Moving Open Science forward at the institutional/departmental level

Authors: Esther Plomp, Emmy Tsang, Emma Henderson and Delwen Franzen

This blogpost summarises a discussion session held during the AIMOS2021 conference (1 Dec – 08:30-9:30 AM UTC). During the discussion, we focused on what our institutes and departments could do to improve the awareness of Open Science practices and support the change towards a more open research culture. We started our session with some of the questions that the participants were currently struggling with, and some of our (not so) success stories: 

  • The Delft University of Technology (the Netherlands) already has a lot of policies and support roles in place that support Open Science practices. There is the Open Science Programme with a dedicated Community Manager that also supports the building and growth of the TU Delft Open Science Community. At the Faculty level, Data Stewards provide support for research data and software management and sharing. Thanks to these Data Stewards, the faculties each have their own Data Management policy.
  • The Flinders University (Adelaide, Australia) is working on policy changes and has an Open Science training in place.
  • The BIH QUEST Center (Charité – Universitätsmedizin Berlin, Germany) has developed a pilot dashboard that provides an up-to-date overview of several metrics of open and responsible research at the Charité. 

Having dedicated roles or policies for Open Science and Data Management is crucial to drive effective change in research practises, but not every institute has these resources. While the uptake of Open Science practises in the last five to ten years has increased, there is also still a lot of frustration at the local level. Not everyone has the time to pay attention to or is enthusiastic about Open Science developments, and participants indicated that some principal investigators did not care about replicability in research. If bachelor/master students are following training on open research practices, they are equipped to take this aspect into account when selecting a supervisor for their PhD research (see also Emily Sena’s contributions in the AIMOS 2021 Panel Discussion on “How to start a revolution in your discipline”). While some institutions offer Open Science training, sometimes the uptake is low. During the session we struggled with some of these obstacles and discussed the following four questions in more detail: 

How can you make the case for hiring professionals that support Open Science practices? 

It helps if other institutes have examples of professional support roles, especially if there is visible impact in the uptake of Open Science practices. A great example of this is the UK Reproducibility Network (UKRN). The UKRN is actively involved in supporting institutions in setting up roles that focus on increasing reproducibility of research, by connecting stakeholders to share best practices and by providing expert advice. 

To build the case for the institution to prioritise investment in Open Science, it is often helpful to illustrate to institutional leadership the effects of (inter)national funders’ commitments to Open Science. Funder mandates on data management planning and sharing are now commonplace (for example, the European Commission, NWO, NIH) and are directly impacting the institution’s researchers. 

It was also noted that support from institutional/faculty leadership alone was often not sufficient: the establishment for these roles should also be driven by the needs of the researchers. Ideally, there is alignment in these bottom-up needs and top-down strategic decisions. 

How do you set up an Open Science policy at your institute? 

To set up an Open Science policy, you may be more successful if you tackle the variety of different aspects of Open Science separately. Open Science is a very broad concept and it may be complicated to address Open Access, Data, Software, Education, Engagement in a single policy. 

Stakeholder engagement is essential when setting up a policy. You should make sure that the policy represents various interests at your institution. Stakeholder mapping is a helpful exercise that could help one understand who to talk to, how and at what stage of policy development. While it may take time to actively engage all of your stakeholders, in the end your policy will be more practically applicable and supported. At the same time, it is also an opportunity to engage in conversation with your stakeholders with this topic, as an upcoming policy that would affect them creates a sense of urgency. It is helpful to run your policy past procedural check points (such as Human Research Ethics committees). 

How do we incentivise/reward researchers practising Open Science?

One way to incentivise researchers to practise Open Science is setting up Awards: 

While it is important to recognise the efforts of individual researchers in practising Open Science, there are discussions on whether incentivising them with awards is the best approach (see Lizzie Gadd’s post ‘How (not) to incentivise open research’ and Anton Akhmerov’s Twitter thread). 

How do you get more people onboard in practising Open Science?

In order to gain more support for Open Science practices, it helps if there are practical examples. It is not always clear from hypothetical or abstract statements what can be done on a daily basis to make research practices more open. 

It was noted that it is easier to start at the beginning of the research career with learning about open research practises, for example, during undergraduate or early graduate school training. Once the students have gained more knowledge, they can also demonstrate to their supervisors that these practices are beneficial. However, it cannot just be up to PhD candidates to drive these changes as they are in a hierarchical relationship with their supervisors. Supervisors should also receive training and support to adjust their practices.

Contributions

This blogpost is written based on contributions by the session participants: Peter Neish (The University of Melbourne, @peterneish), Delwen Franzen (BIH QUEST Center for Responsible Research, @DelwenFranzen), Jen Beaudry (Flinders University, @drjbeaudry), Emma Henderson (University of Surrey, @EmmaHendersonRR), Fiona Fidler (University of Melbourne, @fidlerfm), Nora Vilami and Pranali Patil.

Digital Skills for Researchers: Not only coding

Authors: Meta Keijzer-de Ruijter, Masha Rudneva

Cooking class for researchers  

Some people think that digital skills in research focus on learning how to program (Python, R, C++, MATLAB, etc.) or use digital tools to automate recurring tasks, but it entails a lot more. 

Becoming a digitally-skilled researcher requires more than ‘just’ learning to use individual tools. It is like becoming a star chef: It does not suffice to know how to use the different cooking appliances (knife, mixer, oven, stove, etc). You also need to know how to run a kitchen efficiently, making sure all prepared ingredients for the dish come together on a plate at the right time without mixing up steps in the recipe that affect the final quality of the dish. To summarize, it is essential to consider, plan and prepare all steps and aspects of the research process workflow at the beginning of each research project.

The potential drawbacks  

Implementing best practices in using digital tools requires a significant change in workflow to achieve efficiency and good quality outcomes. If not, code and other scientific outputs can be lost or become unusable by others in the future. Think about the master student who had done a great research and successfully graduated. However, after the student has left, the successors cannot find or re-use the developed code and have to start from scratch. So, the valuable contribution to the project is lost, and the continuity of the work is disturbed.

Also, if researchers do not document the actions and steps during the research project, they may need to figure out things twice when it comes to publication. Reproducibility of the results largely depends on good digital skill practices. So, how could one make sure that the research artefacts remain useful for society and successors?

The Open Science community formulated four main principles or the best practices helping in this process. Those are the “FAIR” principles, which stands for “Findable, Accessible, Interoperable and Reusable”. So, let us analyze a typical life cycle of research software or code creation and see how to build FAIR principles and essential digital skills into your research project.  

What “digital skill” ingredients do you need during your project?  

At the start of a research project, it helps to have a good overview of the elements in the workflow in relation to the various stages of your project. In this section, we provide a roadmap that could help you to plan your work.  

Step 1 – Preparation Phase:    

Defining what you need to build and what tools will be used is essential.  

  • Analysis of the project requirements – What research questions do you need to answer, and what results do you want to achieve? Breaking down big questions into smaller problems/deliverables often helps in building a more modular code in the long run.
  • Investigation of the available codebases – Can you build your project on an existing platform, codebase or use available algorithms, for example, or do you have to “start from scratch”? It is often more efficient to re-use available resources, but you always need to check the licenses and conditions before using, copying or modifying the code of someone. 
  • Learning about the best practices for Research Software development – a high-level understanding of the best practices allows you to avoid the common pitfalls and makes your work more efficient.
  • Choosing the platform, programming language and the concepts for the code produced – is the last preparation step. You are now ready to start the actual work.  

Step 2 – Research project:   

Creating the code or research software is only one piece in the whole story. The other essential aspects one should consider are:    

  • Data Management – consider the best practices for data management at the beginning of the project by drawing up a Data Management Plan, which will detail how the data is structured, stored, and archived. Having a Data Management Plan will save you a lot of work and time later. Data Stewards at the faculties are available to provide you with all the support, training and information required (https://www.tudelft.nl/library/research-data-management/r/support/data-stewardship/contact
  • Backing up the code – think about the storage with periodic automated backup or set up the backup routine yourself. If you use TUDelft research drive or SurfDrive, your code and data are automatically backed up for you. If you use your laptop or external hard drive, you can lose data if the storage drive is damaged. When storing in the cloud, make sure that your credentials are secured, and you will always be able to retrieve them if forgotten.   
  • Documentation – code by itself can be great but not (re)usable by others if no documentation is attached. It might be challenging to remember and understand what the code is doing a year later. So, having proper documentation is a valuable step in making your code reusable by yourself and others.    
  • Metadata to describe your code and results – metadata can be as broad and descriptive as possible. It may contain information about the code creation (author, date, OS, configurations) and describe when and how to use it. Adding appropriate metadata can make your code more findable.  
  • Use of Version Control – this is an essential part of any research project. It allows you to see and manage changes to files over time, keep track of those modifications and ease the collaboration and co-creation of the code for you and your colleagues. The use of GitLab, GitHub or other version control systems ensures that you can always go back to the previous version of your code if something went wrong at the current state. It enhances the reproducibility of the research produced. 
  • Testing / Distribution – you should build tests into the code at various stages to make debugging easier, mitigate potential errors and ensure that you and others can use your code without errors and reproduce results.   
  • Security and Privacy – you often need to build some security features or choose the framework with the built-in security to keep classified and sensitive data well-protected and keep vulnerabilities out of your system.  

Step 3 – Publishing and Sharing

Now, the code has been built, and the first results are obtained. It is a perfect moment to celebrate, but this is not the end of the story. Now think about the sharing and archiving of your results. If you would like the community to use your results, your code should have a license, be stored where others can find it, have explicit metadata attached to it and possess unique identifiers. But no worries, if you have followed the FAIR principles, you are well-covered.   

  • Licensing – Whether you want others to (re)use your code or you are thinking about patenting your software, you should choose a license for it. The most common software license models are Public domain, Permissive, LGPL, Copyleft and Proprietary – they are different types of licenses varying from completely open to fully restricted. 

Often if you are developing software openly, e.g. on GitHub/GitLab, the advice is to choose a license at the beginning. This also has implications for registering the software as per the Research Software policy. 

  • Citations – Citing the sources you used acknowledges and gives credit to the authors. It also allows others to learn more about the previous work your project is built upon. To make your code more citable, it is worth adding a citation file (CFF) to your repository (https://citation-file-format.github.io/)
  • Publishing – there are many platforms on which you can share and publish your code, e.g. GitHub or SourceForge. Publishing and sharing your project on these platforms can attract collaboration and increase visibility. Please remember that the code or any digital object should have a Digital Object Identifier (DOI) to make it easier to find or cite. If the data/code cannot be shared, you can still share the metadata in a repository so that others can find your project and request access to it.  
  • Archiving – when the project is over, you may want to archive your code in a repository to access it in the future. Code can be archived at, for example, 4TU.ResearchData or at Zenodo. 

Digitization brings a lot of opportunities to researchers to do more advanced research and collaborate with others. But it requires adjustments to the workflow, development of a common language and learning skills to effectively use new tools that come available. The good news is that at TU Delft, we have training courses and excellent support available through the Digital Competence Center (DCC, https://dcc.tudelft.nl/ ) and Data Stewards that can help you run your kitchen as a star chef in the digital age. 

Summarises the areas of skills required for each of the three steps of a research project.
The three phases of a research project, and the area of skills required.

Who are we?

Meta Keijzer-de Ruijter:

Meta has a background in Chemical Engineering and Corporate Education. She spent more than 10 years in the ICT Innovation department developing digital assessment in education at TU Delft. Recently, she became a project manager of the FAIR Software project within the Open Science Program. Together with colleagues in ICT Innovation and Research Support at the Library, she set up the Digital Competence Center (DCC) support team. She currently investigates the needs for digital skills for researchers.

Masha Rudneva:

Masha has got her PhD in Physics at TUDelft and recently joined the ICT department as an Innovation Analyst. She focuses on supporting researchers in challenging ICT related requests. 

It is the first in the series of blog posts in which we want to talk about the work we do to support the researchers as the Innovation Department and DCC team to reflect on the things we come across.

MRI Together 2021

Author: Martijn Nagtegaal

In this blog post I want to share my experiences in attending the MRI Together workshop.

MRI (Magnetic Resonance Imaging) research requires a broad range of specialists to make this research effective and useful. MRI disciplines range from engineering and physics to clinicians using the final outcomes: engineers, such as electrical engineers, design RF coils, physicists design specific pulse sequences, mathematicians perform fast and effective reconstructions. While these research fields mainly focus on technical challenges, biomedical scientists and clinicians play their role by asking the more clinically-relevant research questions and testing and applying these novel ideas and designs to study the human body. MRI Together aims to bring together researchers from all these different disciplines and learn about the open science initiatives currently taking place within MRI research and learn from their experiences. For me, this provided an opportunity to learn which different initiatives are taking place at the moment and which open science practices can be included in my research.

A Caucasian woman’s head is being secured by a Caucasian female technician, preparing the patient for magnetic resonance imaging (MRI). Photo by National Cancer Institute on Unsplash.

MRI Together took place online in the third week of December with 2-hour sessions distributed from Monday to Thursday and took place at 1:00, 7:00, 13:00 or 19:00 (CET) to accommodate different time zones. All topical discussions and the opening and closing sessions were held twice with different speakers, to make it possible for everyone to attend sessions at reasonable times. Most sessions included a hands-on session to make attendees acquainted with the proposed research practice or software. In some of these sessions, live MRI scans were performed!

The conference showcased the broad range of open science initiatives that take place and all address their own problem. For me this again showed how broad the field of MRI research is and how much there is to gain if the different parts can be better-aligned with open practices. This ranges from data sharing (with all its legal and ethical challenges) in well-documented formats,  post-processing pipelines that prevent p-hacking, to the possibility to share the exact details in designed MRI sequences.

In my opinion, one of the main challenges in opening MRI research is the central role that vendors of the MRI scanners play. Where the call and need for open science is well heard in most academic research, this might be more conflicting for commercial companies. Close collaboration between research institutes and vendors makes it possible to rapidly prototype new sequences. But, this also leads to intellectual property shared with vendors and vendor-specific (software) implementations of novel research ideas that cannot be easily shared openly. At the same time, close collaboration is advantageous, since the vendors are required to implement new ideas and bring this to non-academic hospitals when clinical advantages are shown. Discussions on how and why vendors can contribute to open science practices does not take place enough I feel, and having the support of vendors can make a substantial difference, for example, in the support of open data formats (or even using them as default).

The talk that stayed with me the most was “Accessibility of imaging in India and how open technology and innovations can help” by Sonal Krishan. We can all try to come up with the most advanced and sophisticated MRI scans, models and analysis, but if this only leads to increased scan time and the requirement for more advanced knowledge for the radiographers, this might only lead to an advantage for a small proportion of the population. In the talk, Dr Krishan addressed again how a large portion (60%) of the Indian population only has access to 10% of the medical imaging facilities, if there is access to MRI or other medical imaging modalities at all. Thus, besides trying to make all research sharable with other users (one part of openness), it is also important to keep thinking about how the latest improvements can be practically implemented in clinical sites with restricted resources, both in equipment, money and expertise.

While attending the conference, I appreciated the broad range of topics. At the same time, almost every talk was relatable because of the shared interest in open science and the natural collaborative atmosphere. I think the organizers did a great job in facilitating a place to share open science practices and projects! For now I will dive back into my own research niche, but I look forward to making this part a bit more open as well!

Behind the scenes of our new open science website

We have launched a new open science website for TU Delft (TUD)- check it out 🎊

Here, we retrace our footsteps and share some of the work behind the scenes and lessons we have learned while constructing this website. We hope that this will be helpful for open research services that are looking to build an online presence to better support and inspire their research and teaching communities.

The starting points

TU Delft has had multiple open science websites; perhaps most notably, the open science guide designed in 2017 has subsequently inspired other institutions’ open science websites. 

So why a new design? The start of the new Strategic Programme Open Science 2020-24 (OSP) represents revitalised efforts from the TUD leadership to invest in 10 areas of open science. The open science guide design was practical and straightforward but not very scalable beyond open access and data. We – the OSP team – wanted and needed a new channel to communicate with our community: one that can represent and host the diverse initiatives and opportunities arising from our work, one that we can easily refer our colleagues, from Faculty staff to librarians from other institutions, to for them to learn more about our work.

We also recognise that open science is an actively evolving and complex topic: from funders’ mandates and institutional policies to training opportunities and support personnel, there are many moving, somewhat related pieces of information that researchers, teachers, students and staff can/should learn about. We would like the new website to be an easy-to-access resource, a trusted source of information from which our community can always rely on to stay up-to-date.

Last but not least, we’d like to recognise the many open champions at TUD and showcase their work through the website. Many TUD researchers and teachers have been pushing boundaries, actively asking themselves how to be more open and inclusive with their work. The website should promote the voices of open advocates from all corners of TUD, inspire others to reflect on their ways of working and encourage discussions around open research and education practices

Telling the many stories

The second goal 👆 was particularly challenging for us: researchers and staff at TUD have varying levels of understanding in open science. The information they would like to have to practise open science would differ based on their career and research fields. 

TUD researchers and staff have different levels of engagement with open science. Avatars designed by Vitaly Gorbachev from Flaticon

To better understand our audience, their motivations for engaging with open science and the obstacles in their ways, we created four user personas together with the OSP team during 1-hour workshops. This exercise helped us reflect on our interactions with TUD researchers, teachers and staff, and helped us prioritise goals and features for the first version of the website.

One of the OSP website’s primary user persona, co-developed by the OSP team. User persona template adapted from Development Impact and You by Nesta (CC-BY-NC-SA).

Less is more

How can we design for all the different paths our users will take in their open science journeys? Our initial plan was to provide an elaborate set of interlinked resources so that users can naturally start where they find most useful (and indeed, we expect most website users to not land on the site via the homepage). Users will then be guided (e.g. through “related resources” and menus) to other pieces of content that may interest them.

A first design for the OSP website’s information architecture – very comprehensive but too complex for both users and maintainers!

A key lesson from the persona exercise and feedback from the team was that this is too overwhelming: not only for newcomers to open science who maybe don’t have a concrete idea of what open science is but also for the team that has to maintain this site. 

Marieke Roggeveen, the OSP’s former communication advisor, suggested trimming down the site to three sections that form a central narrative:

  • Define: What is open science? This section provides a gentle introduction to newcomers.
  • Apply: How can you practise open science? This section lists selected opportunities, resources and experts contact that users can read about to learn or get help on practising open science in their work. 
  • Contribute: Share your experience and inspire others to learn and follow. Sharing and learning are central to the ethos of open science, and we want to create a space for our users to do just that.

For the Apply and Contribute sections, we will build filters to enable users to find and navigate the content they are interested in quickly. Instead of putting all the services and resources we offer on the website, we can use web analytics to help refine and update the selected list in future iterations of the site.

Assembling the building blocks

Once we had identified a rough structure and critical goals, we worked with UX/UI designer Sammy de Keijne, who turned our ideas into wireframes and prototypes.

So far, all our designs are based on our understanding of and assumptions about users’ behaviours. For that reason, we needed to involve real target users in our work as soon as possible to (in)validate our assumptions and identify areas needing attention and improvement.

The design prototype of the OSP website for testing, designed by Sammy de Keijne.

We tested our interactive prototype with five users from the TUD community: researchers from different faculties and career stages and research support staff not in the OSP. We learnt a lot from seeing how they navigate through the prototype and listening to their questions and thoughts in that process.

Through this exercise, we understood that language and word choices significantly impact users’ experience, and we need to test them more carefully. For example, we initially had a heading called “open science 101”, and user testing showed that many did not understand what “101” meant. We also learnt that numbers and data intrigued and appealed to our audience.

A picture speaks a thousand words

The visual identity is like the “personality” of our website and work, and it helps set expectations, contextualise our work and create recognition. We wanted to have a distinct, coherent visual identity across our website and communication assets.

For this, we worked with visual designer Martijn van Overbruggen. Based on a mood board that we curated, Martijn built colour schemes and a graphical style that we felt represented what open science meant to us: leaves that symbolise growth, lines and circles that capture the dynamic nature of open science, a rough texture that invites refinement, vibrant colours the resonate with freshness and creativity (while still aligned with the TU Delft colour palette). 

Creating a coherent visual identity for the open science programme. Designs by Martijn van Overbruggen at WIM Ontwerpers

While we understand the power of visual illustrations, building one that is intuitive enough to understand at a glance yet captures the right amount of nuance has proven to be a huge challenge. One of our biggest challenges was to create the graphic to “define open science”: how can one showcase the fluid and contextual nature of open science with a static graphic? We went through many iterations, re-scoping, rearranging and rewording various elements, to arrive at our current version.

Our many attempts to gently introduce the audience to open science. Designs by Marieke Roggeveen, Martijn van Overbruggen, Marieke Hopley and Emmy Tsang.

Wrestling with the CMS

The TUD website’s “technical backbone” is the content management system (CMS) TYPO3. We prioritised exploring the capabilities of TYPO3 at the start of our design process. It allowed us to understand design constraints and estimate the time and resources required to implement various website elements. For example, having an interactive graphic is possible but would require additional front-end development capacity. 

Having these possibilities and constraints in mind helped keep our graphics and wireframes realistic for implementation – our colleagues at Online Solutions were able to construct the web pages based on our designs efficiently.

Feedback, feedback, feedback

With the first version of our test site online, we shared this with the OSP team for feedback. The feedback cycle at this stage was essential: fresh eyes on our work allowed us to check if we had delivered what we intended and helped us spot errors from strange layouts on mobile devices to typos.

It was vital to manage expectations, both our own and of those who contributed, at this stage: we want to go live with the site as soon as possible, without critical errors. For that, we provided instructions for giving constructive feedback and roughly parcelled the feedback we received into three categories: “easy to fix”, “hard but critical”, and “hard and for later”. This helped us prioritise the changes to implement before launch.

With our new communications advisor Marieke Hopley, we addressed some critical issues regarding the narrative and graphics on our homepage based on the feedback. We also added an “about page” to bring transparency to the open science programme. We have a list of suggested improvements for a second iteration of the site, including having Dutch pages.

Only the beginning

The launch is the first step in this journey. Becoming a trusted resource for a community will require maintenance of the site: regular updates, new stories, and more. We have to build a robust management workflow with team members to draft new content, monitor the pages for outdated materials and errors, approve edits and new pages, and implement changes. 

We also have to continue to raise awareness for the website and ensure that new and existing staff members are aware of its existence and purpose. Ultimately, we hope that the website will not only serve as a source of open science information from OSP staff, but a platform on which TUD academics, students and staff can share their knowledge and perspectives, a gateway for our community to learn about and contribute to open science. 

Acknowledgements: In addition to the people mentioned in the post, we would like to take this opportunity to thank:

  • The TUD OSP team for your ideas, feedback and patience throughout the entire process.
  • TUD data stewards and Connie Clare (Community Manager, 4TU.ResearchData) for your help and support especially during the initial brainstorming stages of this site. Your deep understanding of our target user groups had been crucial in guiding our work.
  • Members of the Open Science Community Delft who took time to help us test the design prototype.
  • TUD’s Online Solutions, especially Inge and Noor, for turing our prototype into reality and advising on the various CMS issues.

Response from TU Delft on National Programme Open Science consultation document

Delft University of Technology was delighted to respond to the open consultation for the Dutch National Programme for Open Science 2030. The following summary was drawn from across the university, including researchers and teachers who form part of the university’s Open Science Community, and members of staff working on the university’s Open Science Programme.

Overall, there was satisfaction that a national programme was being developed, providing funding and impetus to make systematic changes to the practice of science within the Netherlands.

However, a number of comments were made indicating where the consultation document to have greater nuance, and awareness of the systematic pressures holding Open Science back.

a. Why three themes? By having three giant themes, the NPOS gives less space for new ideas to grow during the programme. It is logical to take up Open Access in an NPOS context; there is certainly much to be said for FAIR data (though software should also be included); but why Citizen Science should be a priority in NPOS context is unclear. This is not about the importance of Citizen Science as such. But it should not be a priority under the NPOS ‘Open Science’ umbrella. And Open Education would again be the obvious alternative. There should be space for innovation, eg., in open hardware

Photo of TU Delft Aula by Anant Chandra on Unsplash

b. Be wary of ‘subsidiarity’: Individual action by institutions is not enough. There is a need to enable effective knowledge exchange and sharing between stakeholders to avoid reinventing wheels. Dealing with issues such as digital sovereignty and values-based open access will require more than individual action – central leadership is required.

c. Embed Inclusiveness: There is a need to go beyond paying lip service to inclusion and accessibility. These are the barriers, pressures and perceived risks that keep researchers from adopting Open Science practices. This should be accompanied by an open governance structure, not just implementing NPOS via a top-down hierarchy. Such a governance structure should consider power dynamics between stakeholders and inequities that affect participation. NPOS should also be able to forge collaborative, engaged networks and
the skills and expertise required to help achieve the goals of Open Science

d. Pay closer attention to the strategic topics and systematic pressures that influence Open Science. Specifically:

  • Links between Open Science and other major strategic themes, such as Knowledge Security
  • Systemic pressure and perceived risks that keep researchers from adopting Open Science Practices
  • Fundamental issues that influence concepts of openness, such as our relationship to big tech and the large publishers
  • The value of fundamental, blue-sky research that has less apparent links with direct societal impact
Photo by Fahrul Azmi on Unsplash

e. The open access section needs to be more forthright. The goal of open access must emphasise more the need for ‘cost-constrained’ open access. There should be much more done to encourage non-Gold forms of open access, eg national and international collaboration around Diamond OA. This only comes at the bottom of the document. Relatedly, the incentive system must be addressed. Because of this, moving to non-commercial publishers is less attractive to many, especially for young researchers who are still building their careers

f. Research Data: There are many good parts to this section. It would still benefit from broader discussion about how open data can be (E.g. if companies collaborate in and perhaps even co-fund research, what level of data confidentiality / IP ownership is justified?) Other specific topics that need attention in this section include: linked data initiatives (knowledge graphs); long-term archiving and storage of research data; FAIR education for Masters’ students; and a better appreciation of new types of career path needed in software and data

g. One of the key earlier discussions in the Netherlands has been the creation of an Open Knowledge Base for scholarly metadata. This is entirely missing. In general, the lack of focus on creating open infrastructures means that the room for libraries and other research support staff to engage and develop new open tools for open science is neglected.

Gridding through 2021

Author: Esther Plomp

tl;dr: Overview of the year for Esther Plomp.

After I saw the very comprehensive overview of the Turing Way on their year in the December newsletter I got inspired to write my own 2021 overview. Luckily, I already had some documentation lying around, as I started with ‘Gridding’ this year (thanks to a Tweet by Laura Rossi!). At the end of 2020 I read Magdalena Bak-Maier’s book ‘the Grid’, which encourages you to define priorities and goals for the long term. This could be work related goals, but also personal things. For example, my Twitter thread on books is something that resulted from this grid exercise, as I prioritised reading (or listening to) a book every week this year. While I did not reach all my set goals for this year, I think it is a useful tool to consider priorities and plan more realistically. I will therefore continue to use this in the future! 

January 

My 2021 started with coordinating the TU Delft/Leiden Data Carpentry workshop on learning to manage tabular data and beginning with programming using R. I started coordinating the TU Delft Carpentries in September 2020 and learned a lot about online workshop organisation. I also started discussions with our Carpentry instructors on how we could further improve the workshops. Several documents on how we run the Carpentry workshop at TU Delft are now available (such as information sheets on being a helper and on coordinating the workshops).

I also began my activities to reduce the PhD duration at the Faculty of Applied Sciences. Together with Ans van de Schaik from the Faculty Graduate School and Pascale Daran-Lapujade, the director of the Faculty Graduate School, we’re trying to increase awareness around the topic and throughout the year we managed to set up some practical tools. More to follow in 2022!

During the PIDapalooza21 festival I got to talk about the many different aspects of the analysis of human teeth in the ‘Name and describe your favourite collectible’ session. 

February

February was marked by two Open Science events: The Open Science Festival, of which I was a programme committee member and a session organiser, as well as the International Open Science Conference that normally takes place in Berlin. For the latter conferences I presented a poster on the Open Research Calendar, together with Alexandra Lautarescu and Bradley Kennedy from the Open Research Calendar.

In February I also started mentoring for both the Carpentries and the Open Life Science programme (OLS 3). The Open Life Science programme provided training and a lot of support in my mentor journey. Being a part of the programme has been a consistent part of my year, as a mentor and as a presenter/expert on Open Data. Midway 2021 the Faculty Graduate school approved OLS as a course that PhD candidates could follow for credits (OLS-4)! We are looking forward to continuing this partnership in 2022 for OLS-5. 

This year I was also involved in the CSCCE Community Champions meetings. I presented the TU Delft Data Champions initiative and shared our experiences in establishing the community. An outcome of these sessions are tip sheets that will be shared in 2022 on how you can start your own Champion Initiative. 

March 

I gave two workshops on Data Management. The first one was on Data Management Plans for the  Helis Academy. The second one on general Data Management was part of the SeaChanges meeting. 

I participated in two events organised by the Software Sustainability Institute

April

In April I was coordinating the TU Delft Software Carpentry Workshop and co-organising the Physical Samples session during the Research Data Alliance (RDA)’s 17th Plenary Meeting.

I wrote a guest blog post for ‘The Open Archaeobotanist’ and a scholarship reflection post on my Research Data Access & Preservation Association (RDAP) conference experiences. 

May 

May was a very busy month, with multiple workshops and events taking place!

June

The RDA/ESIP Physical Samples webinar series kicked off in June. The series started with sample management, with a focus on RSpace. In July the webinar was focused on persistent identifiers for reagents and materials (RRIDs). In October we invited several speakers from different disciplines to discuss interdisciplinary sample use. You can find more information about these activities in the 2020-2021 overview of the Physical Samples Interest Group.

As a member of Young Science in Transition I contributed to the YoungSiT symposium on Recognition and Rewards.

As part of the csv,conf,v6 birds of a feather session I contributed to a blog post on Tracking Impact and Measuring Success in Data Education Events.

By the end of June I coordinated my final Software Carpentry Workshop! 

July 

July was all about writing! I submitted a data paper on my isotopic research. Together with Emmy Tsang and Paula Martinez Lavanchy we wrote an overview of our efforts in taking the Carpentry Workshops online (currently still under review). 

I also taught spreadsheet management at another Data Carpentry workshop that was coordinated by Leiden University. 

August 

I attended the FSCI2021 event and followed the ‘Train-the-trainer’ course on Reproducibility for Everyone, as well as a course on Open Science assessment. Unfortunately, there are still no clear solutions for the evaluation of datasets, protocols and software.

As part of the Open Science in Practice Series 2021 I gave a presentation on the TU Delft Software Policy. I also attended some of the other presentations and hope to perhaps host a similar Open Science series at TU Delft as it is a great way to generate discussions around Open Science topics. Luckily, the Open Science Coffees from the TU Delft Open Science Community kicked off in September with a session on Code Review

In the months of August and September I took a beginner course on leadership. This course took place in person, which was a nice change of pace, and has helped me enormously with time management, setting priorities and asking for more feedback. 

September

This month was very exciting as I got to present the plans for an Open Science Team to the management team! The following months I worked on gathering team members from each department of the faculty, and on the next steps that the team can take. Around the same time we’re setting up a Publication Task Force together with the Library to address the increasing publishing costs and generate awareness around publishing more sustainably. More to follow in 2022! 

I presented ‘Data sharing is caring’ at the British Association for Biological Anthropology and Osteoarchaeology (BABAO) conference. I think presenting at existing disciplinary specific events is the most effective way to inform researchers about the latest Open Science developments.

I also wrote two blog posts this month. The first post was a collaboration on quality and the journal impact factor in research, together with Emmy Tsang and Antonio Schettino. The second blog post was a follow up on a post I wrote on publishing articles in 2021, but this time with a focus on data: Managing and Sharing Data in 2021.

During the OS FAIR conference I co-organised a Turing Way workshop on collaboration together with Turing Way community members Emma Karoune and Rachael Ainsworth

I also started following a drawing course by Scriberia, inspired by the Turing Way illustrations

October

In October I made several contributions to events and initiatives organised by others: 

  • As part of the SeaChanges workshop I co-organised another workshop together with Lane Atmore that introduced GitHub and Open Science practises. Many thanks to the SeaChanges early career researchers for participating so enthusiastically and being so generous with their feedback! A nice side effect of this workshop is that I now also have a semi up to date website
  • As part of the TU Delft Diversity week I co-organised an Ally Skills Workshop and helped Emmy Tsang to organise the Open Science Coffee on Diversity and Inclusion in Research, Technology and Design
  • As part of the Data Horror Week, an event around Halloween to increase awareness for data management, I wrote a blog about my PhD experiences. This was also partly inspired by a lack of use cases that I see in my work on PhD duration: there is not a lot of public experience sharing of negative experiences. I tried to contribute by writing the blog ‘PhD in 4, 5-6-7’. Many thanks to Lena Karvovskaya for the encouragement to write this blogpost!
  • I also updated my teaching materials for managing tabular data in Excel for the Data Carpentry that took place (25-26 October).

November

I was a bit too enthusiastic this month, deciding that I was going to write 500 words each day (blogs, articles etc, based on the novel writing month NaNoWriMo), as well as finish one drawing per day. While I did manage to do this, I recommend not tackling two challenges in the same month… 

Several events around the Turing Way took place this month. 

November was also a very busy month in terms of researcher requests. I reached the amount of requests that I had in 2020 (n = 186), with 26 requests in total this month (average is ~16). 

December

Originally intended as a quiet, catch-up month, December started with two fantastic conferences that I could not ignore: AIMOS2021 and FORCE2021. For AIMOS (the Association for Interdisciplinary Meta-research and Open Science) I submitted a discussion session on ‘Moving Open Science forward at the institutional/departmental level’ (summary blog post coming up in January!). For FORCE2021, a conference on the latest developments in scholarly communications,  I introduced The Turing Way in a lightning talk

Looking back at 2021 I’m very proud of what I managed to accomplish and set up despite primarily working from home and experiencing some general anxieties around the pandemic. I’m looking forward to working together with the wonderful people from the Faculty Open Science Team,  Publication Taskforce, Open Research Calendar, PhD duration, IsoArcH, YoungSiT, The Turing Way and Open Life Science programme in the upcoming year! 

Happy holidays! 🙂

Rethinking the Scaffolds of Open

Author: Emmy Tsang

tl;dr1: Research libraries need to re-evaluate how we are contributing to our knowledge ecosystem.

Shifting roles of research libraries

Libraries have traditionally had an important role in shaping the knowledge ecosystem: the library’s collection (books, journal subscriptions, heritage artefacts) and services (e.g. the library catalogue and its search functionalities, inter-library loan systems) helped users find the information they need. These services and assets, in turn, determined a large part of what scholars read and build their research and teaching upon. 

Fast forward to today, in response to the ideals of “open science”, academic libraries not only supports scholars in accessing and discovering knowledge, but also in producing and sharing it. For example, negotiating publishing and subscription deals with commercial publishers, and running research data repositories and providing research data management training. These services and infrastructure are established to enable researchers and teachers to share their research and educational output more widely and in more diverse forms, increasing the impact of the university’s work and encouraging collaborations and knowledge exchange between more academics worldwide.

The quest for “open”

So, is science more open? Funders’ and institutions’ commitment to open access has led to a new business model where commercial publishers can charge $10000+ to publish an open-access article. Scholars from outside of Europe and North America already have a harder time publishing in so-called “prestigious journals”. These high publishing fees imposed by commercial publishers only served to exclude these groups in knowledge production further. There is also a push for broader use of data management plans and all data to be published. International alliances and technology companies build infrastructure for the containerisation of research code and collaborative software development. All while large parts of the world struggle with having stable internet access, let alone the resources to access these infrastructures or training in data management and publication. The practise of open science intends to facilitate collaboration and knowledge sharing. Yet, because it has so far fallen short of recognising and addressing the systemic exclusionary and marginalisation issues2, most current open science efforts “unintentionally” widened the divides in research and further excluded those excluded from scholarly discourses.

At the same time, it is ironic that with our advanced technology, privileges and wealth, researchers in the Global North have much less control over how our research output is shared, consumed, discovered and evaluated than our counterparts in the Global South. Because of the failure of the universities in the Global North to work collaboratively on shared infrastructure, our researchers and libraries are left in thrall to the power wielded by commercial companies. These companies are profit-driven, meaning not only do they not prioritise serving the marginalised, we, as users, have little oversight, control or negotiation power over how their products develop. 

Towards agency and equitable participation

Libraries urgently need to reflect on our role in shaping research and knowledge infrastructure: what is the future that we would like to help cultivate, and for that, what values and principles must we follow? Which voices should be amplified and heard in the infrastructure design and construction process? 

Why should all this matter to TU Delft and its Library? The TU Delft Strategic Framework 2018-24 detailed TU Delft’s vision of “contributing to solving global challenges” through our educational, research, and innovation activities. Solutions intended to address global challenges must be developed with stakeholders affected by these global challenges, or they risk becoming white elephants that fail to achieve any real impact, or worse, end up harming the communities they intended to help because of their ignorance of local needs and cultures. For stakeholders worldwide to effectively participate in co-developing interventions and solutions, TU Delft needs to contribute towards a knowledge infrastructure that centres marginalised voices, prioritises stakeholders over shareholders, and is designed for equitable participation.

To achieve this, we, the library and our community, need to have the power, resources and capacity to actively participate in the design of our knowledge infrastructure. We need to learn from the Global South, which has had much more experience with and knowledge in building open, shared and community-driven infrastructure. To (re)gain control over our scientific narrative and ensure that it serves our academics and partners worldwide, we need to invest in shared infrastructure. This is only possible if we start changing our behaviours.

People constructing scaffolds against against a blue-red sky
Photo by Igor Starkov from Pexels

A (rough) roadmap forward

Making changes in the right direction will first and foremost require outlining a vision: what are the qualities of knowledge infrastructure that fosters equitable participation and collaboration? Identifying these will help shape the principles that underlie our investments. We will need to understand the state of research infrastructure, nationally and internationally. 

It will also take capacity and knowledge building, and short- (e.g. assessing our current engagement with commercially and community-driven infrastructures, piloting months-long collaborations with community-driven projects, engaging nationally and internationally), medium- (e.g. hiring developers to contribute to shared, open-source infrastructure or engaging staff to contribute to community management), and long-term (e.g. redesigning repositories) investments. It will need buy-in from stakeholders across the university and from other national and international partners. 

Playing to our strengths

The TU Delft Library is well-positioned to drive change within our institution and nationally:

  • The Library has a historically important role in producing and disseminating knowledge and has been actively rethinking and experimenting with its roles in the digital age. Combined with our experience with driving change management programmes (e.g. the open science programme), we can design a step-wise approach towards changing the status quo.
  • Library staff have close working relationships with other teams, e.g. ICT, research integrity, graduate school, and scholars within TU Delft. We can engage with and galvanise diverse stakeholders to move this conversation forward within the university.
  • The Library is part of many national, European and international alliances. A fundamental change in the knowledge ecosystem will require a collective effort, and the Library can use its connections to influence and drive collective action.

This work naturally builds upon the library’s existing plans to transition into an active space for collaboration and knowledge exchange, with diverse stakeholders, including societal players. It should also be closely linked to the development of the new collection strategy. In addition, our mission here synergises with those of other ongoing, parallel initiatives within TU Delft, such as the Recognition and Rewards programme, the establishment of the Diversity and Inclusion Policy and Office, and the TU Delft Global Initiative. Involving these project teams and communities into the development of this work helps ensure that our roadmap considers the shared interest and vision of wider groups of stakeholders within and beyond the institute. 

We also benefit from growing conversations and research into this issue from all around the world: the work of Invest in Open, the Principles of Open Scholarly Infrastructure, the Global Sustainability Coalition of Open Science Services (SCOSS), the Knowledge Equity Lab, and many others have helped advance our collective understanding in this area, provided space and generated momentum for open discussions and amplified under-represented voices. We must participate in changing the status quo now to play an active role in shaping the future of knowledge and research. 

First steps

This blog post marks the start of reflections and discussions. In the coming months, we hope to approach the key stakeholders and partners that we have identified above to understand individual concerns and needs, further refine what we want to achieve, and build a shared vision towards an equitable and healthy knowledge infrastructure. The journey towards change will be difficult, but we are not alone – we invite you to help shape the conversations and actions forward. Book a chat with me to share your thoughts, or email me at f [dot] tsang [at] tudelft [dot] nl.  

Extended reading/viewing:

Footnotes:

1 Too long; didn’t read: https://en.wikipedia.org/wiki/Wikipedia:Too_long;_didn%27t_read 

2 We have picked examples that highlight geographic and socioeconomic inequities here, but these issues extend beyond geography, e.g. bropenscience, exclusion based on gender, physical abilities, thinking styles, etc.

The Turing Way Book Dash (Online)

Author: Esther Plomp

I co-organised the third online Turing Way book dash event (8-12 November), which may need some explaining:

  • The Turing Way is a ‘lightly opinionated’ online guide to reproducible data science. The book is collaboratively written using GitHub and Jupyter book, an effort led by Kirstie Whitaker and Malvika Sharan.
  • A book dash is normally a short event (1-2 days) where people come together to work on a book. The name book dash derives from a book sprint, where the time taken is longer than a dash (3-5 days). I say normally because pre-covid Turing Way Book Dashes were 2 day events that took place in person at the Alan Turing institute. While the Dash is more of a sprint in its current online form, the name stuck.
Drawing by Scriberia on the very start of the Turing Way, where Kirstie Withaker is sitting in a cafe in Berlin and is thinking of future projects where three concepts are central: bringing together people, inclusive work and open source.

The online version of the Book Dash consists of an onboarding session of ~1 hour in the week before the dash. During this onboarding session you have the opportunity to meet the other participants for the first time and set up your goals for the Book Dash. Setting up your goals early also allows you to collaborate with others on shared ideas. For example, Arielle proposed a chapter on roles in the research infrastructure, which sounded like something I could contribute to. As a result I adjusted my goals so that I could get the most out of the Book Dash. Another session before the week itself was an one hour introduction to GitHub. This session was aimed primarily at participants that were not yet familiar with the inner workings of GitHub, the platform where most of the contributions to the Turing Way take place.


During the Book Dash week there are four online sessions per day. Three of these sessions are ‘developmental’ or co-working sessions and one session is set up for a social discussion. The co-working sessions allow you to collaborate together on an idea in a breakout room, or to just work on your own ideas in a quiet room. In the middle of the week the social session focused on a ‘show and tell’ of anything that you wanted to ‘show and tell’ to the other Book Dash participants. I learned about restaurants in London, TiddlyWiki, grlc and Munchkin! See this Twitter thread for some more topics and images shared in the ‘show and tell’ session.

Drawing of Esther sitting in front of her laptop, looking at the screen where she is joined by several Turing Way Book Dash attendees. Drawing based on an image by Scriberia.

During the Book Dash I had a lot of opportunities to exchange ideas with people. Some of these discussions popped up randomly or naturally – almost as easy as normally happens during in person events. The intentional set up of the event and collaborative attitude of the participants allow for social interactions that are normally difficult to cultivate in online events. 

At the end of the Book Dash everyone shared their contributions in a ‘Share Out’ session which was open to anyone interested in learning more about the Turing Way. During the Share Out session we also saw all of the drawings made by the Scriberia artists (Matt/Katya) during the Book Dash!

Screenshot of the attendees of the first share out session, with nine individuals smiling for the zoomfie.

Exciting additions from this Book Dash include:

  • Batool, Andrea and Alejandro worked on improving the documentation of translation within the Community Handbook
  • Marta led a discussion on data visualisation and is writing a section about this topic together with Emanuelle
  • Arielle, Lena and myself worked on a new chapter on research infrastructure roles
  • Achintya worked on fixing the style of markdown chunks in the book, and reviewed many contributions by others throughout the week
  • Vicky worked on a revision of the section on Open Access
  • Lena and Jessica worked on a chapter on Peer Review
  • Jessica worked on a how-to review a GitHub Pull Request (PR) Guide
  • Reshama worked on a chapter on how to measure the impact of events
  • Emma and Maria worked on a chapter on sensitive data
  • Malvika improved the workflow for archiving the Turing Way using Zenodo
  • Faruk, Abel and Carlos worked on software citation section and recommendations for reusable code
  • Margaret worked on the metadata section
  • Nina and Ali worked on a chapter on reflective practices in ethical research, a topic which Nina also led a very interesting discussion session on
  • Ankur worked on a section about best practices around capturing and sharing analysis pipelines
  • Melissa updated the chapter on Tools for Remote Collaboration

If you would like to contribute to the Turing Way please get in touch or visit the contributing guidelines to learn how to start. You can also drop into the co-working calls on Monday or the bi-monthly Collaboration Café’s on the Wednesdays!

Image of the Data Steward role, where the Data Steward has the tools and knowledge to make sure that the data management of researchers is on track, so that they can safely continue their journey and connect to other researchers from different institutes (represented by different trains on connected train tracks on a bridge). Image by Scriberia.