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