Tagged: Open Science
The Turing Way Book Dash at TU Delft
Authors: Tanya Yankelevich, Esther Plomp, Julien Colomb
The Turing Way is a ‘lightly opinionated’ online guide to reproducible, inclusive and ethical data science. The book is collaboratively written using GitHub and Jupyter book, an effort led by Kirstie Whitaker and Malvika Sharan.
As part of the Turing Way, we co-organised an event at the TU Delft library! This event was part of the Book Dash that is organised twice a year. During each Book Dash people come together to work on the Turing Way and add their contributions within a short period (hence why it is called a ‘dash’). A large part of the event takes place online, and this year there were in-person hubs in London at the Alan Turing Institute and at TU Delft.
At the TU Delft hub we had several people joining from the Dutch eScienceCenter as well as more internationally based that were interested in Open Hardware to work together to include a more extensive guide on Open Hardware in The Turing Way!
What did we work on?
- Tanya worked on including artists and civil society/community-based organisations as alternative ways for Open Communication of research process and research results. The subsections serve to start the conversation and would benefit from feedback of others with experience with both, artists and civil society/communities, and cases to demonstrate different perspectives.
- Azin got familiar with the Turing Way and had discussions with Barbara on ‘Code linting’.
- Lena worked on Research Data Repositories and Data Feminism (together with Maya, Gigi, Esther), and engaging the general public with art.
- Esther helped Luisa adding a contribution on how to link GitLab and Zenodo, and supported Tanya with her issue and Pull Request, and worked together with Lena on the Research Data Repositories draft. She also reviewed some Pull Requests (#2356), and was able to merge a Pull Request on removing duplication of information in the Open Data and Sensitive Data parts of the book (thanks to Johanna – another online attendee!).
- Carlos worked together with Anne and Alejandro (who joined online) on The Environmental Impact of Digital Research.
- The Open Hardware team (Angela, Santosh, Julien, Sacha, Moritz, Julieta, Nico) worked together on a new Open Source Hardware chapter, including two illustrations.
- Barbara and Pablo worked on an old Pull Request on error message management. During the Dash Barbara commented that “This more than anything makes me believe in Git”, as the pull request was already three years old!
- Julien also worked on data versioning via an old PR, and closed issue 310.
The Delft Hubbers demonstrated a fiery passion about Climate Change in our break discussions (yes, we did try to use the breaks to focus on things other than Book Dash work) and took extra care to follow the Code of Conduct. We promised to work with the university, such that all future events organised at the TU Delft will avoid the use of disposable cups and Nescafé machines… We had a great time getting to know each other in an informal atmosphere and testing the bounds of our biases through jokes. The hub attracted a bunch of Open Science enthusiasts from both the Netherlands and Germany, which inevitably led to a lot of collaboration ideas for the future and future-focused discussions.
The thematic focus (on Open Hardware) was a real success, allowing for specific networking and concrete collaborative work. Informal conversations did naturally sprout the idea to have another thematic focus for a future Book Dash in the Netherlands. A proposed theme is Citizen Science and a guide on “how to Citizen Science”. Thoughts?
Another year over!
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:
- What journals does our Faculty publish in?
- Raising awareness of (sustainable) Open Access options that researchers at our Faculty have
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:
- Research integrity starts with responsible Research Data Management: FAIR/Open Data at the TU Delft. A presentation for the RI seminar at Munster Technological University (MTU) organised by MTULibrary.
- ‘FAIR principles: designing and sharing training materials’for the Data Science and AI Educators’ Programme.
- Research Data Management presentation for the bachelor students of Clinical Technology, with Yasemin Türkyilmaz-van der Velden.
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:
- I coordinated the successful submission of ‘A manifesto for rewarding and recognising Team Infrastructure Roles’.
- The IsoArcH editorial ‘The IsoArcH initiative: Working towards an open and collaborative isotope data culture in bioarchaeology’ got published!It was an honour to co-lead this work with Kevin Salesse and a fantastic community of bioarchaeologists.
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.
Survey report on long-term impact of Carpentry workshops at TU Delft
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.
Demographics and Scope
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).
Main Takeaways from Carpentries
The top three takeaways from the carpentry workshops, according to the respondents, were:
- Using programming languages including R, Python, or the Command Line to automate repetitive tasks (16)
- Making code reusable (12)
- Using scripts and queries to manage large data sets (10)
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.
Relevance of the content
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).
Data Carpentry Genomics
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)
Data Carpentry Social Sciences
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)
Use of tools that are taught in the carpentries
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.
Additional training on research data management or software development
Respondents could tick multiple boxes in this question about additional training needs. The top five training topics were:
- Basic programming – 14 votes
- Modular code development – 13 votes
- RDM workflows for specific data types – 13 votes
- Software versioning, documentation and sharing – 11 votes
- Software testing – 10 votes
Impact of attending the carpentry workshops
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.
Recommendation of the Carpentry workshops
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.
And of course..
We (TU Delft) would like to thank all those who participated in the survey….
Open Science is like a buffet*: take what you can and what benefits you now – come back for more!
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
- Training (Research Data Management 101 & Open Science MOOC)
- Research Data Management website
- data refinement fund
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.
A Data Steward journey
Author: Esther Plomp
When I started as a Data Steward at the Faculty of Applied Sciences I attended the Essentials 4 Data Support course to learn more about research data management support. I was therefore happy to accept Eirini Zormpa’s invitation to discuss my Data Steward journey with the participants of the Essentials 4 Data Support course. Together with Zafer Öztürk from Twente University we shared our experiences during the data supporter panel on the 14th of April. This blog post is a summary of what I highlighted during the panel.
The Essentials 4 Data Support course is an introductory course about how to support researchers with the management and sharing of research data. The course materials are helpful to gain an overview of what research data management support entails. The course also provided an opportunity to link up with peers (such as Lena Karvovskaya) and meet experts (such as Petra Overveld).
In December 2018 I started as the Data Steward at the Faculty of Applied Sciences. In my first couple of months I had the privilege to be peer-mentored by Yasemin Türkyilmaz-van der Velden, who showed me the ropes of data management support. Initially, I had to get to know the position, the workings of the faculty, my new colleagues and the researchers I was now supporting.
In this first year I worked together with Yasemin on our Faculties Research Data Management Policies, based on the TU Delft Research Data Framework Policy. This was an arduous process, as we visited all departments of our faculties. The policy was discussed with many stakeholders, including PhD candidates. In the beginning of 2020 the Applied Sciences Policy on Research Data Management was officially released! Yasemin and I also worked together in the Electronic Lab Notebook pilot that took place at TU Delft resulting in TU Delft licences for RSpace and eLABjournal.
In 2019 I followed a Software Carpentry Workshop to learn basic programming skills so I could better support researchers with any software support questions. I later took the train-the-trainer course and became a Carpentries Instructor myself. By being a Carpentries instructor I can teach basic programming lessons set up by the Carpentries community. With the pandemic we had to shift these trainings online, and I coordinated these workshops for a year (2020-2021).
Over the years, I also increasingly supported researchers with Open Science questions. This is an aspect of the role that I very much enjoy and currently try to expand upon. My role differs somewhat from the other Data Stewards at TU Delft: we each have our own preferences and areas of expertise next to data support (such as software, ethics, or personal data). Another difference is my involvement in a side project focused on PhD duration. At TU Delft and at my faculty we try to reduce the amount of time that PhD candidates take to finish their PhD project. While the official duration for a Dutch PhD is four years, the majority of PhD candidates take much longer. This often means that they have to finish the project in their unpaid free time. As someone who has spent seven years on a PhD project I can say that finishing your PhD next to a full time job is no joke.
As a Data Steward I’m also a connection point in the university network. This allows me to address researcher’s questions myself or to connect them with the expert that they need.
- My position at the Faculty itself allows for close contact with researchers. Before the pandemic I regularly hopped between their offices to help them with any questions. At the Faculty I’m embedded in the support team where I work together with the Faculty Graduate School and the Information Coordinator. I’m in regular contact with project officers, managers and researchers from all levels at the faculty.
- As part of the Data Stewards team I meet the other Data Stewards once a week (virtually) and we communicate through Slack/Teams.
- I’m also in contact with colleagues from the Library and the Digital Competence Center, either through collaborative work or because they are the experts that can address questions from researchers.
- Sometimes I reach out to central experts from the Human Research Ethics Committee, the Privacy Team and ICT Security when needed.
Next to my activities as a Data Steward at TU Delft, I’m also involved in several other initiatives that are revolving around data and open research:
- Since 2020 I’ve been a contributor to The Turing Way. I have primarily written about Research Data Management and contributed a Data Steward case study.
- I am also part of the team that is behind the Open Research Calendar.
- Since 2021 I’m a mentor of the Open Life Science programme, which is now also offered for credits for the PhD candidates of my Faculty. In this 16 week mentor programme you will learn about open science practices and apply them practically to your own project.
- I’ve written an essay on the importance of physical samples in data management and I’m one of the co-chairs of the Research Data Alliance group on physical samples and collections.
- I’m the Open Research Ambassador and Secretary General of IsoArcH, a disciplinary specific data repository for isotope data.
Over the years I very much enjoyed writing blogs like this one, summarising my experiences of conferences, activities and learnings.
I very much enjoy the Data Steward role, for various reasons:
- I support researchers in making their research more transparent.
- I work with amazing colleagues and collaborators
- I meet new people interested in similar topics.
- I can continuously develop and learn new skills.
- I have a lot of autonomy over my working activities and schedule.
A lot of this is made possible by a supportive manager, and many individuals that I learned from along the way.
“Create the world you want, and fill it with the opportunities that matter to you.”– Alicia Keys
My tips for people just starting in a data support role:
- Accept that things can take more time than you originally anticipated. Starting in a new role will take some time to adjust and achieving cultural change in university processes will not happen overnight.
- The downside of being able to create your own opportunities is that there might be a lot of things that you want to do. Even if everything seems important or fun to do, it could mean that you will end up with too much on your plate. Sometimes it is good to say no to shiny opportunities.
- In whatever you do I would recommend you to not take the road alone and seek out others to collaborate with, or ask feedback from. Exchanging expertise and experience will not only be more efficient, it will make the road more worthwhile to walk.
Time to re-think the divide between academic and support staff
By Marta Teperek, Maria Cruz and Danny Kingsley
We are pleased to announce that our article “Time to re-think the divide between academic and support staff” has been just published: https://www.nature.com/articles/d41586-022-01081-8. The article speaks about the negative consequences of the divide between academic and professional support staff, and argues that this divide no longer makes sense as it is not conducive to a successful and effective research process.
By publishing this article, we hope to raise awareness about these problems, start discussions within the community and start identifying the steps which have to be taken to stop the divide. We would welcome your comments and reflections on the topic.
We also wanted to use this opportunity to express our gratitude to Jeff Love, Melanie Imming, Alastair Dunning and Shalini Kurapati for their crucial input and support throughout the process of conceiving this article. Their comments and reflections on the early drafts of the article, as well as the numerous constructive discussions we have had with them, were invaluable to us.
Finally, we also wanted to thank Connie Clare, Manuel Garcia, Hans de Jonge, Lena Karvovskaya, Esther Plomp, Diana Popa, Mark Schenk, Jeroen Sondervan, Emmy Tsang, Yasemin Turkyilmaz-van der Velden and Jose Urra for their comments and suggestions on an early draft of the manuscript.
Publishing a Data Article
Author: Esther Plomp. Contributions from Vicky Hellon, Achintya Rao, Yanina Bellini Saibene, and Lora Armstrong.
This blog post has been adapted from the Turing Way (The Turing Way Community, The Turing Way: A Handbook for Reproducible Data Science. 10.5281/zenodo.3233853) under a CC-BY 4.0 licence.
A Data Article (also known as a Data Paper/Note/Release, or Database article) is a publication that is focused on the description of a dataset. It uses the traditional journal article structure, but focuses on the data-collection and methodological aspects and generally not on the interpretation or discussion of the results. Data articles are in line with the FAIR principles, especially since most publishers will encourage you to share the data through a data repository. The benefit of a Data Article is that your output will be peer reviewed, something which is generally not the case for datasets that are archived on data repositories. It also facilitates recognition for datasets through research assessment procedures that are more traditionally focused on publication output. Publishing a data paper will therefore increase the visibility, credibility and usability of the data, as well as giving you credit as a data producer (The Turing Way Community 2022).
Options to publish a Data Article
Below you can find some journals that publish data articles. The costs information was collected in February 2022.
|Discipline||Publisher/Journal||Cost estimate||Deals for TU Delft|
|All||Experimental Results||£775 / €928||100% APC discount for TUD authors|
|All||Scientific Data||€1790||No, but eligible for the TU Delft OA Fund|
|All||Data in Brief||USD 500 / €440||100% APC discount for TUD authors|
|All||China Scientific Data||RMB 3000 / €416||No|
|All||Data Science Journal||£650 / €778||No, but eligible for the TU Delft OA Fund|
|All||Data||CHF 1400||100% APC discount for TUD authors|
|All||GigaScience||€1089||No, but eligible for the TU Delft OA Fund|
|All||Gigabyte||USD 350 / €308||No, but eligible for the TU Delft OA Fund|
|All||F1000Research||USD 800 / €704||No, but eligible for the TU Delft OA Fund|
|Archaeology||Journal of Open Archaeology Data||£100 / €120||No, but eligible for the TU Delft OA Fund|
|Archaeology||Open Quaternary||£300 / €359||No, but eligible for the TU Delft OA Fund|
|Chemistry||Journal of Cheminformatics||0||NA|
|Earth Sciences||Geoscience Data Journal||€1450||No, but eligible for the TU Delft OA Fund|
|Earth Sciences||Earth System Science Data||0||NA|
|Earth Sciences||Big Earth Data||€910||No, but eligible for the TU Delft OA Fund|
For more journals that offer the Data Article format you can see the ‘Data Article’ section in The Turing Way.
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:
- The BIH QUEST Center offers several awards, including an Open Data Award and an Open Data Reuse Award.
- The University of Surrey organised a showcase event on Open Research and Transparency, where researchers from any discipline could present their case studies in 20 minutes. The presentations were followed by an award ceremony and afterwards the case studies were listed on the website.
- The Health and Technology Open Research Awards involved scoring people on their Open Science practices as objectively as possible. This award benefitted from the UKRN primer on Open Research Awards.
- The University of Bristol and University of Groningen also awarded Open Research Awards.
- There is the Parasite Award for rigorous secondary data analysis.
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.
Useful links and resources
- Open Science communities (for example, TU Delft)
- See the Starter Kit
- Open Life Science programme
- Utrecht University Rewards and Recognition model: TRIPLE
- Utrecht University (NL): Open Science Monitor survey
- Academic job offers that mentioned open science
- Open Scholarship Grassroots Community Networks
- UK Reproducibility Network
- Surrey Open Research and Transparency Showcase
- Promoting Open Science: A holistic approach to changing behaviour
- Open Research Toolkit
- CARL Institutional Policy Template
- ODDPub: a text-mining algorithm to detect data sharing statements in biomedical publications by Riedel et al. (2020) (BIH QUEST Center, Charité – Universitätsmedizin Berlin)
- The Seven Deadly Sins of Psychology: A Manifesto for Reforming the Culture of Scientific Practice by Chris Chambers
- Science Fictions by Stuart Ritchie
- Bad Pharma by Ben Goldacre
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.
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.
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.
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 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.
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).
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.
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.