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

[Celia van Gelder]

*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):
https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translational-medicine-using-galaxy/



TARGET AUDIENCE


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.



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. 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.


PREREQUISITE KNOWLEDGE


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.)



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.
   -

   Galaxy setup for teaching and training material development.




Day 1 - Wed Oct 17

Day 2 - Thur Oct 18

Day 3 - Frid Oct 19

Morning

Galaxy 101 + Variant detection
<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 Speech*

I: About bioinformatics workflows

II: About Galaxy and ELIXIR

III: About bioinformatics teaching

TBD

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

Jaap Heringa <https://www.cs.vu.nl/~heringa/>

Afternoon

BWA + 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/>

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

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

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

Evening

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 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 at 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 at 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.
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