Educators:
Georg Zeller, Malvika Sharan, Toby Hodges (HD-HuB)
 
Date:
03 - 04 July
 
Location:
ATC Courtyard Seminar Rooms, EMBL Heidelberg
 
Content:
CWL is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high-performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL is developed by an informal, multi-vendor working group consisting of organizations and individuals aiming to enable scientists to share data analysis workflows. The CWL project is on Github and we follow the Open-Stand.org principles for collaborative open standards development.
 
This hands-on workshop will provide an opportunity for participants to become familiar with analysis pipeline deployment with CWL, and to develop a CWL implementation for their own workflow.
The workshop will be hosted by EMBL Heidelberg and co-sponsored by HD-HuB, ELIXIR, and BioExcel.
 
Learning Goals:
Interested participants (preferably in teams of two or more) are invited to bring an existing workflow (or a tested portion of a workflow in development) to a two-day hands-on workshop. There they will learn through a combination of mini-lectures and hands-on work the current best practice in how using the CWL standards to describe command line tools and the workflows made from them enables easy cross-site collaboration, portability between different computer infrastructures, and future proofing. Also welcome are data analysis tool authors who want to provide 1st class idiomatic CWL descriptions for use by their users.
 
Requirements:
- One or more data analysis workflows consisting of command line (Linux) programs
- and/or a tested portion of a workflow in development
- and/or a command line data analysis tool that you are the author or maintainer for
- A laptop running Linux or OS X with Python 2.7, Docker, and the reference implementation of CWL installed inside a virtualenv.
- Read through and completed all exercises in the Gentle Introduction to the Common Workflow Language
 
Keywords:
Docker, Workflow, Python, CWL
 
Tools:
Docker, Python
 
Contact:
Georg Zeller (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Malvika Sharan (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Toby Hodges (This email address is being protected from spambots. You need JavaScript enabled to view it.)
 

Educators:
Michael Berthold, Greg Landrum, Patrick Winter, Alexander Fillbrunn, Martin Horn, Timo Sachsenberg (CIBI)

Date:
July 26th – 28th

Location:
University of Konstanz

Contents:
This hands-on course will introduce classic and modern techniques for the analysis of various types of data: molecular databases, images, sequences, and mass spectrometry data. Analysis techniques range from standard logistic regression and random forests to deep natural networks. Participants will learn how to process and integrate their data using the open source platform KNIME and gain experience with extensions such as RDKit (cheminformatics), SeqAn (NGS), FIJI (images), and OpenMS (mass spec).

Greg Landrum, the main author of RDKit, will cover the cheminformatics and machine learning part of the course. Further teachers are members of the SeqAn, FIJI, and OpenMS group.

Learning goals:
Using KNIME for Life Science data.

Prerequisites:
None.

Keywords:
KNIME, OpenMS, SeqAn, Workflows, Mass Spectrometry, Sequence Data, ChemInformatics

Tools:
KNIME, OpenMS, SeqAn, RDKit, Fiji

Contact:
Alexander Fillbrunn
University of Konstanz
This email address is being protected from spambots. You need JavaScript enabled to view it.

Educators:
Björn Grüning (RBC), John Chilton, Martin Cech

Date:
Friday, July 21, 2:30 pm – 6:00 pm

Location:
ISMB, Prag

Contents:
This tutorial is aimed at a broad audience. No previous knowledge of Galaxy or particular topics in bioinformatics is required. Participants should have a desire to learn more about Galaxy, or a desire to learn how to wrap their tools and pipelines in Galaxy to facilitate others using these, or just want specific advice on setting up an instance of Galaxy and scaling it up.

Learning goals:
• Create Galaxy compatible tool and workflow definitions that are publicly accessible and that make it easy for any instance administrator to add your work to their server.
• Deploy Galaxy and scale it up to target production-ready resources such as a Postgres database, NGINX webserver, and distributed resource managers such SLURM or PBS.

Prerequisites: 
Some knowledge of the command-line and Unix will be assumed and parts of the tutorial are hands-on so participants are encouraged to bring their laptops.

Keywords:
Galaxy, Workflows, deployment, compute cluster, cloud

Tools:
Galaxy, Ansible, Docker, Planemo

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

Educators:
- Prof. Dr. Frank Oliver Glöckner (BioData)
- Prof. Dr. Oliver Kohlbacher (CIBI)
- Priv.-Doz. Dr. Wolfgang Müller (de.NBI-SysBio)
- Dr. Andreas Weidemann (de.NBI-SysBio)
- Dr. Dr. Ivay­lo Ko­sta­di­nov (Jacobs University, MPI Bremen)
- Dr. Janine Felden (BioData)

Date:
15.11.2017 ca. 14:00 - 18:00
16.11.2017  09:00 - ca. 15:00

Location:
MPI for Marine Microbiology
Celsiusstrasse 1
28359 Bremen

Content:
- GoFAIR (https://www.dtls.nl/go-fair/) - Prof. Dr. O. Kohlbacher
- FAIRDOM (https://fair-dom.org/) - Dr. W. Müller & Dr. A. Weidemann
- SILVA (https://www.arb-silva.de/) - Prof. Dr. F.O. Glöckner
- GFBio (https://www.gfbio.org/) - Dr. I. Ko­sta­di­nov
- PANGAEA (https://www.pangaea.de/) - Dr. J. Felden

More to be announced soon.

Keywords:
GoFAIR, FAIRDOM, SILVA, GFBio, PANGAEA

Tools:
GoFAIR, FAIRDOM, SILVA, GFBio, PANGAEA

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