Workshops » Past workshops

ICTV/EVBC Workshop on Automating Virus Taxonomy

Dates: 31. July — 02. August 2023
Location: Jena, Germany and online

This summer, the EVBC (European Virus Bioinformatics Center) and the ICTV (International Committee on Taxonomy of Viruses) are organizing a Workshop on Automating Virus Taxonomy in Jena, Germany.

Nanopore Sequencing Workshop

Dates: 26. — 28. April 2023
Location: Jena, Germany

This workshop was offered by the Bioinformatics Core Facility Jena.

Preliminary outline:
Day 1 (Introduction): Details about the Nanopore sequencing technology and a general overview of sequencing approaches.
Day 2 (Sequencing): Introduction and specifics about sample (DNA/RNA) extraction and library preparation, and a demonstration of a sequencing run and real-time analysis during sequencing.
Day 3 (Data analysis): Introduction to the command line and Bash as well as installation and configuration of the needed software tools using Conda. Base calling, read quality control, read processing, read mapping, genome/transcriptome assembly, and modification calling

Introductory workshop on Research Data Management, Open Science, and the FAIR data principles

Course instructors: Cora Assmann, Justine Vandendorpe, Luiz Gadelha et al.
Dates: 15./16. August 2022, 9:30am-12:30pm CEST
Location: online

This training workshop is intended for an audience of all-qualification-level researchers in microbiota research who are interested in being introduced to best practices in Research Data Management (RDM). During the workshop, we will first cover fundamental concepts in RDM such as research data, metadata and the FAIR data principles. We will then continue by following the research data lifecycle, starting from planning a research project and ending with searching for and reusing data. We will end the workshop by discussing legal issues such as privacy issues and licenses. Throughout the workshop, we will include examples from microbiota research and, where relevant, the very first results of the German National Research Data Infrastructure for Microbiota Research (NFDI4Microbiota).

Topics to be addressed will include:

  • Research data life cycle
  • Metadata & metadata standards
  • FAIR data principles
  • Data Management Plans
  • Electronic Lab Notebooks
  • Data sharing & publishing
  • Open Science & Open Data
  • Good Scientific Practice (GSP)
  • Policies & guidelines on managing research data
  • Legal issues

Download the slides: Day 1 | Day 2

A practical introduction to software testing in Python

Course instructor: Dr. Terry Jones, Charité – Universitätsmedizin Berlin, Germany
Dates: 9./10. June 2022, 9:30am-12:30pm CEST
Location: online

There is a glaring discrepancy between professional “production” software produced by companies and the vast majority of bioinformatics code. Commercial code, often written by people with a background in software engineering, is heavily tested according to a mature system of hard-won and long-established best practice. On the other hand, bioinformatics software is often written by people with little or no formal training in software engineering and packages frequently have not a single test. The stark contrast between academic and commercial code, is complemented by a similar alarming divide between how those in the biological sciences act when in the lab versus their reckless behaviour when writing code.

This two-day course will provide a practical introduction to software testing. Both days will consist of a hopefully-motivating first session on why to test, followed by a practical discussion and demonstration on how to test. The second day will provide more nuance and depth. Although Python will be used, the course should be useful to programmers using other languages.

To whet your appetite, topics to be addressed will include:

  • Writing failing tests.
  • Coding with (more) confidence. 
  • Structuring code for testing.
  • Refactoring.
  • Pytest.
  • Mocking (file systems, databases, networks, system libraries, etc).
  • Code coverage.
  • The end of debugging.
  • Examples of crap code.
  • Beyond schadenfreude.
  • Reducing multiplicative uncertainty.
  • Learning what to trust.
  • Testing your data.
  • Using tests as documentation.

Nanopore Sequencing Workshop 2022

Course instructors: Sebastian Krautwurst & Dr. Akash Srivastava, Friedrich Schiller University Jena, Germany
Dates: 23.–25. Mai 2022, 10:00am-05:00pm CEST
Location: FSU Jena, Leutragraben 1 (JenTower 8th floor), 07745 Jena, Germany
Capacity: 10 participants | fully booked

This course is organized together with the Bioinformatics Core Facility Jena.

  • Introduction to the Nanopore sequencing technology
  • Introduction and specifics of sample preparation (DNA-/RNA-extraction) for Nanopore sequencing
  • Demonstration of a sequencing run and real-time analysis during sequencing
  • Overview of base calling and read quality control after sequencing with appropriate tools
  • Overview of read processing with appropriate tools
  • Overview of the possible fields of application and questions that can be addressed with nanopore sequencing