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.
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