Educators:
Michael Turewicz (bioinformatician) and Karin Schork (biostatistician) (BioInfra.Prot)

Date:
Sunday, 11th Nov 2018

Location:
ISAS Campus, Dortmund, Germany (as part of Lipidomics Forum)

Contents:
This course will impart knowledge about how to conduct a differential analysis of high-throughput quantitative omics data using R. As we start with a basic introduction to the popular statistical programming language, no prior knowledge on R is required. The statistical background on utilized methods (hypothesis testing, multiple testing) is explained in order to enable the participants to assess their own as well as published workflows critically. The learning goals of this workshop contain the usage of basic R functions including functions for data import and export, basic plots and statistical tests. As the course will include hands-on exercises, bringing an own laptop is required.

Learning goals:  
- Independent usage of basic R functions including
    - data import and export
    - basic plots
    - statistical tests
    - Deeper understanding of statistical methods applied in differential analyses

Prerequisites:
- Basic understanding of high-dimensional data sets from quantitative omics or other life sciences;
- No prior knowledge on R required

Keywords:
R, high-throughput data, omics, differential analysis, multiple testing

Tools:
Download and more information on R here:
https://cran.r-project.org/

We recommend using an editor such as RStudio, see
https://www.rstudio.com

Contact:
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Educators:
Jacobo Miranda Ackermann, Fadi al Machot, Nils Hoffmann (BioInfra.Prot / LIFS)

Date:
November 11th, 2018   

Location:
ISAS Campus, Dortmund, Germany (as part of Lipidomics Forum)

Contents:
In this course, we will work through a typical use-case for bioinformatics processing of shotgun lipidomics data following MS acquisition, starting with PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals, followed by a comparison of the lipidomes using the LUX Score lipidome homology, before finally checking our quantitative lipidome results against those stored in LipidCompass. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to a provided data set. Participants are required to bring their own laptop in order to work on the hands-on exercises.
 
Learning goals:
Participants will be able to understand and explain the shotgun workflow. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline.

Prerequisites:
Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based applications. Participants are required to bring their own laptop in order to work on the hands-on exercises.

Keywords:
Lipidomics, Shotgun, Pipeline

Tools:
PeakStrainer and LipidXplorer, LUX Score and LipidCompass.

Contact:
This email address is being protected from spambots. You need JavaScript enabled to view it.

Educators:
Andreas Weidemann, Martin Golebiewski, Ulrike Wittig, Maja Rey, Wolfgang Müller (HITS gGmbH, Heidelberg, Germany) Sven Thiele, Axel von Kamp, Steffen Klamt (MPI for Dynamics of Complex Technical Systems, Magdeburg, Germany) Frank Bergmann, Jürgen Pahle, Sven Sahle, Ursula Kummer (University of Heidelberg, Germany) (de.NBI-SysBio) in collaboration with educators from UK, South Africa, Japan, Germany, USA

Date:
Saturday, October 27th, 2018

Links:
http://co.mbine.org/events/tutorial2018

Location:
Ecole Normale Supérieure de Lyon, Site Monod
Lyon, France

Contents:
This tutorial workshop is a satellite of the 19th International Conference on Systems Biology (ICSB).
Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats.

Learning goals:
Model setup using different software tools and systems biology platforms • Using experimental data for setting up quantitative models • Parameter estimation, optimization and model fitting • Simulation, analysis and visualization of biochemical models, and multicellular modelling • Constraint-based and logical modeling of metabolic and signaling networks • Database supported modelling: integrated data management and model databases • Community standards and formats for systems and synthetic biology models.

Prerequisites:
Laptop

Keywords:
systems biology,  software tools,  quantitative models,  parameter estimation, model simulation,  logical modeling,  metabolic networks, model databases, community standards

Tools:
SABIO-RK, CellNetAnalyzer, COPASI, BioModels database, CellDesigner, JWS Online, Morpheus, SEEK/FAIRDOMhub

Contact:
Dr. Andreas Weidemann
E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: +49-6221-533-242
Fax:     +49-6221-533-298
HITS gGmbH
Schloss-Wolfsbrunnenweg 35
D-69118 Heidelberg

Educators:
Stefan Albaum (Bielefeld University, DE) (BiGi / de.NBI)
Sebastian Jünemann (Bielefeld University, DE) (BiGi / de.NBI)
Nils Kleinbölting (Bielefeld University, DE) (BiGi / de.NBI)

Date:
13th November - 10:00 - 17:00

Location:
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld

Content:
Aim of this workshop is to give answers to typical questions in omics data analyses, e.g. regarding data normalization strategies and handling of missing values, the detection of groups of transcripts, proteins and/or metabolites with similar patterns of expression/abundance using cluster analyses, the visualization of multi-omics data in the context of metabolic pathways, or the identification of differentially regulated transcripts, proteins, and metabolites.

We will present our new web application Fusion (Brink et al. 2016) and introduce methods for the exploration of single as well as multi-level omics datasets. In hands-on tutorials, some selected data visualizations will be explained in detail and applied on (provided or own) datasets in order to adjust experiments and make new discoveries.

Prerequisites:
This workshop is intended for MSc/PhD students and postdocs with molecular biology background in transcriptomics (e.g. microarrays, RNA-seq), proteomics (e.g. LC-MS/MS) and/or metabolomics (e.g. GC-MS).

Tool:
Fusion (http://fusion.cebitec.uni-bielefeld.de)

Keywords:
data integration, transcriptomics, proteomics, metabolomics, data analysis

Contact:
Name: Stefan Albaum
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 0521/106-4821

Web:
For more information please visit: https://www.cebitec.uni-bielefeld.de/brf/index.php/training/upcoming-workshops/109-fusion-workshop-11-2018

Educators:
Björn Grüning (RBC)

Date:
04.10.2018 - 05.10.2018

Location:
Prague

Contents:
Galaxy for Proteomics

Learning goals:
How to use Galaxy in Proteomics

Prerequisites:
None

Keywords:
Galaxy, Training

Tools:
Galaxy - usegalaxy.eu, PeptideShaker, SearchGUI, moff, OpenMS, msconvert ...

Contact:
This email address is being protected from spambots. You need JavaScript enabled to view it.