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Messages - Reza Salek

1
EMBO course / EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists 2018
EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists

Date:  Monday 5 - Friday 9 February 2018
Venue:  European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
Application deadline:  Friday, November 03 2017

Contact: Reza Salek (reza.salek@ebi.ac.uk)
Registration: https://www.ebi.ac.uk/training/events/2018/embo-practical-course-metabolomics-bioinformatics-life-scientists-4

Overview

This course will provide an overview of key issues that affect metabolomics studies, handling datasets and procedures for the analysis of metabolomics data using bioinformatics tools. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics, from study design to metabolite identification. We encourage you to bring your data, data problems you might have with a particular data set or study for group discussion and activities.  You will be asked to present your work and participate in the discussions from day one.

Audience
This course is aimed at PhD students, post-docs and researchers with at least one to two years of experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis.

seeking to improve their skills in metabolomics data analysis. 

Syllabus, tools and resources

 • Metabolomics study design, workflows and sources of experimental error, difference between target and un-target approaches
• Metabolomics data processing tools: hands on open source R based programs, XCMS, MetFrag, MetFusion, rNMR, BATMAN
• Metabolomics data analysis: Using R Bioconductor, understanding usage of univariate and multivariate data analysis, data fusion concepts, data clustering and regression methods
• Metabolomics downstream analyses: KEGG, BioCyc, and MetExplore for metabolic pathway and network analysis with visualisation of differential expression, understanding metabolomics flux analysis
• Metabolomics standards and databases: data dissemination and deposition in EMBL- EBI MetaboLights repository; PheNoMeNal, workflows4metabolomics
• Metabolomics Flux and Stable Isotope Resolved Metabolomics (SIRM)
5
Online and e-learning / EmTraG coordination of metabolomics training
Announcing launch of EmTraG, a new initiative to improve the coordination of metabolomics training across Europe. The European Metabolomics Training Coordination Group (EmTraG) was formed in 2016 by scientists with a passion for training in metabolomics. It was created to address the considerable need to harmonise the rapidly expanding portfolio of metabolomics training courses in Europe.
EmTraG’s mission is to harmonise metabolomics training across Europe in order to improve its scientific coverage, geographical reach, quality and impact, thereby empowering the next generation of analytical, computational and applied metabolomics scientists.

For more details See Press release
Official website: http://www.emtrag.eu/
7
Online and e-learning / EMBL-EBI Introduction to metabolomics
This course provides a basic introduction to the rapidly emerging field of metabolomics and its importance and applications.

http://www.ebi.ac.uk/training/online/course/introduction-metabolomics

Learning objectives: 
  • Comprehend the purpose and importance of the field of metabolomics
  • Describe some principles of metabolomic study design
  • Evaluate advantages and limitations of some analytical techniques used in metabolomics studies
  • Discuss some of the modern-day applications of metabolomics
  • Access metabolomics resources at the EMBL-EBI
9
EMBO course / EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists 2017
EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists

Venue: European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
Application opens: Monday August 08 2016
Application deadline: Friday November 11 2016
Participation: Open application with selection
Contact: Reza Salek
Registration fee: £350

Overview
This course will provide an overview of key issues that affect metabolomics studies, handling datasets and procedures for the analysis of metabolomics data using bioinformatics tools. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics, from study design to metabolite identification.

Audience
This course is aimed at PhD students, post-docs and researchers with at least one year’s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants ideally must have working experience using R (including a basic understanding of the syntax and ability to manipulate objects).

For more information, please visit https://www.ebi.ac.uk/training/events/2017/embo-practical-course-metabolomics-bioinformatics-life-scientists-3.
12
Compound identification / Re: Metabolomics and clinical practice
As a new Biomarker, yet to materialise. However, there are many new proposed ones. But it needs to pass the test of time and reproducibility. I would be also interested if anyone else came across one with good potentials. 
14
Galaxy / Re: How to implement a 'commerical' MS data processing software in Galaxy ?
You need to check if the commercial tools licensing would allow you to do it, even if you plan to run it locally.
You can generate a "tool config file" or "wrapper" and share that if you wish (without the commercial tool).
There are many tutorial and wikis on this and larger community to ask questions. @Ralf Weber  know quite a lot more.
Best Wishes,
Reza