Educators:
Patrick Winter, Oliver Sampson (CIBI)

Date:
07-08-2017 – 11-08-2017

Location:
KNIME Office Konstanz (Reichenaustr. 11, 78467 Konstanz)

Contents:
The hackathon has two main goals: the integration of new batch processing middleware and finding use cases for the cluster execution in different domains of the life sciences. Already planned is the adaption of the old UniCore integration to the new cluster execution API and the integration of the Torque middleware, as well as various bug fixes. Regarding use cases, there will be people working on image processing on the cluster. You are welcome to bring your data and workflows to run on a cluster. Please note that KNIME cannot provide cluster infrastructure, so you need remote access to your own cluster.

Learning goals:
- Integration of Cluster Middleware into the KNIME Cluster Extension
- Use cases for cluster execution in the life sciences

Prerequisites:
- Knowledge of Java development
- Prior knowledge of KNIME Node development
- Precise formulation of personal hackathon project

Keywords:
KNIME, Integration, Cluster, UniCore, SLURM, Image Processing

Tools:
KNIME

Contact:
Patrick Winter
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Educators:
A. Shevchenko, R. Ahrends, D. Schwudke, J. Miranda, F. Al Machot (BioInfra.Prot - LIFS)

Date:
Sunday, 12th Nov 2017 - 11:00-16:00

Location:
Research Center Borstel, Parkallee 1-40, 23845 Borstel

Contents:
This course will introduce participants to the workflows used to analyse
lipidomics data with the tools Peak Strainer and LipidXplorer and how to compare
lipidomes with LUX Score.

Learning goals:
- Data import and processing
- Comparison of lipidomes
- Interpretation of results

Prerequisites:
Basic understanding of mass spectrometry data sets from lipidomics or other life
sciences.

Keywords:
high-throughput data; lipidomics; differential analysis;

Tools:
Download and more information on the software packages used during the workshop
is available here:
http://lifs.isas.de

Contact:
Dominik Schwudke This email address is being protected from spambots. You need JavaScript enabled to view it.
Andrej Shevchenko This email address is being protected from spambots. You need JavaScript enabled to view it.
Robert Ahrends This email address is being protected from spambots. You need JavaScript enabled to view it.

More information:

Announcement:
http://lifs.isas.de/index.php/news-2

Registration:
http://lipidomics-forum.fz-borstel.de/index.php/registration

Hosts:
http://www.fz-borstel.de/cms/en/science/priority-area-infections/bioanalytical-chemistry.html

Directions:
http://lipidomics-forum.fz-borstel.de/index.php/venue

Educators:
de.STAIR partners
Dr. Dr. Steve Hoffmann (Leipzig)
Prof. Olaf Wolkenhauer (Rostock)
Prof. Wolfgang Hess (Freiburg)

Date:
4.-6.10.2017

Location:
Faculty of Biology, Freiburg (Breisgau)

Contents:
This workshop intends to introduce the Galaxy RNA-workbench for analysis of RNA-Seq data. Therefore, we will present Linux/Unix and Docker backgrounds, introduce methods for exploration of NGS data and fundamental statistics. In practical tutorials, workflow development, functional predictions of RNAs (e.g. miRNA target prediction) and visualization strategies will be trained.

Learning goals:
- Unix Shell basics
- Introduction to Galaxy RNA-workbench
- RNA-Seq data analysis and workflow development
- Fundamental statistics and file formats
- Functional RNA analysis
- Visualization concepts

Prerequisites:
This workshop is intended for MSc/PhD students and postdocs with background in life science research.

Keywords:
Unix Shell, Galaxy, Workflow development, RNA-Seq analysis, Functional RNA analysis, Visualization

Tools:
Galaxy

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

Registration:
http://destair.bioinf.uni-leipzig.de/event/de-stair-1-workshop/

deSTAIR flyer freiburg 1710 1

Educators:
Prof. Knut Reinert, René Rahn, Hannes Hauswedell (CIBI)

Date:
25. – 27.09.2017

Location:
Martin-Luther University, Steintor-Campus, Room SR7, Emil-Abderhalden-Straße, 06108 Halle, Germany

Contents:
The SeqAn user meeting addresses bioinformatics professionals and students who want to develop efficient applications for NGS analysis based on an efficient, well-maintained C++ library.
We offer a dedicated track for users that want to develop computational tools with SeqAn. In addition, we will present the capabilities of SeqAn and its integration into the Workflow system KNIME and discuss your needs and future directions in sequence analysis. The schedule of our meetings is very flexible, allowing discussions and contributions from the participants.

Note, this year’s user meeting is a joint CIBI event featuring SeqAn, OpenMS and MetFrag. All three tools are developed by the Center for Integrative Bioinformatics (CIBI) and funded as a project of the german network for bioinformatic infrastructure (de.NBI).

Participants need to register via https://goo.gl/forms/8WKW2T2OBrosfiuA3.

You will find additional information regarding accommodations and travel directions on our webpage: http://www.seqan.de/seqan-ugm-2017/

See you in Halle!
The CIBI Team

Learning goals:
Using SeqAn for tool development

Prerequisites:
For the developer track, basic knowledge about C++ and fundamental programming experience is of advantage.

Keywords:
Sequence Analysis; NGS Workflows; Proteomics; Metabolomics

Tools:
SeqAn; KNIME

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

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

Date:
Monday, 13th Nov 2017 - 10:00-17:00

Location:
Ruhr University Bochum, 44801 Bochum

Contents:
This course will impart knowledge about how to conduct a differential analysis of high-throughput quantitative proteomics 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 is explained in order to enable the participants to assess their own as well as published workflows critically. In this regard the course will touch upon statistical inference:
- hypotheses, type I and II error
- location tests (t-test and ANOVA)
- multiple testing

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 proteomics 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 http://www.rstudio.com

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

More information:

Announcement:
http://www.rub.de/mpc/medical_bioinformatics/bioinfraprot/training/index.html.de

Flyer:

Flyer R workshop 2017

Registration:
http://goo.gl/forms/mpKHnbT1Um

Hosts:
http://www.rub.de/mpc/medical_bioinformatics/index.html.de

Directions:
http://www.rub.de/anreise/index_en.html