[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
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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)_:
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/%7Efeenstra/>
*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/%7Eheringa/>
*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 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
<http://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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