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@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@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, 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-translational-medicine-using-galaxy/

Application form: https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translational-medicine-using-galaxy/enrollment-galaxy-workshop-2018/

TARGET AUDIENCE

This course consists of two parts, each of which you could register separately in the 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	Introduction to Galaxy	Network analysis with microbiota metatranscriptome	Teaching bioinformatics workflows
Morning	Saskia Hiltemann	Chao Zhang	Anton Feenstra
Keynote	I: About bioinformatics workflows	II: About Galaxy and ELIXIR	III: About bioinformatics teaching
Keynote	Remond Fijneman	Björn Grüning	Jaap Heringa
Afternoon	RNAseq	16S rRNA sequencing with mothur	Galaxy training material development
Afternoon	Björn Grüning	Saskia Hiltemann	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 (celia.van.gelder@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@dtls.nl

websites: www.dtls.nl, www.biosb.nl

skype: celia.van.gelder

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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