September 2018 - Galaxy-training - lists.galaxyproject.org

Fwd: [BBC] Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy - 17- 19 October 2018, Amsterdam
by Dave Clements 20 Sep '18

20 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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GTN - Instructor community - first meeting
by Bérénice Batut 20 Sep '18

20 Sep '18

Hi all, We would like to start a group of instructors that would be interested into supporting other instructors. One of the goal of such group could to be to discuss and collect best pedagogical and technical recommendations for Galaxy training workshops and start a handbook for training with Galaxy. Another goal could be to start regular discussion meetings in which one or two experienced instructors could help and give advices to less experienced instructors (a bit on the same idea as the Instructor Discussion Sessions of the Carpentries). If you are interested to participate to such group, feel free to join one of 2 planned meetings (to fit different time zones and constraints, but similar discussions): September 27, 3pm (UTC+2) Timing for your time zone <http://arewemeetingyet.com/Berlin/2018-09-27/15:00/GTN%20-%20Instructor%20c…> Hangout <https://hangouts.google.com/hangouts/_/calendar/Z2FsYXh5dW5pZnJlaWJ1cmdAZ21…> Google event <https://calendar.google.com/event?action=TEMPLATE&tmeid=NmNkM2Q1azZmaWhtaWQ…> October 5, 11am (UTC+2) Timing for your time zone <http://arewemeetingyet.com/Berlin/2018-10-05/11:00/GTN%20-%20Instructor%20c…> Hangout <https://hangouts.google.com/hangouts/_/calendar/Z2FsYXh5dW5pZnJlaWJ1cmdAZ21…> Google Event <https://calendar.google.com/event?action=TEMPLATE&tmeid=NG9tamJqYmd0Y2JuYmY…> We will also take notes during the meeting and send the notes afterwards. I hope to see some of you there, Best, Bérénice Batut ----------------------------------------------------------------------------------- PhD in Bioinformatics and Computational Biology Post-doc in Bioinformatics ----------------------------------------------------------------------------------- http://bebatut.fr

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GOBLET Question: Renew or not?
by Dave Clements 06 Sep '18

06 Sep '18

Hi All, There's a discussion happening on the GTN Gitter channel <https://gitter.im/Galaxy-Training-Network/Lobby> about renewing our GOBLET membership (or not). If you are interested and/or have something to say, please join us there. Thanks, Dave C -- https://galaxyproject.org/ https://usegalaxy.org/

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