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EMBL Heidelberg

This course will teach the biological researchers how to analyse biological data sets using open-source software. Most of the analysis will be performed with docker4seq and rCASC packages, which was developed to facilitate the use of computing demanding applications in the field of NGS data analysis. Docker4seq and rCASC packages use docker containers that embed demanding computing tasks (e.g. short reads mapping) into isolated containers. This approach provides multiple advantages: the user does not need to install all the software on its local server, the results generated by different containers can be organised in pipelines and reproducible research is guarantee by the possibility of sharing the docker images used for the analysis. Computers for hands-on exercises will be provided along with demo data sets.

EMBL Events;     Email: events@embl.de

Data Analysis and Bioinformatics,

EMBL Heidelberg

Spatial biology is a rapidly evolving scientific topic with frequent and novel technological advances that have powerful application potential in the context of basic and translational research. The aim of the course is to provide participants a comprehensive conceptual introduction and intensive hands-on practical training on the main techniques of Imaging-based spatial-omics, i.e. multiplex immunofluorescence and spatial transcriptomics. We will provide a general overview of the field through lectures from scientific experts, assist the participants on how to choose and implement the right method for their scientific needs, and finally also share practical tips and experience of developing these techniques thanks to the presence of the original developers of such methods. Through hands-on practicals and computer sessions, the course will teach participants how to carry out open-source imaging-based methods for cost-effective spatial transcriptomics (hybridization in situ sequencing) and multiplex immunofluorescence (immune-SABER and IBEX).

Iva Gavran;     Email: iva.gavran@embl.de

Data Analysis and Bioinformatics, Genome Biology, Transcription, Translation, Technology, Imaging, Methods, #EMBOSpatialOmics

ecSeq Bioinformatics GmbH

The purpose of this intense one-week summer course is to get a deep understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. You will be trained on understanding NGS data formats and handling potential problems/errors therein. In the summer school, we will use a real-life RNA-seq dataset from the current market leader illumina.

Events Team;     Email: events@ecseq.com

NGS, Next-Generation Sequencing, Illumina, RNA-Seq

EMBL Heidelberg

This course will provide training in genome editing and cell engineering in mammalian cells and mouse embryos using the highly efficient CRISPR/Cas9 system. Participants will learn design of CRISPR targets using bioinformatics tools, generation of gene knock-outs/knock-ins, and target validation using the most current technologies. The course will be split into two groups (mammalian cells OR mice) based on participants’ expertise. Please note that all participants are expected to engage in all sessions. Participants should plan for approximately 1 hour extra per day for self paced learning modules.

EMBL Events;     Email: events@embl.de

Biologie,    Molekularbiologie