[ELIXIR-ITA_ml] Fwd: [Galaxy-wg] Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach it! - 17- 19 October 2018, Amsterdam

General ELIXIR-Italy Mailing list elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it
Ven 13 Lug 2018 18:24:59 CEST

ELIXIR-NL Course: Bioinformatics for Translational Medicine using 
Galaxy: see it, do it, teach it!

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: _This course is an ELIXIR-EXCELERATE course and is 
organised by ELIXIR-NL by Chao (Cico) Zhang (VU), Sanne Abeln (VU), 
Anton Feenstra (VU), Saskia Hiltemann (ErasmusMC), Mateusz Kuzak (DTL) 
and Celia van Gelder (DTL).

_Course page (incl. Application Form)_: 


1) Biomedical & translational medicine researchers/students who are keen 
on bioinformatics and 2) educators in the “bio” domain who would like to 
start using Galaxy in their courses as an introduction to Bioinformatics.


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. 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 recognised 
researchers in the fields of Biomedicine, Bioinformatics education and 
Galaxy workflows. The confirmed speakers include Jaap Heringa, who is 
the scientific director of the Netherlands Bioinformatics Centre; and 
Björn Grüning, who is the leader of Galaxy training network, also 
actively involved in Bioconda.


The attendees of Part I are assumed to have the basic knowledge of 
biomedicine (molecular biology and genomics) and be interested in 
analysing 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.)


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.
  * Galaxy setup for teaching and training material development.


*Day 1 - Wed Oct 17*


*Day 2 - Thur Oct 18*


*Day 3 - Frid Oct 19*



Galaxy 101 + Variant detection 


Network analysis with microbiota metatranscriptome 


Teaching bioinformatics workflows

Saskia Hiltemann <https://shiltemann.github.io/>


Chao Zhang <https://hi-it.org/>


Anton Feenstra <http://www.few.vu.nl/%7Efeenstra/>

*Keynote Speech**


I: About bioinformatics workflows


II: About Galaxy and ELIXIR


III: About bioinformatics teaching



Björn Grüning <https://galaxyproject.org/people/bjoern-gruening/>


Jaap Heringa <https://www.cs.vu.nl/%7Eheringa/>



BWA + RNAseq 


16S rRNA sequencing with mothur 


Galaxy training material development 

Saskia Hiltemann <https://shiltemann.github.io/>


Saskia Hiltemann <https://shiltemann.github.io/>


Saskia Hiltemann <https://shiltemann.github.io/>



Social dinner


*About the instructors*:  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), Chao Zhang 
(VU), Leon Mei (LUMC), Ruben Vorderman (LUMC) and Sanne Abeln (VU).

*Note*: The course is held in a computer classroom, so you don’t need to 
bring your own laptop.


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 <mailto: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 <mailto:celia.van.gelder a dtls.nl>

websites: www.dtls.nl <http://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.

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