4. Helmholtz Reproducibility Workshop

Tuesday 25 Mar 2025, 09:00 → 15:00 Europe/Berlin

Reproducibility is central to the open science discourse, promoting scientific integrity and strengthening society's trust in scientific results. With this event we want to contribute in shaping the future of reproducible, robust, and transparent research within the Helmholtz community. 

In this 4th Helmholtz Reproducibility Workshop we will delve into the core of reproducible science and its transformative potential for science. The workshop begins with two keynotes on reproducibility, one by Altuna Akalin (MDC - Software reproducibility of data processing and machine learning in the era of AI) and the other by Frieder Paulus (Lübeck University - Contextualization of reproducibility in the organization of academic work) - both of which will also be livestreamed, to make them easily accessible for researchers from all Helmholtz Centers. Following the keynotes, attendees can choose one of two hands-on workshops that will equip them with the tools and insights needed to make reproducibility a cornerstone of their scientific endeavors.

After a shared lunch, providing ample networking opportunities, the event will conclude with a round table discussion on "Reproducibility in Research Assessment: Shaping transparent and measurable health research", including, e.g., Mathijs Vleugel (Head of the Helmholtz Open Science Office), Wolfgang zu Castell (Director Department Geoinformation and CIO at GFZ), Miriam Kip (Berlin Institute of Health at Charité), Sven Rank (Digital Change at Forschungszentrum Jülich), moderated by Jess Rohmann (Postdoc at Charité - Universitätsmedizin Berlin). 

 

4. Helmholtz Reproducibility Workshop at a glance

When? March 25, 2025

Where? MDC - BIMSB, Hannoversche Straße 28, 10115 Berlin

How? Keynotes = hybrid setting (live & online), Workshops = only live

 

How to participate?

Participation is free of charge (incl. lunch). During the registration process, you will be asked to choose one of the two workshops on offer. They will take place in parallel so you can only attend one. 

Registration for the onsite event is now open and will close on March 10, 2025.  Seats are limited and will be handed out on a first come, first serve basis. 

Please only register if you are able to come. Otherwise you might block a seat that someone else would have liked to actually use. 

Should you not be able to attend in person, the keynotes will be streamed in a hybrid setting. Registration for the keynotes is open until March 23, 2025. 

Speakers

We have five inspiring speakers setting the stage through keynotes and short impulses. Please follow this link to find short biographies and useful information.

	Dr. Altuna Akalin MDC
	Dr. Frieder Paulus University of Lübeck
	PD Dr. Ulf Toelch BIH QUESR Centre for Responsible Research @ Charité Universitaetsmedizin Berlin
	Deborah Schmidt Helmholtz Imaging/ MDC
	Dr. Ella Bahry Helmholtz Imaging/ MDC

Organizers

The Helmholtz Open Science Office supports the Helmholtz Association as a service provider in shaping the cultural change towards open science. It represents Helmholtz in various open science initiatives, is involved in third-party funded projects, and in this way communicates the Helmholtz positions on open science on a national and international level.

HIDA - the Helmholtz Information & Data Science Academy - is Germany’s largest postgraduate training network in the field of information and data science. We prepare the next generation of scientists for a data-intensive future of research.

This year, HIDA and the Open Science Office are supported by colleagues from this year's host center, namely the Research Data Management Unit at Max Delbrück Center , who provide information, consultation, support, and training to researchers through all phases of the research data life cycle at MDC. 

09:00 → 10:10 Opening

09:00 Welcome

Speakers: Anna-Lisa Döring (HIDA), Lea Maria Ferguson (Helmholtz Open Science Office), Steffi Genderjahn (Helmholtz Open Science Office), Stephanie Schworm (HIDA)

09:10 Keynote 1: Software reproducibility for data processing and machine learning workflows in the era of AI

In the era of AI, ensuring software reproducibility for data processing and machine learning workflows is more critical than ever, particularly in computationally intensive fields like bioinformatics. Reproducibility guarantees consistent outputs across different environments, which is essential for validating research findings and disseminating workflows widely. However, the complexity of managing software dependencies, especially as versions rapidly evolve, poses significant challenges.
This talk presents a principled approach to building reproducible analysis pipelines using tools like GNU Guix, demonstrated through the PiGx pipelines for RNA sequencing and other bioinformatics applications. We explore how these pipelines, by encapsulating dependencies and providing standardized outputs, serve as a model for reproducibility in AI-driven workflows. Additionally, we discuss the implications of integrating AI and machine learning in research, emphasizing the need for reproducible practices to maintain the integrity of AI applications across various scientific domains.

Speaker: Dr Altuna Akalin (Max-Delbrück-Center (MDC))

Altuna_Akalin_2025_HelmholtzReproducibility.pdf

09:40 Keynote 2: Contextualization of reproducibility in the organization of academic work

Academics are under considerable pressure when it comes to managing their visibility and reputation as their careers develop. Similar to non-academic work, their competition to coexist is shaped by the unique incentive structures of their work environment. In this talk, I will argue for the importance of envisioning reproducibility and its “crisis” in the context of an academic system that values visibility through publications and confuses measures of journal rank with quality and those of good scientific practice. In addition, I will draw attention to currently discussed novel ideas for the distribution of third-party funding that may have the potential to reduce discrimination against marginalized groups and lower costs in the academic workforce.

Speaker: Dr Frieder Paulus (Lübeck University)

ReplicationCrisis_Helmholtz_FMP.pdf

10:10 → 10:30 Coffee break

10:30 → 12:30 Workshops

10:30 Workshop 1: From Methods to Results Reproducibility

Reproducibility is often seen as an important cornerstone for the advancement of science. But what does it actually mean and how does it affect your daily work? In this workshop, we will explore different types of reproducibility, strategies to improve it, and also some probabilistic thoughts on why we will never achieve full reproducibility.

Requirements: A laptop.

Speaker: Dr Ulf Toelch (BIH QUEST Centre for Responsible Research @ Charité)

Reproducibility_WS_Helmholtz_250325.pdf

10:30 Workshop 2: Image Prevalidation

In this workshop on image prevalidation, we will introduce the importance of ensuring that image data is suitable for the analysis it is intended for. Images can contain hidden quality issues, inconsistencies, or artifacts that can impact analysis results, often in subtle ways. Through real-world examples, we will explore how to detect these challenges early on, discussing image quality and consistency across data collections. We aim to create an open, interactive environment where participants can share their experiences and challenges with image data. We will introduce practical approaches to assessing image data before analysis begins, while encouraging discussion on best practices and common pitfalls. Our goal is to foster communication and mutual learning, helping everyone to improve their image validation workflows.

Any Specific Requirements or Equipment Needed?
Python knowledge is helpful, but not required.

Speakers: Dr. Ella Bahry (Helmholtz Imaging / MDC), Deborah Schmidt / Helmholtz Imaging Support Unit (MDC)

Image Prevalidation: Replicability through Data Knowledge

12:30 → 13:30 Lunch & Networking

13:30 → 14:15 Round table

13:30 Round table: Reproducibility in Research Assessment: Shaping transparent and measurable health research

In this scientific round table, invited guests will discuss the topic "Reproducibility in Research Assessment: Shaping transparent and measurable health research".

Speakers: Jess Rohmann (Charité - Universitätsmedizin Berlin), Mathijs Vleugel (Helmholtz Open Science Office), Miriam Kip (Berlin Institute of Health at Charité), Sven Rank (Forschungszentrum Jülich), Wolfgang zu Castell (GFZ Helmholtz-Zentrum für Geoforschung)

14:15 → 14:30 Wrap up

14:15 Wrap up