Educators:
Alexander Goesmann, Sven Griep, Oliver Rupp, Tobias Zimmermann, Oliver Schwengers, Andreas Hoek, Jochen Blom, Sebastian Jaenicke (BiGi)

Date:
23.-25.04.2018

Location:
Heinrich-Buff-Ring 58, Justus-Liebig-Universität, Gießen

Content:
The first day will introduce software tools for the quality control of short read data. For conducting basic sequence read processing steps we will use our local Galaxy server. In the last session we will explain the basic approaches for genome assembly and run various genome assemblers:

- Introduction to quality control
- Automatic trimming of sequencing reads
- The basics of genome assembly

On the second day we will take a closer look at the genome assembly results. Afterwards, we provide a comprehensive introduction to microbial genome annotation. Available tools and algorithms for the different genome analysis and annotation steps will be explained and used within Galaxy. The GenDB genome annotation pipeline will be presented as well as a new stand-alone high-throughput genome analyses pipeline (ASA3P) that can be used to process thousands of genomes on a single day:

- The basic principles of region and function annotation
- Genome annotation tools and pipelines in Galaxy
- Manual and distributed genome annotation using GenDB
- Introduction to the ASA3P software

The third day will give an introduction into comparative genomics with a focus on differential gene content analysis using the EDGAR platform.  The use of the BLAST score ratio values (SRVs) to measure the similarity between coding sequences and to assess orthology will be introduced. All features of EDGAR will be introduced in detail:

- Genomic subset calculations (core-genome, pan-genome, singleton genes)
- Core-genome-based phylogenetic analyses
- Sequence based phylogeny
- ANI, AAI
- Statistical analyses (core/pan/singleton development plots)
- The public EDGAR database

Agenda:

Day 1: Quality control & genome assembly

13:00 – 13:15   Welcome & introduction (Alexander Goesmann)
13:15 – 13:30   Transfer of data sets
13:30 – 15:00   Read quality control & trimming incl. hands-on session (Sven Griep, Oliver Rupp)
15:00 – 15:30   Coffee Break
15:30 – 17:00   Introduction to genome assembly incl. hands-on session (Sven Griep, Oliver Rupp)

Day 2: Microbial Genome Annotation

  9:00 – 10:30   Introduction to microbial genome annotation (Alexander Goesmann)
10:30 – 11:00   Coffee Break
11:00 – 12:30   Genome annotation with Galaxy & GenDB hands-on session (Sven Griep, Oliver Rupp, Tobias Zimmermann)
12:30 – 13:30   Lunch
13:30 – 14:30   Introduction to ASA3P (Oliver Schwengers)
14:30 – 15:00   Coffee Break
15:00 – 17:00   ASA3P practical session (Oliver Schwengers, Andreas Hoek)
17:30                Optional: Tour to Gleiberg castle

Day 3: Comparative Genomics

  9:00 – 10:30   EDGAR (Jochen Blom)
10:30 – 11:00   Coffee Break
11:00 – 12:00   EDGAR hands-on (Jochen Blom, Sebastian Jaenicke)
12:00 – 12:30   Course evaluation & closing remarks (all hands)

During the afternoon of the last day participants are invited to discuss open questions or individual projects or data sets with the course experts.

Learning goals:
On all three days the program includes extensive hands-on training to allow participants to get familiar with the presented software. Participants can bring their own datasets that fit the topics of the workshop. The data can be analyzed in the hands-on sessions.

Prerequisites:   
None

Keywords:   
Quality control, genome assembly, Microbial Genome Annotation, Comparative Genomics

Tools:
Galaxy, GenDB, ASA3P, EDGAR

Registration:
To register for this training course just send a short email to our contact address below so that we have your full name and email address. Due to the fact that that the number of participants is limited to 20, we will schedule according on a first come first serve basis. We have to demand a 30 Euro fee to cover our expenses for catering, apart from that the workshop is free.

For more information see: http://www.uni-giessen.de/fbz/fb08/Inst/bioinformatik/Education/courses/content/course042018

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

Educators:
Alexander Sczyrba (Bielefeld University), Jan Krüger (Bielefeld University), Sebastian Jünemann (Bielefeld University)

Location:
Bielefeld University, Centrum für Biotechnologie - CeBiTec , Universitätsstraße 27, 33615 Bielefeld, Room G1-106

Date:
March 8th, 2018

Content:
The German Network for Bioinformatics Infrastructure (de.NBI) is operating an  OpenStack cloud computing infrastructure for the life science community (https://cloud.denbi.de/). The goal of this course is to give a fundamental introduction to the underlying OpenStack infrastructure and is dedicated to bioinformaticians or experienced computational data analyst who want to utilize scalable and flexible cloud resources for their research. Participants will learn how to setup a cloud project and work with virtual instances, how to efficiently utilize cloud computing resources, about networking and security issues, means of deploying bioinformatics tools in the cloud, and how to set up a customized compute cluster in a cloud environment using BiBiGrid. Course subjects will be covered by short talks and practical hands-on sessions.

Keywords:
OpenStack, Cloud Computing, virtual machines (VMs)

Tools:
OpenStack, BiBiGrid

Prerequisites:
- practical experience in Linux/Unix derivatives, the command line interface and file system required
- basic knowledge of networking recommended

Application:
Please send your application to This email address is being protected from spambots. You need JavaScript enabled to view it. (subject cloud-course-03-2018) including a very brief motivation, a few words about your background, and if you already have some knowledge of cloud infrastructures. There will be no participation fee, yet travel and accommodation expenses need to be paid by the participants. Available course places will be assigned on a first come, first serve basis.

Contact:    
Name: Dr. Alexander Sczyrba
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 0521/106-2910

Name: Jan Krüger
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 0521/106-2494
       
Name: Sebastian Jünemann
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 0521/106-4827

Educators:
Alex Sczyrba (Bielefeld University), Sebastian Jaenicke (Giessen University), Sebastian Jünemann (Bielefeld University)

Location:
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Room V6-113

Date:
March the 27th to 29th, 2018

Content:
The aim of this 3-day workshop will be to give students a brief overview of the tools and bioinformatics techniques available for the analysis of next generation sequence (NGS) data from microbial communities. The format will comprise a mixture of lectures and hands-on tutorials where students will process example data sets in real-time in the de.NBI cloud environment. After covering general aspects of sequence based analysis (e.g. pre-processing, quality measurements, error handling, and so on) the course is divided into two parts: targeted (16S rDNA operon gene amplicons) and untargeted (whole-genome shotgun; WGS) metagenome analysis. On demand, a compact introduction into the Linux operating system and the usage of the command line interface will be given upstream to the introducing part to guarantee a consistent baseline for the following lectures. The main aspects of the 16S part are the common pipeline steps beginning with pre-processing and filtering followed by e.g. OTU clustering, taxonomic classification, and different statistical measurements like rarefaction analysis. In addition, the recent emerging ASV/zOTU approach will be introduced and discussed with the attendants in conclusion. In the third part, advantages and disadvantages of whole metagenome sequencing will be illustrated. As WGS metagenomics has the potential to address the full spectra of genome-based issues, the focus here will be on taxonomic and functional analysis with the aid of different bioinformatic tools. Two different techniques to analyze WGS metagenome data are part of this section: (1) in the read-based approach the software solution MGX, an integrated platform for metagenome analysis and data visualization, will be demonstrated. (2) the assembly-based approach to potentially recover near-complete genome by assembling reads into contigs which are subject to binning methods to group individual contigs into genome bins.

Prerequisites:
- basic knowledge in microbiology and NGS-based analysis
- practical experience in a Linux/Unix derivatives, the command line interface and file system required

Prerequisites for the workshop plus the Linux introduction:
- basic knowledge in microbiology and NGS-based analysis

Please note that participation to this course does not depend on the actual Linux experience of the applicant. Both, experienced as well as inexperienced Linux users are encouraged to submit an application. However, the Linux introducing session in the morning of the first day is optional only for applicants fulfilling the Linux prerequisite.

Application:
Please send your application to This email address is being protected from spambots. You need JavaScript enabled to view it. (subject MG­course2018) including a short motivation, a few words about your background, your level of experience on the command line (Linux/Unix), and your experience within the field of metagenomic analysis and related bioinformatic tools. There will be no participation fee, yet travel and accommodation expenses need to be paid by the participants.

Contact:    
Name: Sebastian Jünemann
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 0521/106-4827

Name: Alexander Sczyrba
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 0521/106-2910

Name: Sebastian Jaenicke
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 0641/9935-802

Website:
For more information see: http://www.cebitec.uni-bielefeld.de/polyomics/index.php/training/upcoming-workshops/103-metagenomics-workshop-03-2018

Educators:
René Rahn, Hannes Hauswedell (CIBI)

Date:
11.03.2017 – 18.03.2017

Location:
Mallorca, Spain

Contents:
During this developer meeting we will continue to integrate several projects into the SeqAn-3 library.
With the new C++ standards C++11/14 and 17 the language and the STL have been majorly evolved and support now many useful features that feel like a new programming language. Based on the current standard of C++17 we plan a major redesign of the SeqAn library targeting the novel design concepts.
During a presentation day the concepts and implementation designs are presented. In the subsequent days different task forces will be assembled to work on the implementation.

Learning goals:
- Working with modern C++ 11/14/17 (Concepts, Ranges, STL-Features).
- Working with the SDSL (Succinct Datastructure Standard Library).
- Documenting code with Doxygen.
- Writing unit tests with google test framework.
- Designing and implementing core modules of SeqAn-3.

Prerequisites:
Target audience: This developer retreat is for invited members only. Participants must be familiar with the design principles of SeqAn and with the current c++ standards: ISO/IEC 14882:2011, ISO/IEC 14882:2014 and the current draft of C++17 as well as the working draft of N4641 (Concept TS) and N4651 (range TS).
Software requirements: For the retreat we require a working installation of the gcc-7 compiler, cmake >= 3.2, git, doxygen

Keywords:
Modern C++, SeqAn

Tools:
No special tools are required or used.

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

Educators:
Vedran Franke, Jonathan Ronen (RBC)

Date:
20 Feb 2018

Location:
MDC-Berlin

Contents:
1) Processing drop-seq data with PiGx pipelines available via GNU guix. The pipeline uses popular scRNA-seq tools via snakeMake interface.
2) Clustering, imputation and plotting using netSmooth and other R based tools

Learning goals:
Learn how to process and analyze scRNA-seq data

Prerequisites:
- BYOL (bring your own laptop)
- Experience with R (know how to read/write data, being able to make basic plots)
- Experience with unix terminal ( knowing how to run commands on the terminal)

Keywords:
RNA-seq, single-cell, scRNA-seq

Tools:
netSmooth, drop-seq-tools, scater

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

apply here (the room capacity is limited, we might have to select applicants):
https://goo.gl/forms/oZhfxu23tL7YB0lM2