[BBC] Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy - 17- 19 October 2018, Amsterdam

[Celia van Gelder]

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 ( <https://goo.gl/maps/CphwJEFDegt> O|2 Lab Building,
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
ional-medicine-using-galaxy/>
https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translati
onal-medicine-using-galaxy/

Application form:
<https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat
ional-medicine-using-galaxy/enrollment-galaxy-workshop-2018/>
https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translati
onal-medicine-using-galaxy/enrollment-galaxy-workshop-2018/ 

 

TARGET AUDIENCE

 

This course consists of two parts, each of which you could register
separately in the
<https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat
ional-medicine-using-galaxy/enrollment-galaxy-workshop-2018/> application
form.

 

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

 <http://galaxyproject.github.io/training-material/topics/introduction/>
Introduction to Galaxy

 <https://www.ncbi.nlm.nih.gov/pubmed/26342232> Network analysis with
microbiota metatranscriptome

Teaching bioinformatics workflows


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

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

 <http://www.few.vu.nl/~feenstra/> Anton Feenstra


Keynote

I: About bioinformatics workflows

II: About Galaxy and ELIXIR

III: About bioinformatics teaching


 <https://www.nki.nl/people/fijneman-remond/> Remond Fijneman

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

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


Afternoon

 <http://galaxyproject.github.io/training-material/topics/transcriptomics/>
RNAseq

 <http://galaxyproject.github.io/training-material/topics/metagenomics/> 16S
rRNA sequencing with mothur

 <http://galaxyproject.github.io/training-material/> Galaxy training
material development


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

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

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


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 ( <mailto:celia.van.gelder at dtls.nl> 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:  <mailto:celia.van.gelder at dtls.nl> celia.van.gelder at dtls.nl

websites:   <http://www.dtls.nl/> www.dtls.nl,  <http://www.biosb.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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