Open yet everywhere in chains: Where next for open knowledge?
Presentation given at VOGIN-IP-Lezing, Public Library of Amsterdam, March 2023
Presentation given at VOGIN-IP-Lezing, Public Library of Amsterdam, March 2023
Authors: Maribel Barrera, Ashley Cryan, Cecile van Heukelom, Paula Martinez Lavanchy, Iulia Popescu, Madeleine de Smaele, Maaike Smit, Marta Teperek, Carlos Utrilla Guerrero, Yan Wang, Aleksandra Wilczynska
The year 2022 has been one of great achievements for the RDS team. Apart from the running existing services and business-as-usual activities, here’s an outline of our successes and accomplishments over the last year:
People responsible for this work:
People responsible for this work:
People responsible for this work:
TU Delft is currently writing a digital strategy for 2024-30. It’s due to be approved in spring 2023, but work is already beginning on its implementation.
The strategy has eight sections
Along with Robert van Bremeen from ICT, I am responsible for the research and innovation section. We have identified four key areas where the university’s approach to digital can have a positive impact on the practice of research. These followed discussions with those writing the Digital Strategy and workshops involving researchers and others from the university.
The workshops identified some broad themes. For example, the crucial importance of a trusted infrastructure for sharing data; the amount of unstructured data that was created by researchers but never reused; the importance of good training, and staff support; and the growing importance of software.
The themes were summarised as the four areas shown in the image below.
We then took this a step further, and identified both existing initiatives and new ones that are needed in order to turn the four areas into specific, actionable projects.
This draft diagram still needs some work, but it gives an indication of these initiatives.
This discussion is of course just the first step. The work now begins of turning these fine ideas into practice.
For this step, ICT and the Library will appoint a kwartiermaker to explore how this list of initiatives can be turned into a programme with specific projects under it. The programme currently has the name of the Research Hub.
The kwartiermaker will be discussing these initiatives with researchers, support staff, managers and others across the university – in conversations, meetings, workshops and other forums. The goal is to have a defined programme for the Research Hub, including a list of projects by mid 2023.
Author: Esther Plomp
tl;dr: Overview of 2022 for Esther Plomp.
For 2021 I wrote an extensive overview of what I did, which I found a helpful process. I also got motived to do this again thanks to Yanina and Danielle with their overviews. So here we go again!
Last January I started with my activities for the PhD duration team at the Faculty of Applied Science. The team consists of myself, Ans van Schaik (Faculty Graduate School) and Pascale Daran-Lapujade (director of the Faculty Graduate School). This year we set up a procedure to reduce the PhD duration (PhD-in-4 policy). This procedure required a communication plan (for which I gave an interview – as in house expert on taking too long on your PhD..).
I also gave a crash course on Open Science, together with Emmy Tsang (then Community Engagement manager at the TU Delft Library). This included a presentation on Open Data (made in R Markdown!).
The participants of the AIMOS discussion session wrote up their experiences in a blogpost ‘Moving Open Science forward at the institutional/departmental level’. I repeated this session in March for the Open Science Barcamp, which is summarized in another blog.
And I presented on Sharing Mortuary Data!
Last February I started with mentoring activities for the Carpentries and Open Life Science. This year I continued this for Open Life Science and co-mentored Adarsh Kalikadien, together with Maurits Kok from the Digital Competence Center. The Faculty of Applied Sciences continues to provide PhD candidates that participate in Open Life Science with credits (read more on intranet). Later this year I had the honour of co-mentoring Saranjeet Kaur Bhogal, with Fotis Psomopoulos.
In February we also started with our Faculty’s Publication Task Force. We had two main goals:
As part of my efforts for The Turing Way, more information on data articles was added. Many Turing Way Community members contributed, as well as Lora Armstrong (Data Steward CitG).
I was invited by the 3mE PhD council to talk about Metrics in academia, based on a blog that I co-wrote with Emmy Tsang and Antonio Schettino in 2021. In July I co-organised a similar session on Metrics in Academia with the Applied Science Faculty’s PhD council.
I had the honour to be one of the panellists of ‘The Turing Way Fireside Chat: Emergent Roles in Research Infrastructure & Technology’.
This month marked the official start of our Faculty’s Open Science Team! This team consists of at least a member of each of the Faculty’s departments (Flore Kruiswijk, Jean Marc Daran, Xuehang Wang, Sebastian Weingärtner, Sabrina Meindlhumer, Anton Akhmerov). This year we discussed how to increase awareness of Open Science and how to determine the focus of every department is for the upcoming years. Each of the team members engaged their department in a discussion or send out a survey in the months October-December. We will discuss the results with the Faculty management team in the next year.
I gave a lightening talk on The Turing Way for the Collaborations Workshop 2022 (save the date for 2023!).
Together with Zafer Öztürk, I discussed my experiences as a Data Steward for the Essentials 4 Data course. I wrote a summary of my Data Steward Journey in a blogpost.
I was on the FAIR data podcast and discussed several things FAIR (Findable, Accessible, Interoperable, Reusable) that I’m involved in with Rory Macneil. (Can recommend to reach out to Rory if you have anything FAIR to discuss!)
Together with Chris Stantis we organised an IsoArcH workshop on responsible data sharing.
Thanks to Valerie Aurora, I was able to follow the Ally Skills train-the-trainer workshop.
Our article on Taking the TU Delft Carpentries Workshops Online was published and was one of the most popular articles that month in JeSLIB!
I was involved in several presentations:
In June I gave a repeat of the Data Management Plan workshop for the DCC Spring Training Days.
I was involved as a Subject Matter Expert for Open Data for TOPS (Transform to Open Science).
And I presented the ‘Open Science Buffet’ poster for the Faculty of Applied Sciences Science Day.
Next to this, I followed a training on change management. This was very helpful in my efforts for the Open Science & PhD duration teams.
For the TU Delft BioDay I presented two posters on Open Science (the Buffet one mentioned earlier and one on the Open Life Science programme).
I was one of the panellist of the IFLA open data infrastructures panel organised by Emmy Tsang.
July was the month where I started to record the things that I am saying no to (since tracking things motivates me to actually work on them!). I also managed to get corona in August..
In August I learned how to use Quarto by making the materials of the RDM 101 course available online. I’m organising a faculty version of this course in March 2023.
I co-organised one of the workshops by The Turing Way for Carpentry Con: Git Good: Using GitHub for Collaboration in Open Open Source Communities. Many thanks to Anne Lee Steele, Hari Sood and Sophia Batchelor for this collaboration!
Together with Yan Wang we presented on Data Stewardship at TU Delft for a swissuniversities webinar.
Co-organised a session on FAIR discussions for the VU Open Science Festival, for which we’re currently writing a checklist article.
I described my career trajectory in an interview for the NWO magazine.
Presented a poster on the Removing Barriers to Reproducible Research work I did with Emma Karoune for the BABAO 2022 conference.
September was a busy article month:
Also, my husband defended his thesis!
I attended the NWO BioPhysics conference, where I coordinated the data/software workshop ‘Plan ahead: practical tools to make your data and software more FAIR’. We gave a similar workshop in May for NWOlife2022.
I gave an invited talk on Open Science for the Tools, Practices and Systems programme. The presentation was based on the blogpost : ‘Open Science should not be a hobby‘ (written in May).
I again participated in AcWriMo (write 500 words each day for blogs, articles etc, based on the novel writing month NaNoWriMo). (I learned from last year and did not include a drawing each day…)
I gave my first in person Ally Skills training for the How are You week. There may be more of that in the upcoming years!
November is also the month for the second The Turing Way Book Dash. This (currently mostly online) event takes place over four days in May and November. Participants contribute to The Turing Way during the event and join social discussions related to data science. I reviewed a lot of pull requests! Thanks to my AcWriMo I managed to write something on Cultural Change, Code Review for journals, updating the RDM checklist, and Open Peer Review.
I also met the team of Young Science in Transition in person for the first time!
I followed a course on policy writing. This has hopefully improved my writing.
The article I co-wrote with Emma Karoune, on Removing Barriers to Reproducible Research in Archaeology, got recommended!
I also finalised my review activities for swissuniversities’ Open Research Data calls.
November was again the busiest month for researcher requests (n=27), comparable to last year (n=26). In total I had 196 requests this year, a bit lower compared to 2021 (n=211), but more than 2020 (n = 186).
And I managed to figure out how Mastodon works (follow me @toothFAIRy@scholar.social)
I used December to recover from November, and round up some things for the year. This included updating the Open Science Support Website, which now has over 72 posts that answer frequently asked questions by researchers. Not all posts are finalised, and feedback is always welcome.
I’d also like to add a couple of things that I didn’t manage this year: Work on some of the older research data management survey data, reach inbox zero, write an article based on one of my thesis chapters, and get through my to-do list. I guess we have 2023 for that!
Happy New Year!
PS: check this Mastodon thread for my favourite books of 2022.
In his novel The Kingdom (link to WorldCat), which concerns the origin of the Biblical Gospels, French novelist Emmanuel Carrère makes a sudden detour into the difficulties of digital preservation:
In the more than twenty years that I’ve been using computers, everything I’ve written by hand is still in my possession, for example the notebooks I base this book on, while without exception everything I typed directly onto the screen has disappeared.
Of course, I made all kinds of backups, and backups of my backups, just like everyone said I should, but only the ones I printed out on paper have survived.
The others were saved on floppy disks, sticks, external drives—all supposedly much safer but ultimately obsolete one after the next—and are now as inaccessible as the tapes we listened to in our youth.(page 56)
In his book, The Universe: A Biography, Paul Murdin charts the history of the universe via the astronomers that have explored and researchers it.
In this quote here (page 55 of the book), he explains how the open data from the Sloan Digital Sky Survey (SDSS) helped nourish a community of researchers who could understand more about the development of the universe.
The Open Science Festival at Vrij Universiteit Amsterdam inspired many ideas. Here are a few that struck me (mainly from the strategic rather than research practice perspective)
5. And nothing will really change without changing the incentives – how do we reward and recognise all staff involved in (open) science? (Dutch approach – https://recognitionrewards.nl/)
Written by: Meta Keijzer-de Ruijter
Digitalisation offers a lot of opportunities for researchers to boost their research: automation of repetitive tasks, collection of more (complex) data, increase in computing capacity, re-use of data and code plus new ways to collaborate with colleagues within and outside of the research group.
At TU Delft, Library Research Data Services and ICT/Innovation are working closely together to define a vision and strategy to improve the support for developing digital competencies amongst the research community. In this process, we are looking at workshops and activities that are already being organised to assess their impact and possible improvements. With that aim in mind, a survey was developed to be sent to former participants of Data and Software Carpentry workshops. Our survey was based on the standard questions of the long-term impact survey that The Carpentries use, but we added questions on the actual usage of the tools taught and additional learning needs on the topics that were addressed in the workshops.
The survey was sent to 315 former participants of Data and Software Carpentry workshops held by TU Delft between 2018 and the summer of 2021. We received 45 responses. In addition, the feedback from both instructors/helpers and participants over the years was considered in this report.
Most of the respondents were PhD candidates (37 out 45) that attended the workshops during their first or second year (21 out of 37). Respondents came from all faculties, but the majority from Applied Sciences (8), Civil Engineering and Geosciences (6), Architecture and the Built Environment (6) and Mechanical, Maritime and Materials Engineering (6).
Most respondents provided feedback on the software carpentry workshops (30 of 45).
The top three takeaways from the carpentry workshops, according to the respondents, were:
The workshop(s) helped them to improve their efficiency, data analysis and data management skills.
It should be noted that eight respondents wrote that they are not using any of the tools. The main reason for that was that they use alternative tools that better match their practice or that are easier to use on an ad hoc basis.
Most of the respondents found programming with Python (partly or very) relevant. But there is a lot of debate on the level of Python being taught. Although it was communicated that the level is very basic beginner, a recurrent note (also in the surveys right after the Software Carpentry Workshops) was being made that the topics addressed are too basic and the pace of the course too slow for those who want to refresh. The reason they still attended was that in order to get the full Graduate School credits for this course, everyone should attend all parts of the carpentry. In an online setting this seemed to result in less engagement in the breakout rooms.
Figure 1 Response to the question ‘How relevant was the content of the Software Carpentry for your research’? (n=22).
In the Genomics carpentry the command line part was found most relevant to the participants, closely followed by data wrangling.
Figure 2 Response to the question ‘How relevant was the content of Data Carpentry Genomics for your research?'(n=3)
In this data carpentry the data analysis and visualization with R is most valued. The relevance (and eventual) use of OpenRefine was questioned. None of the respondents (n=5) in the long-term survey reported using OpenRefine in their current work.
Figure 3 Response to the question ‘How relevant was the content of Data Carpentry Social Sciences for your research?'(n=5)
In the survey, respondents were asked about their usage of the tools that were taught in the workshops. Did they start using the tools and to what extent, or did they quit using the tools or never even started using them. On each tool they were also asked if and how they would like to advance their skills.
The use of Unix was picked up by a good number of respondents, those that didn’t use Unix mentioned that it did not serve their purpose. Two respondents stated that they did not feel confident enough to use it. Additional materials for self-paced learning or help with how to apply it in their work might help them get started.
It appeared that the respondents that already used Python increased their usage from occasional to more frequent. Those who reported not using Python stated that they use an alternative tool.
Both frequent and occasional Python-users would like to improve their skills either by attending more advanced workshops, self-paced materials or talking with peers. Examples of topics they are interested in include data analysis, (big) data management, packaging, Jupyter Notebooks, libraries (including scikit and numba), handling large databases and automating tasks.
Only three people responded to the usage of R question, one of them started using R from that moment on, the other two report that they were using a different tool to do their data management. The respondent that used R said that additional training, learning materials and talking to peers would be appreciated to improve the skills.
Amongst the respondents the use of Git increased. Those who didn’t use the tool (7 respondents) said either that it didn’t fit their purpose (4 respondents) or that they did not feel confident enough to start using it (3 respondents). This last group would like access to additional learning materials, guided practice or consultation on how to apply Git in their own work.
Most of the Git users would love to improve their skills in various ways. Topics that are mentioned are dealing with complex files, comparing different versions of code, collaborative use of Git and building more confidence using Git.
None of the respondents (n=5) used OpenRefine after the workshop. Three of them stated that the tool doesn’t fit their purpose, while two respondents would like to have additional materials or consultation on how to apply it in their work.
The use of spreadsheets remained about the same after the workshop. And the respondents did not feel the need to improve their skills.
None of the respondents (n=3) had been using this prior to the workshop. After the workshop two of them started using it and they would like to learn more. No specific topics were mentioned.
The respondent that did not start using cloud computing stated that it did not fit his/her purpose.
Respondents could tick multiple boxes in this question about additional training needs. The top five training topics were:
Most respondents agreed that attending the carpentries had an impact on their work. They gained confidence in working with data, made their analysis more reproducible, were motivated to seek more knowledge about the tools, advanced their career, improved their research productivity and improved their coding practices.
The only topic where there was a wide spread of (dis)agreement was on the impact of the carpentry workshops on the professional recognition of their work.
Most respondents recommended or would recommend the carpentry workshops to their colleagues.
From the survey we learned that the carpentries fulfill an important role in the introduction of tools that help members of the research community to carry out their work more efficiently, but additional means and support are necessary. The translation of the carpentry materials to the daily practice can be challenging, causing some to quit or not even start using the tools. In the discussions with observers, helpers, and instructors of the software carpentry workshop we identified the need to link the carpentry topics more clearly to the research workflow, in order to increase the understanding of the ‘why’ we teach these topics and tools.
We (TU Delft) would like to thank all those who participated in the survey….
Author: Esther Plomp
This overview highlights resources that are available for TU Delft researchers in their Open Science journey. Please see the poster for the full visual representation with the links embedded.
Research Support TU Delft Library
Digital Competence Center (Data Managers)
Managing and Sharing Data in 2021
Policy: Research Data at TU Delft & Faculties
GitHub/GitLab (& 4TU.ResearchData/Zenodo integration)
Support from the Digital Competence Center (Research Software Engineers)
Training: Carpentries/Code Refinery
TU Delft Research Software Policy facilitates sharing of Research Software
Engagement is part of the TU Delft Core values (DIRECT)
‘Outreach and public engagement are core elements’ (TU Delft strategic priorities 2022)
Online discussion and presentation platforms such as the Virtual Science Forum
A new policy on Open Educational Resources will be ‘a starting to point to make Open Education the default approach for teaching at TU Delft’ – TU Delft Strategic Priorities 2022
TU Delft Open Access Fund (up to €2000 for gold open access)
Publishing deals (check the Journal Browser)
Support for sustainable publishing (SciPost)
How to publish Plan S compliant?
You share, we take care (Taverne)
‘There is no open science if science is not open to all’ (Whitaker and Guest 2020)
Open Science Community TU Delft (@OSCDelft)
Diversity and Inclusion at TU Delft
Electronic lab Notebooks (RSpace/eLABjournal)
‘Open science and education can play an important role in improving the quality of our work and stimulating the use of our knowledge and findings by others’ – TU Delft Recognition & Rewards Perspective 2021 – 2024
The Dutch position paper Room for everyone’s talent aims to recognise a wider range of academic contributions
Strategy Evaluation Protocol (SEP) – 2021-2027 has Open Science as a main assessment criteria
Open Hardware Community Delft (@DelftOpenHW)
TU Delft Open Science Programme 2020-2024
*The term Open Science Buffet has been coined by Christina Bergmann in 2019.