Helmholtz Reproducibility Workshop

Europe/Berlin
Potsdam

Potsdam

Telegrafenberg
Description

Reproducibility is central to the open science discourse, promoting scientific integrity and strengthening society's trust in scientific results. Helmholtz is a central actor in the discussion on the promotion of reproducible and robust research on a national as well as international level.

Following the success of our first two (online) workshops of our reproducibility series (Enabling reproducibility in data science & Love your data? Make it reproducible!), we are excited to bring together the Helmholtz community in person for our third edition at the Telegrafenberg in Potsdam, hosted by the Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences.

In our third workshop, again jointly organized by the Helmholtz Open Science Office and Helmholtz Information & Data Science Academy (HIDA), we will delve into the core of reproducible science and its transformative potential for science across disciplines. With this event we want to contribute in shaping the future of reproducible, robust, and transparent research within the Helmholtz community.

The workshop begins with two keynotes on reproducibility, one focusing on Image Data Analysis by Deborah Schmidt and the other on open science and research software engineering by Oliver Bertuch (both sessions will also be livestreamed). Following the keynotes, attendees can choose from a selection of three workshops that will equip you with the tools and insights needed to make reproducibility a cornerstone of your scientific endeavors.

The event will conclude with a shared lunch, providing ample networking opportunities for all participants.

 

How to participate?

Participation is free of charge (incl. lunch). Please register for the event by clicking on "Apply for Participation". During the registration process, you will be asked to choose one of the three workshops on offer. They will take place in parallel so you can only attend one. 

The event will take place on the Telegrafenberg in Potsdam! Given that workshop seats are still available, registration will be open until October 31st, 2023. 

Should you not be able to attend in person, the keynotes will be streamed in a hybrid setting. Registration for the keynotes only is possible on site or online and is open from September 27, 2023 until November 15, 1pm.

 

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.

 

Speakers

Deborah Schmidt is head of the Helmholtz Imaging Support Unit at the Max Delbrück Center for Molecular Medicine in Berlin. Her team develops and maintains Album, a decentralized distribution platform for digital solutions to specific scientific problems. She is a media computer scientist experienced in basic research data analysis, human computer interaction, computer vision, deep learning, data visualization, and generative graphics. She is passionate about open science, frugal science, citizen science, and decentralized systems.

Oliver Bertuch is a research software engineer working on solutions for managing, publishing and archiving research data and research software. His mission is to bring these two worlds together to promote open science and reproducibility. Based at the Central Library, he works closely with the IQSS, Harvard, as part of the Dataverse Core Team (https://dataverse.org). His focus there is on issues such as containerisation and research software readiness of Dataverse repositories. As Co-PI of HERMES (https://software-metadata.pub), he is developing a new key infrastructure element for automated, metadata-rich research software publications. 

Kainat Khowaja is a Statistical Consultant at the Core Facility Statistical Consulting team at Helmholtz Munich and Postdoc at Bielefeld University's Data Science Group. She brings expertise in statistics, machine learning, and data analytics. During her work at the Core Facility Statistical Consulting, she is offering support for research questions and addresses challenges in (bio-) statistics by ensuring the quality of analyses and applying modern statistical methods to data.

Adina Wagner is a research associate at the Forschungszentrum Jülich and doctoral researcher at the Heinrich Heine University Düsseldorf. She is a software developer for the DataLad project, an open source data management tool built upon Git and git-annex, and a proponent of open science, open source, and reproducible research.

Tracey Weissgerber leads the Meta-research and Automated Screening Group at the QUEST Center for Responsible Research within the Berlin Institute of Health at Charité – Universitätsmedizin Berlin. Her team’s research focuses on improving data visualization, methodological reporting, transparency, and reproducibility in scientific publications. Dr. Weissgerber organizes ScreenIT, a group of software developers and researchers who have created tools to screen preprints and papers for common problems and beneficial practices. She has also developed a series of courses where participants gain hands-on experience in designing and conducting meta-research (science of science) studies, writing and depositing protocols, and implementing other reproducible research practices in their own research.

Location

You can find information on how to get to the location here.

The workshop will take place in House H (purple box in the map).

 

    • 09:00 10:15
      Opening
      • 09:00
        Welcome 10m Haus H und Online

        Haus H und Online

        Telegrafenberg 14473 Potsdam
        Speakers: Anna-Lisa Döring (HIDA), Antonia Schrader (Helmholtz Open Science Office), Lena Messerschmidt (Helmholtz Open Science Office), Steffi Genderjahn (Helmholtz Open Science Office), Stephanie Schworm (HIDA)
      • 09:10
        Keynote 1: Replicability along the imaging pipeline 30m Haus H and Online

        Haus H and Online

        Telegrafenberg 14473 Potsdam

        Helmholtz Imaging is a platform providing support to scientists across domains along the whole imaging pipeline, from data acquisition to model training and visualization. Containerization is often touted as the solution to achieving reproducibility in such complex digital processes. However, when it comes to replicating a scientist's image analysis workflow, the reality frequently involves a series of custom steps and zero containers. This talk explores openly accessible strategies and technologies for user friendly replicability, based on experience acquired within the Helmholtz Imaging platform.

        Speaker: Deborah Schmidt
      • 09:40
        Keynote 2: It takes a village: building paths between Open Science, Reproducibility and Research Software Engineering 30m Haus H and Online

        Haus H and Online

        Telegrafenberg 14473 Potsdam

        Science has acknowledged in many disciplines it needs to be more "open" and "reproducible". But what it actually means and how to get there is yet mostly uncharted territory. This talk will introduce you to the HELIO model of Open Science, outline how documentation is key to both goals and why research software engineering is now more important than ever before.

        Speaker: Oliver Bertuch (Forschungszentrum Jülich)
    • 10:10 10:30
      Coffee break 20m
    • 10:30 12:30
      Workshops Haus H

      Haus H

      Telegrafenberg 14473 Potsdam
      • 10:30
        Workshop 1: Data and reproducibility management with DataLad 2h

        The path to reproducible science is paved with many open source software tools - this workshop introduces one of them. Using hands-on examples centered around the tool DataLad (http://datalad.org ), we will discover core concepts for reproducibility, such as version control, digital provenance, containerization, or data publication. The workshop focuses on technical and conceptual aspects alike, and aims to equip everyone with skills they could transfer to the real-world data collected during their research.

        Speaker: Adina Svenja Wagner (INM-7)
      • 10:30
        Workshop 2: Statistical and Computational Reproducibility: Experiences of a Statistical Consultant 2h

        In this interactive workshop, we will delve into the intricacies of enhancing research reproducibility. Drawing upon our collective expertise as statistical consultants, we will combine theoretical discourse with practical experiences, fostering a comprehensive understanding of technical, statistical, and computational facets of reproducibility. Engaging discussions will provide a platform for sharing experiences and expectations in this domain. Live demonstrations featuring tools such as RMarkdown and Git will introduce attendees to the essential resources required to advance their research reproducibility practices.

        Requirements: Basic knowledge in statistics (hypothesis testing/linear regression) and programming is advantageous.

        Speaker: Kainat Khowaja (Helmholtz Munich)
      • 10:30
        Workshop 3: How to use RRIDs, and identify and fix common data visualization problems 2h

        In this hands-on workshop, participants will learn to use research resource identifiers (RRIDs) to specify exactly what materials were used, and learn to identify and fix common data visualization problems. RRIDs are unique persistent identifiers for cell lines, plasmids, antibodies, model organisms (e.g. mice, flies), software and tools, and core labs. We’ll also address common data visualization problems, including understanding why you shouldn’t use bar graphs for continuous data and determining what to use instead, strategies for creating colorblind accessible figures, and techniques for creating informative image-based figures and western blots. Participants may also design flow charts to show the number of included and excluded observations at each phase of the experiment. This information is essential to assess the risk of bias.

        Format: This will be a flipped workshop, where participants watch instructional videos prior to the workshop. During the workshop, participants will apply what they have learned by critiquing visualizations from published papers and adding research resource identifiers to their methods section or supplies list.

        What to bring to the workshop:
        Your methods section, or a list of materials used in your research that require RRIDs
        A laptop computer

        Speaker: Tracey Weissgerber (BIH at Charité)
    • 12:30 12:40
      Short break 10m
    • 12:40 13:00
      Wrap up Haus H

      Haus H

      Telegrafenberg 14473 Potsdam
      • 12:40
        Wrap up 20m
        Speakers: Adina Svenja Wagner (INM-7), Dr Kainat Khowaja, Tracey Weissgerber (BIH at Charité)
    • 13:00 14:30
      Lunch & Networking 1h 30m Hallway (Haus H)

      Hallway

      Haus H

      Telegrafenberg 14473 Potsdam