfw%7Ctwcamp%5Eembeddedtimeli…> . See you in the new year, Dave C [image: 2018-12-26_12-01-57-martins-tree.png] -- https://galaxyproject.org/ https://usegalaxy.org/

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Fwd: Please nominate training topics for GCC2019 by Dec 31
by Dave Clements 06 Dec '18

06 Dec '18

Hi All, In case you missed it, the call for training topic nominations is now open. See below for details. I would particularly like to encourage people on this list to consider nominating topics. Thanks, Dave C ---------- Forwarded message --------- From: Dave Clements <clements(a)galaxyproject.org> Date: Wed, Dec 5, 2018 at 2:40 PM Subject: Please nominate training topics for GCC2019 by Dec 31 To: Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Cc: Bérénice Batut <berenice.batut(a)gmail.com> Hi All, The *2019 Galaxy Community Conference (GCC2019)* <https://galaxyproject.org/events/gcc2019/> will be held in be held in *Freiburg, Germany, 1-6 July*. Like previous Galaxy Community Conferences <https://galaxyproject.org/gcc/>, GCC2019 will feature invited keynotes, accepted talks, posters, demos, birds-of-a-feather gatherings and *training*. The format of GCC2019 will be a bit different than the previous years: it starts with 1 day of training and then 3 days with more specialized training sessions aligned with talks. *You can read more about the new format on the conference FAQ <https://galaxyproject.org/events/gcc2019/faq/#what-will-be-the-format-for-g…>.* *The training topics that are offered are determined by the community so BY YOU! <https://docs.google.com/forms/d/1fBPjEmw7Td52rhBnC0SvflnQCD7Ue5IMJ9RkM0SjnY…>* Please give some thought to what topics you would like to see offered, or that you would like to offer, and then submit them as topic nominations <https://docs.google.com/forms/d/1fBPjEmw7Td52rhBnC0SvflnQCD7Ue5IMJ9RkM0SjnY…> . Nominated topics can cover a wide range. For example: - Introduction to Using Galaxy - Scientific topic oriented trainings - Community specific trainings - Development and administration around Galaxy - Train the trainers This list only shows some examples. *Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic.* If you are looking for ideas, see the topic nominated in: 2016 <https://galaxyproject.org/news/2018-12-galaxy-update/bit.ly/gcc2016noms>, 2015 <https://galaxyproject.org/news/2018-12-galaxy-update/bit.ly/gcc2015vote>, 2014 <https://galaxyproject.org/news/2018-12-galaxy-update/bit.ly/1s6NtMN>, 2013 <https://galaxyproject.org/news/2018-12-galaxy-update/bit.ly/1i2j1gN> and the Galaxy Events page <https://galaxyproject.org/news/2018-12-galaxy-update/galaxyproject.org/even…> . Training nomination is open from *December, 1st* to *December, 31*. Topics will be compiled into a uniform list by the GCC2019 Organizing Committee, and topics will be voted on by the Galaxy Community from *January, 15th* to *January, 31st*.

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Galaxy Training Material (online) CoFest - 15th November (next week)
by Bérénice Batut 08 Nov '18

08 Nov '18

Dear all, The Galaxy Training Network is organizing regular online CoFests (Collaboration/Contribution Fests) every 3 months on the 3rd Thursday for a day of the collaborative work on the training content. The next one will be next Thursday (the 15th of November). We plan to focus on genome annotation training; but anyone who would like to contribute on any other topics is very welcome to join. We will coordinate via Hangout <https://hangouts.google.com/hangouts/_/calendar/Z2FsYXh5dW5pZnJlaWJ1cmdAZ21…> (drop-in channel we will keep open the whole day) and the GTN Gitter channel <https://gitter.im/Galaxy-Training-Network/Lobby>. More details about this event can be found on the Galaxy website (https://galaxyproject.org/events/2018-11-gtn/ <https://galaxyproject.org/events/2018-11-gtn/>) and the dedicated GitHub issue <https://github.com/galaxyproject/training-material/issues/1082>. During the day, we plan to have a GTN meeting to discuss the recent changes and future directions. To accommodate different time zones and schedules, we will have 2 calls (with similar discussions) at 7am (UTC + 2) <http://arewemeetingyet.com/Berlin/2018-11-15/07:00/GTN%20meeting> and 4pm (UTC + 2) <http://arewemeetingyet.com/Berlin/2018-11-15/16:00/GTN%20meeting> via Hangout <https://hangouts.google.com/hangouts/_/calendar/Z2FsYXh5dW5pZnJlaWJ1cmdAZ21…>. More details about the meeting will be posted on the dedicated GitHub issue <https://github.com/galaxyproject/training-material/issues/1088>. We hope to see you there Best, Bérénice Batut ----------------------------------------------------------------------------------- PhD in Bioinformatics and Computational Biology Post-doc in Bioinformatics ----------------------------------------------------------------------------------- http://bebatut.fr

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Galaxy Training Material (online) CoFest - 15th November
by Bérénice Batut 15 Oct '18

15 Oct '18

Dear all, The Galaxy Training Network is organizing regular online CoFests (Collaboration/Contribution Fests) every 3 months on the 3rd Thursday for a day of the collaborative work on the training content. The next one will be on the 15th of November. We plan to focus on genome annotation training; but anyone who would like to contribute on any other topics is very welcome to join. We will coordinate via Hangout <https://hangouts.google.com/hangouts/_/calendar/Z2FsYXh5dW5pZnJlaWJ1cmdAZ21…> (drop-in channel we will keep open the whole day) and the GTN Gitter channel <https://gitter.im/Galaxy-Training-Network/Lobby>. More details about this event can be found on the Galaxy website (https://galaxyproject.org/events/2018-11-gtn/ <https://galaxyproject.org/events/2018-11-gtn/>) and the dedicated GitHub issue <https://github.com/galaxyproject/training-material/issues/1082>. During the day, we plan to have a GTN meeting to discuss the recent changes and future directions. To accommodate different time zones and schedules, we will have 2 calls (with similar discussions) at 7am (UTC + 2) <http://arewemeetingyet.com/Berlin/2018-11-15/07:00/GTN%20meeting> and 4pm (UTC + 2) <http://arewemeetingyet.com/Berlin/2018-11-15/16:00/GTN%20meeting> via Hangout <https://hangouts.google.com/hangouts/_/calendar/Z2FsYXh5dW5pZnJlaWJ1cmdAZ21…>. More details about the meeting will be posted on the dedicated GitHub issue <https://github.com/galaxyproject/training-material/issues/1088>. Feel free to forward this email to any potentially interested individuals and groups. We hope to see you there Best, Bérénice Batut ----------------------------------------------------------------------------------- PhD in Bioinformatics and Computational Biology Post-doc in Bioinformatics ----------------------------------------------------------------------------------- http://bebatut.fr

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Training material missing
by LI Jiaxin 09 Oct '18

09 Oct '18

Hi I found that the training material in fold 1. Galaxy Australia Training Material<https://usegalaxy.org.au/library/list#/folders/F62e701d3f176b13d> 2. RNA-Seq<https://usegalaxy.org.au/library/list#/folders/F716028a8851ce294> 3. Fly RNA-Seq KO 03 R2.Fastq are missing. ? Thanks for upload it. Best wishes! Jiaxin

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regarding transcriptome read cleaning
by Rahul Shelke 05 Oct '18

05 Oct '18

Dear sir, I am using Australia Galaxy for assembling transcriptome lib. For cleaning of Illumina nextera 500 reads, I am using a trimmomatic program. This program contains nextera paired end adapter cleaning option. Now I am confused whether I should use galaxy nextera adapter or use specific nextera 500 adapter for cleaning. Kindly provide your suggestion. -- Rahul G. Shelke PhD Scholar Department of Biosciences and Bioengineering. Indian Institute Of Technology. Guwahati,Assam, India.781039 +91-9954919129 Skype ID:- rahulshelke2

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Fwd: [BBC] Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy - 17- 19 October 2018, Amsterdam
by Dave Clements 21 Sep '18

21 Sep '18

Hi All, The second part of this workshop is about using Galaxy in courses as an introduction to bioinformatics. Space is limited. Cheers, Dave C ---------- Forwarded message --------- From: Celia van Gelder <celia.van.gelder(a)dtls.nl> Date: Sat, Sep 15, 2018 at 10:47 PM Subject: [BBC] Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy - 17- 19 October 2018, Amsterdam To: <bbclist(a)psb.vib-ugent.be> ELIXIR-NL Course: Bioinformatics for Translational Medicine using Galaxy Please circulate this email to those who might be interested. *Date*: 17-19 October, 2018 *Location:* VU Amsterdam (O|2 Lab Building <https://goo.gl/maps/CphwJEFDegt>, Gustav Mahlerlaan 665, 1082 MK, 1082 MK Amsterdam) *Organizers:* Chao (Cico) Zhang (VU), Sanne Abeln (VU), Anton Feenstra (VU), Saskia Hiltemann (ErasmusMC), Mateusz Kuzak (DTL) and Celia van Gelder (DTL). *Course page*: https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat… *Application form*: https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat… *TARGET AUDIENCE* *This course consists of two parts, each of which you could register separately in the **application form* <https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat…> *.* *Part 1 (Day 1 and 2)*: biomedical & translational medicine researchers/students who are keen on bioinformatics *Part 1 and 2 (Day 1, 2 and 3)*: educators in the “bio” domain who would like to start using Galaxy in their courses as an introduction to bioinformatics. *COURSE DESCRIPTION* Analysing molecular data in translational medicine involves a multitude of computational steps. Here, we introduce the basics of how to design and run these steps within Galaxy, a free and easy-to-use web platform that enables users to connect bioinformatics tools into a workflow without any prior programming expertise. This course consists of two parts, each of which you could register separately. Part 1 will let you get familiar with Galaxy; it will introduce some bioinformatics workflows used for RNAseq, variant detection and metagenomics; and how to easily connect different computational steps in Galaxy. Part 2 will focus on how to teach bioinformatics with Galaxy and to design bioinformatics courses using Galaxy. Participants can register for both parts separately. This course is also interspersed with a few keynotes, from recognized researchers in the fields of biomedicine, bioinformatics education, and Galaxy workflows. The confirmed speakers include Remond Fijneman (Day 1), a scientist in oncology from NKI; Björn Grüning (Day 2), the leader of Galaxy training network, who is also actively involved in Bioconda, and Jaap Heringa (Day 3), the scientific director of the Netherlands Bioinformatics Centre. *PREREQUISITE KNOWLEDGE * The attendees of Part I are assumed to have the basic knowledge of biomedicine (molecular biology and genomics) and be interested in analyzing patient-derived sequencing data. The attendees of Part II are assumed to have some teaching experience in the relevant field (e.g., bioinformatics, computational biology, systems biology, quantitative biology, etc.) *COURSE SCHEDULE* The course consists of six modules, as the table below shows, covering a list of topics as follows: - Introduction to Galaxy. Run bioinformatics tools and workflows in Galaxy without the need for any programming expertise. - Reference-based RNA-Seq data analysis - Module detection in differential gene expression in meta transcriptomics samples. - Microbiota Analysis: 16S rRNA sequencing analysis in Galaxy - How to teach bioinformatics workflows. - How to prepare training material development. *Day 1 - Wed Oct 17* *Day 2 - Thu Oct 18* *Day 3 - Fri Oct 19* *Morning* Introduction to Galaxy <http://galaxyproject.github.io/training-material/topics/introduction/> Network analysis with microbiota metatranscriptome <https://www.ncbi.nlm.nih.gov/pubmed/26342232> Teaching bioinformatics workflows Saskia Hiltemann <https://shiltemann.github.io/> Chao Zhang <https://hi-it.org/> Anton Feenstra <http://www.few.vu.nl/~feenstra/> *Keynote* I: About bioinformatics workflows II: About Galaxy and ELIXIR III: About bioinformatics teaching Remond Fijneman <https://www.nki.nl/people/fijneman-remond/> Björn Grüning <https://galaxyproject.org/people/bjoern-gruening/> Jaap Heringa <https://www.cs.vu.nl/~heringa/> *Afternoon* RNAseq <http://galaxyproject.github.io/training-material/topics/transcriptomics/> 16S rRNA sequencing with mothur <http://galaxyproject.github.io/training-material/topics/metagenomics/> Galaxy training material development <http://galaxyproject.github.io/training-material/> Björn Grüning <https://galaxyproject.org/people/bjoern-gruening/> Saskia Hiltemann <https://shiltemann.github.io/> Saskia Hiltemann <https://shiltemann.github.io/> *Evening* Social dinner *About the instructor*: Each session is led by one instructor listed in the table above but strongly supported by multiple co-instructors, including, but not limited to, Saskia Hiltemann (ErasmusMC), Björn Grüning, Chao Zhang (VU), Leon Mei (LUMC), Ruben Vorderman (LUMC) and Sanne Abeln (VU). *Correction*: An earlier version of this announcement mentioned that you don’t need to bring your own laptop, this is NOT TRUE. We regret the error. *You do need to bring your own laptop*. *COURSE FEE* Course participation is free of charge. A workshop dinner will be organized on Thursday (at participants’ own expenses) Should you have any question about this course, please contact Celia van Gelder (celia.van.gelder(a)dtls.nl) Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: www.dtls.nl, www.biosb.nl skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours. _______________________________________________ BBClist mailing list BBClist(a)psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/bbclist -- https://galaxyproject.org/ https://usegalaxy.org/

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