Educators:
Oliver Kohlbacher, Julianus Pfeuffer, Timo Sachsenberg (CIBI)

Date:
19.09.2018 - 21.09.2018

Location:
Arnimallee 6, 14195 Berlin, Germany

Contents:
During the meeting we will present the capabilities of OpenMS, provide training in a dedicated tutorial session and discuss your needs and future directions in mass spectrometry. This year’s meeting will include an optional OpenMS tutorial session on the first day (Wednesday) with the general conference starting on Thursday, September 20. You can bring your data, an OpenMS wish list, ideas for collaboration projects, and also give a talk about your project. This may include suggestions in areas where currently available software solutions were unsatisfactory. In addition, we will offer a dedicated session for attendees that want to get started developing with OpenMS.

Keynote speakers:
Tsung-Heng Tsai, NU Boston

Learning goals:
Capabilities of the OpenMS library and tools; How these tools are combined in flexible and powerful workflows in order to analyze LC-MS based, high-throughput metabolomic and proteomic data; How the powerful workflow engine KNIME is employed to build these workflows, perform statistical analysis and visualize results.

Prerequisites:
Basic to expert level knowledge of MS based proteomics or metabolomics

Keywords:
LC-MS based proteomics and metabolomics, OpenMS, workflows, KNIME, data analysis

Tools:
OpenMS, KNIME

Contact:
Scientific and program questions: This email address is being protected from spambots. You need JavaScript enabled to view it.
Please register at: https://sites.google.com/view/cibi-user-meeting-2018/home

Educators:
RBC Freiburg

Date:
17.09.-21.09.2018

Location:
Uni Freiburg

Contents:
1-week full-day hands-on workshop in Freiburg.

Topics:
- Galaxy Introduction
- Data analysis of RNA-seq, ChIP-seq, Exome-seq, MethylC-seq data
 
Learning goals:
Using Galaxy for data analysis of HTS data. Topics:
- Quality control
- Mapping
- Differential expression analysis
- Workflow design
- Statistics
- Visualization.

Prerequisites:
No. Beginner training course!

Keywords:
Galaxy, NGS, HTS,  RNA-seq, ChIP-seq, Exome-seq, MethylC-seq

Tools:
Galaxy

Contact:
Freiburg Galaxy Team: http://galaxy.uni-freiburg.de/

Registration:
https://docs.google.com/forms/d/e/1FAIpQLSckq6Zwa9AHlww07744r2bTwJywUmWUoEmNAJYMvouXTaaf4A/viewform

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

Educators: 
Steffen Neumann (PhenoMeNal Project, Leibniz Institute for Plant Biochemistry) (CIBI)
Christian Henke (Virus-X Project, Bielefeld University) (BiGi)
Marius Dieckmann (Bioinformatics and Systems Biology, Justus University Giessen) (BiGi)
Liren Huang (SparkHit, Bielefeld University) (BiGi)
Björn Grüning (BioContainers, Bioinformatics Group Freiburg University) (RBC)
Helena Rasche (Bioinformatics Group Freiburg University) (RBC)
Lukas Jelonek (Bioinformatics and Systems Biology, Justus University Giessen) (BiGi)
Peter Belmann (Cloud Governance, Bielefeld University) (CAU)

Date:
29-31.10.2018

Location: 
Bielefeld University

Contents:
The de.NBI Cloud offers compute power for life science research in Germany. Active for about a year now, many projects of all sizes and with a variety of use cases are using the vast capacity of the de.NBI Cloud. Due to the diversity of approaches that arise in this exciting and rapidly evolving cloud computing technology niche, this meetup should help to exchange ideas and approaches in the growing de.NBI Cloud community.

Learning goals:
The de.NBI Cloud User Meeting is your chance of meeting users, developers and administrators using the de.NBI Cloud. In a 3-day event (29.-31.10.2018) at Bielefeld University you can learn about life science projects hosted in the de.NBI Cloud. Talks and workshops will be given about current de.NBI Cloud projects and state of the art cloud computing technologies like Spark, Docker and Kubernetes.

Talks/Workshops:

- Kubernetes
- Rancher
- CWL
- Docker
- Nextflow
- OpenStack Basics
- OpenStack Advanced
- BioContainers

Prerequisites:
We welcome people from all background, no matter if you are new to the de.NBI Cloud or considering to submit a project application, to learn and network in our growing community.

Keywords:
de.NBI Cloud, Cloud Computing, Kubernetes, Nextflow, Docker, BioContainers, OpenStack, CWL, Rancher

Tools:
Kubernetes, Nextflow, Docker, BioContainers, OpenStack CLI, CWL, Rancher

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

Registration:
https://docs.google.com/forms/d/e/1FAIpQLSfRhEk2o4Lo4r0B5P-ClVigGuoO8runIIhaLdH4ep9QP-0GlA/viewform?usp=sf_link

Educators:
René Rahn (SeqAn), Hannes Hauswedell (SeqAn), Svenja Mehringer (SeqAn), Jeanette Prinz (KNIME) (CIBI)

Date:
19.09. – 21.09.2018

Location:
Berlin, Freie Universität Berlin

Contents:
We are delighted to announce this year’s SeqAn User Meeting 2018 from 19th to 21st of September in Berlin. For the second time we will host it as a common User Meeting of the de.NBI Center for Integrative Bioinformatics (CIBI) and cordially invite researchers in the fields of genomics, proteomics, metabolomics, data mining and bioimage analysis to come together and share their knowledge. 

We are excited to demonstrate for the first time the brand-new design of SeqAn3. In this context, we have a dedicated training day for beginners and advanced users on implementing applications with SeqAn3. With the help of your feedback and our experiences from past years we are convinced that SeqAn3 will make it genuinely easier to write applications with our library, while still providing the familiar performance of our algorithms and data structures.
Furthermore, we will have a training course for data scientists to learn how to process genomics data within KNIME using SeqAn and external NGS tools and the KNIME REST Web service functionality to query information from online web services such as ENSEMBL.

In addition, we will setup bring-you-own-data (BYOD) sessions, where you can bring your data and meet the developers and other scientists to discuss and implement solutions for analysing your own data.

The program will be complemented with key notes and talks from researchers in the field that give you new insights in the most recent development of our tools and show you demonstrations of current projects using multi-omics analysis.

Learning goals:
- What SeqAn 3 is and is capable of
- How to write tools with SeqAn 3
- What KNIME is and is capable of
- How to incorporate and share existing tools within KNIME
- Practical experience with KNIME through an exercise on sequence analysis

Prerequisites:
The tutorials are suited for beginners and intermediate programmers and users in the domain of sequence analysis (read mapping, variant detection, metagenomics, RNseq, assembly, etc.). Prior knowledge of SeqAn or KNIME is not required, albeit it can be very helpful.
For the programming part a basic knowledge in C++ is required. Also, the following compilers and command line tools for the programming part are required:
- MacOS (g++-7 or higher) or Linux or BSD (g++-7 or higher)
- Git
- Cmake-3.0 or higher
For the KNIME part the latest version 3.6 will be used.

We will provide an ubuntu virtual machine with preinstalled software ready to use (requires virtual box installation and at least 40 GB of free disk space.)

Registration:

Please register here: https://sites.google.com/view/cibi-user-meeting-2018/home/registration

Please follow us either on Twitter @SeqAnLib, on the mailinglist This email address is being protected from spambots. You need JavaScript enabled to view it. (subscribe here: https://bit.ly/2v6AIXn) or at http://www.seqan.de/news to stay updated. More information and registration can be found at: https://sites.google.com/view/cibi-user-meeting-2018/home

Keywords:
SeqAn, KNIME, Sequence Analysis

Tools:
KNIME 3.6, SeqAn 3, [optional] VirtualBox (We will provide a fully integrated Ubuntu VM with all necessary software preinstalled)

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

Educators:
Julianus Pfeuffer, Timo Sachsenberg (CIBI)

Date:
08.09.2018

Location:
17TH EUROPEAN CONFERENCE ON COMPUTATIONAL BIOLOGY
Athens, Greece

Contents:
Computational mass spectrometry provides important tools and bioinformatic solutions for the analysis of proteomics and metabolomics data. Non-targeted methods are ideal for unbiased discovery studies and scale well for large-scale studies (e.g., clinical proteomics/metabolomics). This de.NBI training event introduces key concepts of non-targeted label-free analysis and workflow-based processing using real-life datasets. We will introduce several open-source software tools for proteomics, primarily focusing on OpenMS (http://www.OpenMS.org). In a hands-on session, we will demonstrate how to combine these tools into complex data analysis workflows including visualization of the results. Participants will have the opportunity to bring their own data and design custom analysis workflows together with instructors. If requested by participants, we can also guide in implementing novel methods or tool into the OpenMS framework.
Training material and handouts will be prepared for both users that want to design proteomic workflows, as well as training material for algorithm and tool developers.

Learning goals:
Capabilities of the OpenMS library and tools; How these tools are combined in flexible and powerful workflows to analyze LC-MS based, high-throughput proteomic data; How the powerful workflow engine KNIME is employed to build these workflows and visualize results.

Software Requirements:
The participants should bring their own laptop computers. Installer versions of all required software will be available.

Keywords:
LC-MS based proteomics, OpenMS, workflows, KNIME, data analysis

Tools:
OpenMS, KNIME

Registration:
http://eccb18.org/registration/

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