Day 1
Location: ETH Zurich Main Building, HG D3.2
10:00-10:30 Coffee and registration
10:30-10:45 Welcome and Introduction. Bernd Rinn, ETH Zurich Scientific IT Services
10:45-11:15 Building a FAIR data infrastructure for biomedical research. Sven Fillinger, QBiC, University of Tübingen
11:15-11:45 TX-MS: Rapid determination of quaternary protein structures. Lars Malmström, S3IT, University of Zurich
11:45-12:15 OpenNGS – managing Next Generation Sequencing data and analysis with openBIS. Tomasz Zielinski, SynthSys and SBS, University of Edinburgh
12:15-13:30 Lunch
13:30-14:00 The RITE way: nuclear pore complexes moving into an ELN. Elisa Dultz, ETH Zurich
14:00-14:30 Streamlined data management of shared laboratory resources with the openBIS Importer Toolset. Aaron Ponti, Single Cell Unit, ETH Zurich
14:30-15:00 Complete lab record keeping using the openBIS Jupyter extension. Andreas Cuny, ETH Zurich
15:00-15:30 Coffee break
15:30 -16:00 Experiences from openRDM.swiss. Andreas Fürholz, ZHAW
16:00-16:30 Latest openBIS developments and outlook. Caterina Barillari, ETH Zurich Scientific IT Services
16:30-17:00 Discussion
Day 2
Location:ETH Zurich Main Building, HG E 33.1; HG E 33.3; HG E 33.5
We will host three parallel workshops. The same workshops will run twice, so users have the option to choose one in the morning and one in the afternoon. It is also possible to attend only one workshop in the morning session.
Users are required to bring their own laptops for the workshop sessions.
Workshops schedule:
09:00-12:00 First workshop session (with coffee break)
12:00-13:00 Lunch
13:00-16:00 Second workshop session (with coffee break)
Workshop 1: User training on openBIS ELN-LIMS
The goal of this workshop is to familiarize new users with the ELN and LIMS functionalities of openBIS. We will also cover analysis of data stored in openBIS using Jupyter and MATLAB.
Topics
- Defining an openBIS data model
- Creation of an inventory of materials
- Registration of laboratory protocols
- Registration of experiments and data upload
- Basic customisation of openBIS
- Analysis of data stored in openBIS with Jupyter & MATLAB
Target audience
Master and PhD students, postdocs, staff scientists, data managers.
Prerequisites
The workshop is intended for beginners and existing openBIS users who are not yet familiar with the ELN and LIMS functionalities of the software.
Workshop 2: Programming with openBIS.
The goal of this workshop is to provide users with an overview of the many options available to use openBIS programmatically.
This workshop will have four topics and users are requested to choose two of them at registration. If users are interested in all topics, they can choose two topics for the morning session and two for the afternoon session.
Topics
- BigDataLink : Using obis with openBIS to manage your data outside the DSS
- V3 API: Python. Programming with PyBIS for integrations and pipelines using Jupyter
- V2 API: Jython. Dropboxes for data imports
- V3 API: Java/Javascript. Writing client applications for integrations and pipelines
Target audience
Developers, openBIS system admins.
Prerequisites
Programming knowledge in at least one of these languages: Python, Java, Javascript.
Workshop 3: Reproducible data analysis workflows
The goal of this workshop is to give the participants conceptual and practical knowledge on combining data analysis workflows and data management for their research projects. We will present current software solutions and best practices for reproducible and traceable data analysis workflows.
Topics
- Overview of current workflow systems and their features related to data management
- Introduction to conda and containers with hands-on examples
- Quick introduction to snakemake as a popular workflow manager, openBIS-snakemake interfacing, examples from genomics with hands-on examples
Target audience
Master and PhD students, staff scientists, data managers, developers.
Prerequisites
Familiarity with the terminal and openBIS. Python knowledge is an advantage.
