BioNT Community Event & CarpentryConnect Heidelberg 2024 Conference Program

Provisional Conference Programme

Day 1 - Tuesday, November 12, 2024

Time Event
09:00 - 09:45 Refreshments & Networking
09:45 - 10:15 Welcome back
10:15 - 11:00 Keynote #1
30min presentation + 15min Q&A
11:00 - 11:30 Break & Networking
11:30 - 13:00 Panel discussion Coding and Data Science Skills Training for Industry
Radhika S Khetani, Isabela Paredes Cisneros, Lisanna Paladin
Workshop 1 Training material: thinking of reusability
Bruna Piereck
Workshop 2 Building a miniHPC for delivering HPC Carpentries workshops
Jannetta Steyn
Workshop 3 Research data management: how to start and maintain a project
Justine Vandendorpe
Breakout Discussion 1 Lesson Development Training for Existing Lesson Projects
Toby Hodges, Aleksandra Nenadic
Breakout Discussion 2 Cloud-based Virtual Environments for Hands-On Bioinformatic Training Courses
Sebastian Jünemann, Alexander Sczyrba, Sina Barysch, Alain Becam
13:00 - 14:30 Lunch & Networking
14:30 - 16:00 Panel discussion Coding and Data Science Skills Training for Industry
Radhika S Khetani, Isabela Paredes Cisneros, Lisanna Paladin
Workshop 1 Training material: thinking of reusability
Bruna Piereck
Workshop 2 Building a miniHPC for delivering HPC Carpentries workshops
Jannetta Steyn
Workshop 3 Research data management: how to start and maintain a project
Justine Vandendorpe
Workshop 4 Practical introduction to Knowledge Graphs - exploring how to extend the Library Carpentry Wikidata lession and make it useful for researchers
Rabea Müller, Konrad Förstner
Breakout Discussion 8 The future of SWC Lessons Programs
Samantha Ahern
16:00 - 16:30 Break & Networking
16:30 - 17:15 Lightning talks
17:15 - 17:45 Day 1 closing remarks
17:45 - 19:00 Posters & Networking
19:00 -21:00 Dinner

Day 2 - Wednesday, November 13, 2024

Time Event
09:00 - 09:45 Refreshments & Networking
09:45 - 10:15 Welcome back and program overrview
10:15 - 11:00 Keynote #2
30min presentation + 15min Q&A
11:00 - 11:30 Break & Networking
11:30 - 13:00 Workshop 5 Glosario Contribution Drive
Toby Hodges, Angelique Trusler
Breakout Discussion 3 Tools for creating training materials - carpentries workbench, the google suite, and beyond
Sarah Kaspar
Breakout Discussion 4 Escaping the circles of installation hell
Raniere Gaia Costa da Silva, Jannetta Steyn
Breakout Discussion 5 Developing and Delivering Training Material at the Intermediate Level
Matthew Bluteau, Aleksandra Nenadic, Stephen Crouch
Breakout Discussion 6 Managing the HPC curriculum: from core to specialized topics.
Alan O'Cais, Marc-André Hermanns
Breakout Discussion 7 How to maintain a community of trainers in the DACH region
Rabea Müller
13:00 - 14:30 Lunch & Networking
14:30 - 15:15 Keynote #3
30min presentation + 15min Q&A
15:15 - 15:45 Final remarks and feedback session

Day 2 - Wednesday, November 13, 2024 - Mini-hackathon and Curriculum Development Session

Time Event
15:45 - 16:15 Break & Networking
16:15 - 17:45 Mini-hackathon and Curriculum development Introduction
17:45 - 19:30 Social program
19:30 - 22:00 Dinner

Day 3 - Thursday, November 14, 2024 - Mini-hackathon and Curriculum Development Session

Time Event
08:30 - 09:15 Refreshments & Networking
09:15 - 09:30 Welcome back
09:30 - 11:00 Mini-hackathon 1 Converting Carpentry-Style Lessons from Jekyll to the Workbench Lesson Format
Aleksandra Nenadic, Matthew Bluteau
Mini-hackathon 2 Julia-novice: A lesson exploring the Julia language
Dr. Simon Christ
Mini-hackathon 3 Find out what the Galaxy Training Network is by actively tackling a small task on the GTN or for our citizen science online game
Saskia Hiltemann, Teresa Müller
Mini-hackathon 4 The Epiverse-TRACE curricula for outbreak analytics and research software practices
Andree Valle-Campos, Hugo Gruson
Mini-hackathon 5 Adapting existing lessons for CarpentriesOffline
Jannetta Steyn
Mini-hackathon 6 SWC Core Lesson Improvement - Git and Python
Samantha Ahern
Mini-hackathon 7 Advanced Git Curriculum
Ivelina Momcheva
11:00 - 11:30 Break
11:30 - 13:00 Mini-hackathon 1 Converting Carpentry-Style Lessons from Jekyll to the Workbench Lesson Format
Aleksandra Nenadic, Matthew Bluteau
Mini-hackathon 2 Julia-novice: A lesson exploring the Julia language
Dr. Simon Christ
Mini-hackathon 3 Find out what the Galaxy Training Network is by actively tackling a small task on the GTN or for our citizen science online game
Saskia Hiltemann, Teresa Müller
Mini-hackathon 4 The Epiverse-TRACE curricula for outbreak analytics and research software practices
Andree Valle-Campos, Hugo Gruson
Mini-hackathon 5 Adapting existing lessons for CarpentriesOffline
Jannetta Steyn
Mini-hackathon 6 SWC Core Lesson Improvement - Git and Python
Samantha Ahern
Mini-hackathon 7 Advanced Git Curriculum
Ivelina Momcheva
13:00 - 14:30 Lunch Break
14:30 - 15:00 Groups report
15:00 - 15:30 Final remarks and feedback session

Abstracts

Workshops

Speaker(s)

  • Radhika S Khetani — AstraZeneca
  • Isabela Paredes Cisneros — EMBL - European Molecular Biology Laboratory
  • Lisanna Paladin — EMBL - European Molecular Biology Laboratory

Abstract

In this interactive panel, we aim to delve into the broader challenges of training in the industry landscape and identify potential blind spots and solutions for BioNT, as well as for other initiatives and projects with similar questions around training of computational skills in life sciences. Kicking off with a short introduction about their expertise to stimulate questions, our panel of experts will explore various key topics, including the expectations of industry professionals regarding training, the role of certificates, the importance of the training language, and what knowledge exchange programmes/structures exist in different business contexts. We will also address the preference between proprietary and free software, strategies for advertising training initiatives to industry stakeholders, and the sustainability of training activities.

Throughout the panel, attendees will have the opportunity to gain insights into how industry leaders tackle the training needs of their current employees and how can jobseekers best use open training resources to improve their employability in the bio-computational field. We will discuss the relevance of digital skills and explore how academic expertise can be leveraged to meet industry demands effectively. Additionally, we will examine the importance of assessment in certifying self-paced and lifelong training and explore potential benefits for the broader community.

The format of the event will involve panellists sharing their experiences and insights on stage, followed by facilitated discussions and audience interaction. Participants are encouraged to submit questions in advance, which will be clustered and presented to the panellists for discussion. With a focus on fostering collaboration and knowledge exchange, this workshop promises to be an enriching experience for all attendees, providing valuable insights into the evolving landscape of coding and data science skills training in the industry.

Speaker(s)

  • Bruna Piereck — VIB/ELIXIR-BE
  • Alexander Botzki — VIB/ELIXIR-BE

Abstract

Going FAIR (Findable, Accessible, Interoperable and Reusable) is a growing effort in the training communities. In this training session, we present an extract of the co-created ELIXIR-BE and ELIXIR-SE course - FAIR training material by design - that is embedded in the ELIXIR Training Platform offering. Focusing on the ‘R’ of the FAIR practice, our objective is to demonstrate and guide participants into trying out a few steps to create Reusable material. Although our main focus is to create reusable material by design, we reflect on it from two complementary perspectives: on one hand the initiative of making it reusable and secondly the practice of reusing other materials. By doing this, we empower participants in creating and reusing training material while actively and critically thinking about their efforts in a FAIR way.

We will discuss, exemplify and give opportunities to participants to look into different aspects of Reusability. Activities are thought to increase the technical skills and discerning mindset during the development of a new training course. By the session’s conclusion, participants should be able to incorporate aspects of reusability in their fresh training material as much as FAIRifing aspects regarding reusability of existing resources.

Speaker(s)

  • Jannetta Steyn — Newcastle University

Abstract

There are several problems with gaining access to an HPC to run a workshop for students. An alternative is to build a mini HPC out of single board computers (SBC) such as Raspberry Pi computers but this is not an easy task. This tutorial aims to introduce the CarpentriesOffline miniHPC solution which allow instructors without specialised HPC hardware and software knowledge to run HPC Carpentries workshops.

Speaker(s)

  • Justine Vandendorpe — ZB MED - Information Centre for Life Sciences

Abstract

Have you ever wondered how to properly manage your research data from the start of a project? And how to apply best practices during your project to make your data reusable after the project? During this workshop we will answer these questions as well as the most common questions researchers have regarding Research Data Management (RDM): What is RDM? How to write a Data Management Plan (DMP)? How to properly organise, share, publish and archive your data? How to choose a trusted repository? And how to apply RDM skills to industry? This will be an introductory and interactive workshop.

Speaker(s)

  • Rabea Müller — ZB MED - Information Centre for Life Sciences
  • Konrad Förstner — ZB MED - Information Centre for Life Sciences

Abstract

Wikidata is a freely accessible knowledge base that acts as a central repository for structured data used in Wikipedia and beyond. It provides a collaborative platform for storing and managing structured data about entities, concepts, and relationships between them. Wikidata’s structured data can be utilized by various projects, including research endeavors, to enhance data integration, exploration, and analysis.

This workshop focuses on extending the reach of the existing Library Carpentry Lesson on Wikidata, originally designed for librarians and information professionals, to cater to a broader audience including researchers. Participants will engage in a collaborative exploration of the lesson’s structure and content, aiming to adapt examples and concepts to resonate with individuals from research backgrounds. Additionally, there will be discussions on strategies for broadening the lesson’s appeal and tailoring it to the needs of diverse research communities. The workshop will also contemplate the potential transition of the lesson to a Software Carpentry format, aligning with the methodologies and practices of The Carpentries. Through interactive sessions and group activities, attendees will collectively brainstorm ideas and solutions to enhance the accessibility and relevance of the Library Carpentry Wikidata Lesson for researchers.

Speaker(s)

  • Toby Hodges — The Carpentries
  • Angelique Trusler (joining online) — The Carpentries

Abstract

In data science and programming, breaking down language barriers is pivotal for creating an inclusive learning environment. Glosario (https://glosario.carpentries.org/) is an open source, multilingual glossary for computing and data science terms. It currently contains definitions for more than 600 terms in 25 different languages, from German to IsiZulu.

This "Contribution Drive" will increase the number of supported languages and enrich the glossary with additional data science terms, making it an even more comprehensive resource for learners worldwide. Participants will be shown how to contribute to Glosario in the first part of the session. The second part will be devoted to making contributions: submitting new terms, translating existing definitions, and reviewing existing entries. This is a great opportunity to build a valuable resource that increases global access to coding and data skills and gain experience contributing to open source projects in a supportive environment.

Breakout Discussions

Moderator(s)

  • Toby Hodges — The Carpentries
  • Aleksandra Nenadic — UK Software Sustainability Institute

Abstract

The Carpentries Collaborative Lesson Development Training was launched in October 2023. Currently in beta testing, the curriculum (https://carpentries.github.io/lesson-development-training/) teaches concepts, skills and good practices in lesson design and iterative development, use of The Carpentries lesson infrastructure, and effective collaboration.

In its current form, the training is aimed at groups of collaborators who wish to begin working on an idea for a new lesson, but many of the same concepts and skills it teaches would be valuable to those wishing to adapt, expand, or update an existing lesson.

This breakout discussion will bring together community members with experience of – or interest in – curriculum design principles and making updates to existing curriculum, to discuss the potential content of a hypothetical Collaborative Lesson Development Training program aimed at those working on an existing lesson.

Moderator(s)

  • Sebastian Jünemann — Forschungszentrum Jülich
  • Alexander Sczyrba — Forschungszentrum Jülich
  • Sina Barysch — EMBL Heidelberg
  • Alain Becam — University Of Heidelberg

Abstract

Hands-on training in bioinformatics often requires participants to follow an instructor by entering commands or running tools in a specific execution environment (e.g. Linux). These environments often require a specific set-up of tools and libraries to be prepared in advance, which can be an obstacle for potential participants if they have to do the work on their own. This also poses a risk to the course delivery if participants are using different systems and versions or have not been able to complete the preparation. In the German Competence Center Cloud Technologies for Data Management and Processing (de.KCD), we are using the de.NBI Cloud along with the course module of the SimpleVM solution to specify, configure, prepare and deploy virtual environments for course participants. Thereby, we can also make use of the flexibility and scalability of the de.NBI Cloud and its IT infrastructure to tailor resource, tool and environment requirements specifically to the needs of a given course.

In this breakout discussion, we will introduce the de.NBI Cloud and SimpleVM and showcase how we use this system for our training activities. Based on that, we would like to start a discussion if and how this environment can be adopted by trainers and institutes outside of the current scope of de.NBI and de.KCD, also potentially including industrial partners. In addition, we want to identify current needs and obstacles for other trainers with regard to the use of virtual (trusted) research and learning environments, what systems or solutions they are currently using, and how such systems can be incorporated into online- and self-learning content and offerings.

Moderator(s)

  • Sarah Kaspar — EMBL Heidelberg

Abstract

This session is a comparison of the carpentries workbench to other tools for preparing training materials. In particular, I can share my experiences with google slides for presenting concepts and visuals, the R package learnR (https://rstudio.github.io/learnr/), which is tailored to creating interactive tutorials for self-study, and google colab. Questions to be discussed in the session include:

  • Which tool is suitable for which purpose?
  • What other tools do participants use?
  • How can the tools be combined in one training project? (e.g. use a lesson in the workbench to create plots using code, export the plots to google slides)
  • If you use different tools for the same project, how do you keep your materials in sync?
  • Moderator(s)

    • Raniere Gaia Costa da Silva — GESIS Leibniz Institute for the Social Sciences
    • Jannetta Steyn — Newcastle University

    Abstract

    Since the first Sofware Carpentry workshop in 1998, guarantee that the software was installed correct on the user's computer was a challenge. Every instructors have their personal collection of lessons learnt. In 2025, could our instructors be free from the installation hell? In this breakout discussion session we will talk about (1) the use of cloud computing like mybinder.org, Google Colaboratory, and GitHub Codespaces and (2) WebAssembly powered computing like JupyterLite and WebR. If time allow, we will also talk about code execution from within the lesson using tools like Thebe and learnr.

    Moderator(s)

    • Matthew Bluteau — UK Atomic Energy Authority (UKAEA)
    • Aleksandra Nenadic — SSI
    • Stephen Crouch — SSI

    Abstract

    The original mission of Software Carpentry to address the computational skills gap among researchers has been highly successful, yet there remains a growing demand for more advanced training beyond the novice level. With the increasing complexity of modern research workflows and the emergence of roles such as Research Software Engineer (RSE), there is a pressing need to develop tailored curricula for competent practitioners who seek to enhance their existing knowledge—e.g. software testing, continuous integration, software design, etc. One manifestation is the frequent question from learners at the end of a novice workshop that any instructor will have doubtless received: “what course should I take next?” The Carpentries Incubator is one place learners can go for courses beyond novice level, and a rough estimate is that one third of the 153 courses there target an “intermediate” level topic. Whilst these are undoubtedly valuable additions to the Carpentries canon, to our knowledge there has been no systematic assessment of how these resources should differ from the novice lesson template that the Carpentries employs. How does the content of the lesson change when targeting learners at this different level? How should the delivery of the material change?

    In this breakout discussion, we hope to explore these broad questions, drawing upon the experiences of attendees and commence creating a shared knowledge around intermediate-level teaching material. The session will commence with a brief perspective from some of the maintainers of the Intermediate Research Software Development course about how they approach these questions, providing some inspiration for subsequent discussion. Then, attendees will be polled to prioritize the topics that the group would like to cover.

    Moderator(s)

    • Alan O'Cais — University of Barcelona
    • Marc-André Hermanns — RWTH Aachen University

    Abstract

    "HPC Carpentry is the first entry to the Carpentries Lesson Program Incubator. As such it has a proposed core curriculum, which will be outlined at the beginning of this session. HPC Carpentry exists in an ecosystem that is constantly developing however. Beyond the core curriculum, we would like to discuss other existing and proposed lessons that are relevant to HPC Carpentry and how to adequately integrate them so that they complement the core and each component is sufficiently maintained. Questions we would like to address are:

  • Anchoring the discussion: our learner profiles and the core curriculum
  • How can we promote the adoption/adaption of the HPC Carpentry core curriculum?
  • How do we foster engangement of instructors for core topics taking them beyond their own specific interests?
  • How to spread engagement for specialized topics that are initiated by single instructors or small groups?
  • How to integrate HPC Carpentry in the training initiatives that are being funded in the wider HPC ecosystem (including large initiatives such as ACCESS-CI in the US and EuoHPC-JU in Europe, but perhaps more importantly regional HPC training initiatives)
  • Perhaps also, how to do the reverse?"
  • Moderator(s)

    • Rabea Müller — ZB MED - Information Centre for Life Sciences

    Abstract

    Join us for a breakout session focused on maintaining a Carpentries community in the DACH region. We'll discuss tailored strategies for overcoming regional challenges, leveraging technology, and fostering collaboration among trainers. Whether you're new to Carpentries or a seasoned member, discover practical insights to sustain a thriving community of trainers in our region.

    Moderator(s)

    • Samantha Ahern — University College London and SWC Lesson Programmes Governance Committee

    Abstract

    Part of the remit of the SWC LPGC is to oversee the maintenance and evolution of the SWC Lesson Programme. What support does the community need in maintaining the current programme? How could/should this evolve? What new programme(s) would the community like to see?.

    Mini-hackathons and Curriculum Development Sessions

    Moderator(s)

    • Aleksandra Nenadic — UK Software Sustainability Institute
    • Matthew Bluteau — UK Atomic Energy Authority

    Abstract

    We are not suggesting to start on a new lesson, rather to run a mini hack session to help people convert from the old Carpentry lesson format that relies on Jekyll to the new Workbench format.

    An outcome of the session would be an increased knowledge around the use of the Workbench, improved content of some lessons, one or more lessons converted to the new Workbench format (or well on their way to be converted), and potential improvements to the lesson migration guide.

    Moderator(s)

    • Simon Christ — Leibniz Universität Hannover

    Abstract

    To be provided

    Moderator(s)

    • Saskia Hiltemann — Institute of Pharmaceutical Sciences, Faculty of Chemistry and Pharmacy, University of Freiburg
    • Teresa Müller — Freiburg Galaxy team, Technical Faculty, University of Freiburg

    Abstract

    "The Galaxy training community (GTN) has empowered scientists to learn how to take their data analysis into their own hands. It is an open-access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework.

    The GTN has a very active and vibrant community, which happily welcomes new members and contributors. The mini-hackathon is a perfect entryway to get to know the GTN its learning materials and the community.

    Within the mini hackathon, first, a general onboarding to the GTN will highlight its material and infrastructure. For the active contribution part a set of entry-level tasks are collected, which are feasible to solve within this one day. The tasks include the curation and updating of tutorials with e.g. new screenshots or tool annotations as well as quiz questions and teaching material development for our educational online game, the DNAnalyzer.

    Moderator(s)

    • Andree Valle Campos — Epiverse-TRACE at the London School of Hygiene and Tropical Medicine
    • Hugo Gruson — Epiverse-TRACE at data.org

    Abstract

    The Epiverse-TRACE initiative aims to provide a software ecosystem for outbreak analytics with integrated, generalisable and scalable community-driven software. We support the development of R packages, make the existing ones interoperable for the user experience, and stimulate a community of practice.

    We structure our training materials into two complementary curricula. The Outbreak Analytics curriculum focuses on streamlining the utilisation of R packages tailored for outbreak analytics tasks to enhance decision-making processes. Meanwhile, the Research Software curriculum aims to broaden our suite of R tools to develop open, reproducible, and sustainable data analysis projects, adhering to best practices in research software development.

    In the Outbreak Analytics curriculum, we built three lessons around an outbreak analysis pipeline split into three stages: Early, Middle, and Late tasks. Early tasks include reading and cleaning case data and accessing delay distributions to estimate transmission metrics. Middle tasks include estimating forecasting, severity and superspreading from case data and simulating transmission chains. Late tasks include scenario modelling to simulate disease spread and investigate interventions (https://epiverse-trace.github.io/tutorials-late/).

    In the Research Software curriculum, we have two lessons focused on best practices for your outbreak analytics R projects and data. The Version Control with Git in Rstudio lesson is a forked repository from the Software Carpentry Version Control with Git lesson reframed to an outbreak response scenario. The Improve Your Code for Epidemic Analysis with R lesson (https://epiverse-trace.github.io/research-compendium/) focuses on three skills to increase project reliability and reusability by the community: using a research compendium template with {rcompendium}, making reproducible analysis with {renv}, and writing informative READMEs following good community practices.

    Moderator(s)

    • Jannetta Steyn — Newcastle University

    Abstract

    The CarpentriesOffline project is slowly but surely gaining momentum. However, some of the existing lessons, such as Version Control with GitHub and Intro to HPC need to be adapted. We also are working on an onboarding to CarpentriesOffline lesson which needs to be developed further. We started work on some of the lessons but these need to be checked and updated.

    Moderator(s)

    • Samantha Ahern — University College London and SWC Lesson Programmes Governance Committee

    Abstract

    Some of the core lessons need some improvements. This would either be the planned improvements to the Git lesson or the Python lessons.

    Moderator(s)

    • Ivelina Momcheva — Max Planck Institute for Astronomy

    Abstract

    A curriculum for advanced git which I co-developed was recently accepted to the Carpentries Incubator (https://datacarpentry.org/astronomy-python/). There are other similar efforts. I would like to work with others on developing advanced git materials, either as a general curriculum or as specialized lessons. Looking to meet like-minded people interested in teaching advanced git concepts..

    Lightning Talks

    Diversity - a well-known term by now. But what does that mean in particular and how is this concept to be implemented in modern-day workshop culture? What barriers can and must be taken into consideration - and what impact this will lead up to further in research communities. A quick dive into equal opportinities and equity.

    Methods Hub is a new service offer from GESIS Leibniz Institute for the Social Sciences for computational social scientists working with digital behavioral data to learn about social and socio-technical phenomena. Methods Hub hosts an index of software packages that computational social scientists can use and avoid reinventing the wheel. Additionally, Methods Hub also host documentation and tutorials related with the indexed software packages. One key feature of Methods Hub is to be a 1-click bridge to mybinder.org where users have access to ready to use computational environment.

    The Netherlands houses an extensive Carpentries community: seven Academic institutions have become member organizations and a total of 125 instructors have been certified and are spread across the country. Despite the considerable size of the Dutch community, it faces challenges too: not all instructors keep active after certification, which makes it difficult for workshop coordinators to find instructors. Currently, the Dutch community is (non-officially) coordinated by the Netherlands eScience Center, a Dutch national expertise centre that strives to increase awareness of the importance of research software and digital technologies in and around academia. The eScience Center and other Carpentries member organizations across the Netherlands would like to work together to build a stronger community that fosters its instructors to keep their certification active, to keep in close contact and support each other on providing training and lesson development initiatives.

    There are already some national networks initiated. For example, NL-RSE: the Netherlands Research Software Engineers' Community. We are also building a community on training initiatives in research software called RST-NL: Research Software Training NL, to share resources, tips and tricks and exchange advice on digital training. Next to this, the Netherlands eScience Center also (co-)develops new lessons in the Carpentries Incubator. Finally, we are developing training on “Research Software Support” for onboarding and to skill up RSEs and research support staff at Dutch research performing organizations.

    We hope to use this opportunity at Carpentries Connect to bring together new and seasoned community members to share knowledge, network, and develop strategies for building a strong local training community so that we can help build digital literacy of researchers in the Netherlands. Please share your thoughts and advice on community building!

    Community-led training is an increasingly important tool in life sciences research. Networks like ELIXIR work with academic and commercial researchers. They depend on software tools such as FAIRDOM-SEEK which are used by individuals based at institutions across Europe. Peer-to-peer support is an essential way for the community to develop their skills with such tools. The Carpentries lesson template could form part of this. This lightning talk will describe my first six months working in the life sciences FAIR research data field, comparing against my previous work with the Library Carpentry community.

    The FAIR (Findable, Accessible, Interoperable, Resusable) principles have become a cornerstone for more impactful and reusable science. In line with their growing adoption by the scientific community at large, the bioimaging domain has experienced a significant shift in mindset towards FAIR in recent years. As a European research infrastructure, Euro-BioImaging shapes the development of FAIR bioimaging data by fostering the exchange of knowledge and know-how between bioimaging communities across disciplines, scales and geographical locations. Through its national and international activities, Euro-BioImaging leverages input from European projects and grassroots initiatives to advance the field of bioimaging to a place where data and software sharing is a top priority.

    In line with our mission, we provide several online training events on the implementation of FAIR principles to bioimage researchers as well as the general public. Although individual researchers must be aware of the FAIR principles, it is also crucial to recognize that the burden and workload of creating FAIR data should not fall solely on their shoulders. To this end, our latest workshop is designed for bioimaging core facilities to provide them with actionable steps on how to support more FAIRness in their projects, thus lowering the barriers for individual researchers on their path to FAIR. The workshop will be developed through a collaborative effort between experts from our Euro-BioImaging facilities as well as from the wider bioimaging communities. The outcomes will be shared with the whole world to facilitate the adoption of FAIR bioimage data.

    "For the past 20 years, the University of Vienna (UNIVIE) has offered Research Data Management services to its researchers, students, and support staff. More recently, UNIVIE has begun embedding Data Stewards within interested faculties. One of the goals of this approach is to provide tailored, discipline-specific support. An additional focus of this program is the education and support of the next generation of researchers.

    In June of 2023, the Data Stewards at the Faculty of Life Sciences and the Centre for Microbiology and Environmental Systems Science) launched a new workshop dedicated to introducing Ph.D. candidates and Masters students in the life sciences to basic research data management. This course, entitled Research Data Management for Ph.D. Candidates in the Life Sciences, employs a blended learning approach that combines instruction with a variety of activities designed to encourage students to test their skills. Students are given an online module (~4 hours) to complete before attending two in-person half-day seminars. While the online module focuses on information transfer, the seminars prioritize activities, discussions, and questions + answers. Since the workshop’s launch, the UNIVIE Data Stewards working in the life sciences have continued to hone both the online module and the in-person seminars to evaluate which approaches perform well and which leave room for improvement. In January 2024, the online module, which was written in LiaScript, and the seminar materials were released on Zenodo (https://zenodo.org/doi/10.5281/zenodo.10512974) as an open educational resource that can easily be reused and modified by others.

    This poster/lightning talk provides an overview of the content of the course, the lessons learned by the UNIVIE Data Stewards working in the life sciences in the past 18 months, and future directions that include the launch of an Open Science Community to facilitate more advanced and specialized information exchange.

    More than 8 years, the Galaxy training community (GTN) has empowered scientists to learn taking their data analysis into their own hands. It is an open-access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework. Galaxy is an open, web-based platform designed to enable computational research in the life sciences. With more than 390 different tutorials spanning over 30 topics, the GTN provides Galaxy users, developers, and admins support in diverse learning endeavors.

    The GTN provides online learning materials for learners and instructors, which are both suited to synchronous and asynchronous learning. The content is grouped by topics and fields, and a search will help to find the materials for a preferred topic. More recently the GTN also additional introduced learning pathways.

    The GTN community not only offers e-learning materials suitable for self-paced learning but also provides regular on-site workshops at different locations, webinars as well as a massive yearly online learning event - the Smörgåsbord (a global, 5-day, 24/7, and free-of-cost event). This concept was not only helpful in times of pandemics, but it also provided people from every corner of the continent to participate and get support within their working hours. Galaxy and the GTN are part of the BioNT consortium and are providing online workshops for its basic curriculum. Additionally, Galaxy and GTN offer the Training Infrastructure as a Service (TIaaS), which provides dedicated computing resources for a workshop.

    The GTN has a very diverse community with more than 340 contributes the platform is constantly growing and taking new tutorials as well as the updates of the existing tutorials. The infrastructure of the GTN is open and easily accessible via GitHub and building and changing learning materials can be all done in markdown, lowering contribution burdens.

    The Carpentries workbench is a set of R packages that provides the infrastructure for all Carpentries lesson materials since 2023. It can be considered as a free, open-source and fully reusable Learning Management System (LMS). The code is available on GitHub under an MIT license and the hosting and automation setup are provided transparently as configuration as code, and for free via GitHub Pages and GitHub Actions. This makes the workbench a prime candidate for any external community that wishes to use a well-tested, free and replicable LMS. In this presentation, I investigate the use of the workbench in external communities, beyond the Carpentries, and I present our experience as one of these communities: the Epiverse-TRACE community. This presentation thus targets multiple audiences and serves multiple purposes:

  • Strengthen the case for the further funding of the workbench as a critical piece of technical infrastructure, not just for the Carpentries, but also for adjacent external communities
  • Potentially inform the future development of the workbench by highlighting our struggles as an external community adopting this framework, and by analyzing forks of the workbench packages
  • Demonstrate to external communities the steps they can follow to use the workbench for their own training materials, including how to define and implement a custom theme
  • CodeRefinery is a project funded by Nordic e-infrastructure collaboration (NeiC) supporting students and researchers across all research domains by teaching "good enough" FAIR (Findable Accessible Interoperable Reproducible) research software development practices. Among other activities, the project has enabled us to conduct interactive hands-on online and free workshops for over 300 registrants at a time. The workshops are live streamed and combine co-teaching, asynchronous questions and answers as well as parallel local meetups. A few years ago we switched from the traditional online teaching style to this new format, which required adjusting to alternative technologies and mindset. With this contribution we would like to share our current teaching strategy as well as our main lessons learned from developing our workshop style and open lesson materials over the years.

    Software Carpentries are a great way for beginners to engage for the first time with code. Participants learn the basics of a programming language, the way of thinking behind programming and how to help themselves after the Carpentries. However, after participating in a Software Carpentry workshop a gap between your skill set and your daily challenges in your research remains. The participants may struggle being on their own with insufficient experience to solve their own challenges without helpers. This leads not only to frustration, but may result in not adopting the practices taught in the Carpentries. There are often insufficient resources to support programming beginners individually and we often do not know what happens with Carpentry participants after the workshops.

    To ensure a follow-up check and to provide a continuous learning path for coding beginners, we introduced an inclusive programming cafe at our university (Vrije Universiteit Amsterdam). A programming CAFE (Code Along, Feel Empowered) is a community event that brings together programmers - both researchers and research supporters - to share knowledge about programming and learn with each other in an open and informal setting. Everyone is welcome to join a short demo of selected programming related topics (such as visualisation and AI in programming), present their projects and bugs, work on smaller challenges, and connect with fellow researchers and advanced programmers outside their domains.

    We would to share our experience with our programming cafe "Bytes & Bites", inspire other institutions to provide a similar experience for Carpentry participants, and discuss best ways to continue the learning journey of Carpentry participants.

    Posters

    The Carpentries Workbench, a recent innovation, has revolutionised lesson development by offering an accessible, inclusive, and intuitive platform for curriculum creators. This tool simplifies the deployment of Markdown-written lesson content to a stylised website, requiring minimal coding knowledge and abstracting away most technical details so that creators can focus on the content.

    A standout feature of the Workbench is its automatic tracking of R package dependencies and updating them via the package cache. This is achieved through the renv package, which creates a lesson-specific R environment, detecting and recording any third-party R packages used throughout the lesson. This ensures a consistent environment between deploying lessons on GitHub and building them locally.

    However, a significant gap exists for Python dependencies, despite Python being a popular language widely used in the Carpentries curriculum. To address this, I have contributed a feature to the sandpaper package, which is responsible for lesson deployment. This feature enables the tracking of Python dependencies in a manner consistent with the current package cache in R. This enhancement can be easily integrated when creating new lessons and added to existing ones, without altering the general sandpaper interface. It aims to alleviate the manual maintenance burden for lesson developers working with Python.

    In this poster, I will outline the process of implementing this feature, share the lessons learned, and discuss my experience contributing to the Carpentries Workbench infrastructure. This contribution hopes to further streamline the lesson development process and improve the overall user experience.

    Methods Hub is a new service offer from GESIS Leibniz Institute for the Social Sciences for computational social scientists working with digital behavioral data to learn about social and socio-technical phenomena. Methods Hub hosts an index of software packages that computational social scientists can use and avoid reinventing the wheel. Additionally, Methods Hub also host documentation and tutorials related with the indexed software packages. One key feature of Methods Hub is to be a 1-click bridge to mybinder.org where users have access to ready to use computational environment.

    The Netherlands houses an extensive Carpentries community: seven Academic institutions have become member organizations and a total of 125 instructors have been certified and are spread across the country. Despite the considerable size of the Dutch community, it faces challenges too: not all instructors keep active after certification, which makes it difficult for workshop coordinators to find instructors. Currently, the Dutch community is (non-officially) coordinated by the Netherlands eScience Center, a Dutch national expertise centre that strives to increase awareness of the importance of research software and digital technologies in and around academia. The eScience Center and other Carpentries member organizations across the Netherlands would like to work together to build a stronger community that fosters its instructors to keep their certification active, to keep in close contact and support each other on providing training and lesson development initiatives.

    There are already some national networks initiated. For example, NL-RSE: the Netherlands Research Software Engineers' Community. We are also building a community on training initiatives in research software called RST-NL: Research Software Training NL, to share resources, tips and tricks and exchange advice on digital training. Next to this, the Netherlands eScience Center also (co-)develops new lessons in the Carpentries Incubator. Finally, we are developing training on “Research Software Support” for onboarding and to skill up RSEs and research support staff at Dutch research performing organizations.

    We hope to use this opportunity at Carpentries Connect to bring together new and seasoned community members to share knowledge, network, and develop strategies for building a strong local training community so that we can help build digital literacy of researchers in the Netherlands. Please share your thoughts and advice on community building!

    BioNT is dedicated to providing a comprehensive training program and fostering a community for digital skills relevant to the biotechnology industry and biomedical sector.

    In our efforts to attract employees from SMEs, industries, and job-seekers, we looked for an approach that would prioritise privacy while maintaining interactivity.

    After analysing various approaches, we have formulated our workshop delivery strategy at BioNT. Our approach draws inspiration from leading learning communities such as The Carpentries, Coderefinery, and the Galaxy Training Network (GTN), but is tailored to meet the unique needs of our participants.

    Through this poster, our aim is to introduce the setup, organisation, and structure of a BioNT workshop focusing on how we tried to maintain anonymity using the Zoom webinar format and how we ensure interactivity with the HedgeDoc document.

    "The FAIR (Findable, Accessible, Interoperable, Resusable) principles have become a cornerstone for more impactful and reusable science. In line with their growing adoption by the scientific community at large, the bioimaging domain has experienced a significant shift in mindset towards FAIR in recent years. As a European research infrastructure, Euro-BioImaging shapes the development of FAIR bioimaging data by fostering the exchange of knowledge and know-how between bioimaging communities across disciplines, scales and geographical locations. Through its national and international activities, Euro-BioImaging leverages input from European projects and grassroots initiatives to advance the field of bioimaging to a place where data and software sharing is a top priority.

    In line with our mission, we provide several online training events on the implementation of FAIR principles to bioimage researchers as well as the general public. Although individual researchers must be aware of the FAIR principles, it is also crucial to recognize that the burden and workload of creating FAIR data should not fall solely on their shoulders. To this end, our latest workshop is designed for bioimaging core facilities to provide them with actionable steps on how to support more FAIRness in their projects, thus lowering the barriers for individual researchers on their path to FAIR. The workshop will be developed through a collaborative effort between experts from our Euro-BioImaging facilities as well as from the wider bioimaging communities. The outcomes will be shared with the whole world to facilitate the adoption of FAIR bioimage data.

    "For the past 20 years, the University of Vienna (UNIVIE) has offered Research Data Management services to its researchers, students, and support staff. More recently, UNIVIE has begun embedding Data Stewards within interested faculties. One of the goals of this approach is to provide tailored, discipline-specific support. An additional focus of this program is the education and support of the next generation of researchers.

    In June of 2023, the Data Stewards at the Faculty of Life Sciences and the Centre for Microbiology and Environmental Systems Science) launched a new workshop dedicated to introducing Ph.D. candidates and Masters students in the life sciences to basic research data management. This course, entitled Research Data Management for Ph.D. Candidates in the Life Sciences, employs a blended learning approach that combines instruction with a variety of activities designed to encourage students to test their skills. Students are given an online module (~4 hours) to complete before attending two in-person half-day seminars. While the online module focuses on information transfer, the seminars prioritize activities, discussions, and questions + answers. Since the workshop’s launch, the UNIVIE Data Stewards working in the life sciences have continued to hone both the online module and the in-person seminars to evaluate which approaches perform well and which leave room for improvement. In January 2024, the online module, which was written in LiaScript, and the seminar materials were released on Zenodo (https://zenodo.org/doi/10.5281/zenodo.10512974) as an open educational resource that can easily be reused and modified by others.

    This poster/lightning talk provides an overview of the content of the course, the lessons learned by the UNIVIE Data Stewards working in the life sciences in the past 18 months, and future directions that include the launch of an Open Science Community to facilitate more advanced and specialized information exchange.

    More than 8 years, the Galaxy training community (GTN) has empowered scientists to learn taking their data analysis into their own hands. It is an open-access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework. Galaxy is an open, web-based platform designed to enable computational research in the life sciences. With more than 390 different tutorials spanning over 30 topics, the GTN provides Galaxy users, developers, and admins support in diverse learning endeavors.

    The GTN provides online learning materials for learners and instructors, which are both suited to synchronous and asynchronous learning. The content is grouped by topics and fields, and a search will help to find the materials for a preferred topic. More recently the GTN also additional introduced learning pathways.

    The GTN community not only offers e-learning materials suitable for self-paced learning but also provides regular on-site workshops at different locations, webinars as well as a massive yearly online learning event - the Smörgåsbord (a global, 5-day, 24/7, and free-of-cost event). This concept was not only helpful in times of pandemics, but it also provided people from every corner of the continent to participate and get support within their working hours. Galaxy and the GTN are part of the BioNT consortium and are providing online workshops for its basic curriculum. Additionally, Galaxy and GTN offer the Training Infrastructure as a Service (TIaaS), which provides dedicated computing resources for a workshop.

    The GTN has a very diverse community with more than 340 contributes the platform is constantly growing and taking new tutorials as well as the updates of the existing tutorials. The infrastructure of the GTN is open and easily accessible via GitHub and building and changing learning materials can be all done in markdown, lowering contribution burdens.

    The Intermediate Research Software Development Course is now at the beta stage in the Carpentries Incubator. Along the course of its maturity, many pilot sessions have been conducted, asynchronous contributions made, and lessons learnt as a result. A brief summary of the current status of the course will be delivered, including topics like successful delivery styles that have been used, alternate tooling options such as the popular VS Code IDE, and recent changes to the course content on software design and architecture. As course maintainers, we are always looking for new contributors, so we hope that creating awareness of this course and its status will peak interest within the Carpentries community. To facilitate this, we will signpost routes and resources that new contributors can use to get involved.

    The Carpentries workbench is a set of R packages that provides the infrastructure for all Carpentries lesson materials since 2023. It can be considered as a free, open-source and fully reusable Learning Management System (LMS). The code is available on GitHub under an MIT license and the hosting and automation setup are provided transparently as configuration as code, and for free via GitHub Pages and GitHub Actions. This makes the workbench a prime candidate for any external community that wishes to use a well-tested, free and replicable LMS. In this presentation, I investigate the use of the workbench in external communities, beyond the Carpentries, and I present our experience as one of these communities: the Epiverse-TRACE community. This presentation thus targets multiple audiences and serves multiple purposes:

  • Strengthen the case for the further funding of the workbench as a critical piece of technical infrastructure, not just for the Carpentries, but also for adjacent external communities
  • Potentially inform the future development of the workbench by highlighting our struggles as an external community adopting this framework, and by analyzing forks of the workbench packages
  • Demonstrate to external communities the steps they can follow to use the workbench for their own training materials, including how to define and implement a custom theme.
  • CodeRefinery is a project funded by Nordic e-infrastructure collaboration (NeiC) supporting students and researchers across all research domains by teaching "good enough" FAIR (Findable Accessible Interoperable Reproducible) research software development practices. Among other activities, the project has enabled us to conduct interactive hands-on online and free workshops for over 300 registrants at a time. The workshops are live streamed and combine co-teaching, asynchronous questions and answers as well as parallel local meetups. A few years ago we switched from the traditional online teaching style to this new format, which required adjusting to alternative technologies and mindset. With this contribution we would like to share our current teaching strategy as well as our main lessons learned from developing our workshop style and open lesson materials over the years.

    At the Netherlands eScience center we have been teaching “Image Processing with Python” both to an internal eScience group of research software engineers and general multi-disciplinary groups of researchers. There is excitement about image processing, particularly from researchers who deal with medical data. We therefore decided to extend the Carpentries curriculum with a course that covers the basics of medical image processing in Python.

    The goal of this material is to teach some of the basic concepts necessary for medical image research using Python. We believe the “Image Processing with Python” course provides a general introduction to working with images, but lacks the unique and challenging specifics of working with medical images. Therefore, we began developing a workshop tailored to life science and medical scientists with little to no experience with computational approaches to medical images, but with a familiarity (i.e., basic knowledge) with Python and topics covered by “Image Processing with Python '' Carpentry's course.

    Existing materials related to medical imaging data under development at Carpentries cover only one imaging modality (i.e., MRI). We add materials on common toolkits for medical image processing in Python, e.g., SITK. Theoretical materials on patient/data anonymization in relation to medical image formats along with an introduction to PyDICOM will also be provided. Our specific curriculum will include a diagnostic images overview, an introduction to working with MRI, registration and segmentation taught with SITK, an introduction to working with CT/Pathology data, data anonymization for images and files, preparing and processing images for machine learning and a unit on generative algorithms. The first edition of the course is scheduled for September 2024. Here we propose to use a poster and lightening talk to introduce our new course. We can cover the material we created and discuss the course reception.

    The Epiverse-TRACE initiative aims to provide a software ecosystem for outbreak analytics with integrated, generalisable and scalable community-driven software. We support the development of R packages, make the existing ones interoperable for the user experience, and stimulate a community of practice.

    We structure our training materials into two complementary curricula. The Outbreak Analytics curriculum focuses on streamlining the utilisation of R packages tailored for outbreak analytics tasks to enhance decision-making processes. Meanwhile, the Research Software curriculum aims to broaden our suite of R tools to develop open, reproducible, and sustainable data analysis projects, adhering to best practices in research software development.

    In the Outbreak Analytics curriculum, we built three lessons around an outbreak analysis pipeline split into three stages: Early, Middle, and Late tasks. Early tasks include reading and cleaning case data and accessing delay distributions to estimate transmission metrics. Middle tasks include estimating forecasting, severity and superspreading from case data and simulating transmission chains. Late tasks include scenario modelling to simulate disease spread and investigate interventions (https://epiverse-trace.github.io/tutorials-late/).

    In the Research Software curriculum, we have two lessons focused on best practices for your outbreak analytics R projects and data. The Version Control with Git in Rstudio lesson is a forked repository from the Software Carpentry Version Control with Git lesson reframed to an outbreak response scenario. The Improve Your Code for Epidemic Analysis with R lesson (https://epiverse-trace.github.io/research-compendium/) focuses on three skills to increase project reliability and reusability by the community: using a research compendium template with {rcompendium}, making reproducible analysis with {renv}, and writing informative READMEs following good community practices.

    Global BioImaging (GBI) stands as a unifying force, mobilizing imaging scientists and facilities from across 61 countries and 13 networks. With a mission to provide a panoramic view of the imaging landscape, GBI champions the global impact of imaging scientists. Through inclusive programs and initiatives, GBI transcends geographical, technological, and thematic barriers, fostering exchange, innovation, and community building (see also "i4A").

    GBI's offerings include comprehensive training, immersive job shadowing experiences, and impactful advocacy efforts designed to empower imaging scientists and influence policy and decision-makers. Collaborative papers and working groups embody the collective commitment to advancing imaging science, covering various topics from career pathways to infrastructure development.

    These guidelines often translate into workshops or breakout sessions according to the matters of interest from local imaging communities: "How to make a case for fair career paths for imaging scientists working in core facilities", "How to talk to our funder", "How to build a network and community", "How to organize training courses in your core facility", "How to showcase the value and impact of your core or network", and "How to talk to your IT department when setting up a RDM infrastructure" are pivotal in shaping the trajectory of imaging science. GBI maintains a strong commitment to equitable access and opportunities, promoting travel grants and funds dedicated to imaging scientists from underserved communities.

    As anticipation grows for the annual meeting in Japan (#GBI_EoE2024), GBI remains at the forefront, accelerating exchange and innovations across the globe, propelling progress, and fostering collaboration in the field of imaging science (https://globalbioimaging.org/exchange-of-experience/exchange-of-experience-ix)

    Researchers from a broad spectrum of scientific fields use computers to aid their research, often starting at their own laptop or institutional workstation. At some point in the research, additional help in form of algorithmic or software engineering consultancy or even additional computational resources in form of access to high-performance computing (HPC) systems may become necessary. Furthermore, on the side of AI, it may be unclear how practices of machine learning and artificial intelligence could be employed for their specific research.

    With state-level HPC competence centers, NHR ("Nationales Hochleistungs-Rechnen") centers, and German national AI service centers, there is a broad spectrum of support available for researchers across Germany. Training opportunities offered by these centers may include topics focused on and courses provided by the "HPC carpentry", "Software Carpentry", and "Data Carpentry", yet, may also go beyond the Carpentries' current spectrum of courses and capabilities.

    This lightning talk and poster is meant to raise awareness for these opportunities and aid researchers in finding the right contact for such services to advance their research. Furthermore, the awareness for such services within the Carpentries' community of instructors may also lead to a better connection between the Carpentries and these centers to enable synergies for the benefit of researchers across Germany.