Nami Writes

(Speech Note) Why I nominated myself to be a board member for the Open Science Community Netherlands (OSC-NL)

2025-10-18T00:00:00Z

Below are my notes for the speech. They may be different from what I actually said. Nevertheless, I wanted to share.

Good afternoon, everyone, my fellow open science and scholarship enthusiasts.

It's special that we gathered here today to think together about the future of our grass-roots, bottom-up Open Science efforts in the Netherlands.

My name is Nami Sunami. I am a member of Open Science Community (OSC) Eindhoven. At the university, I work as a Data Steward.

I nominated myself to become a Board Member of OSC-NL because I want to give back to the Netherlands' Open Science Communities.

In 2019, 6 years ago, I came to the Netherlands for the first time to attend an Open Science-themed conference, hosted by the Society for Improvement of Psychological Science. Up to that time, I had been doing open science practices in my PhD in the US. But I always felt like I was alone, a bit lonely, doing these practices in my own bubble.

At the conference, I felt first-hand the power of the grass-roots community. I was surrounded by people who are passionate about improving how scholarship is done, fighting for freedom and equity for knowledge. I was no longer alone.

The experience changed my life. The Netherlands became the place that I want to be. The rest is history. I decided to come to the Netherlands, and now I'm standing here in front of you.

I feel grateful to be part of the Dutch Open Science effort, and I do hope that it's inspiring many people, like it did for me.

However, I also would like to acknowledge that Open Science is becoming more and more institutionalized rather than community based, top-down rather than bottom-up efforts. Institutions require researchers to do open science practices. Often it’s a good thing, but sometimes doing open science becomes just another checkbox-ticking activity. Top-down decision-makers may forget about bottom-up community voices. For me, the recent consultation process for the Open Science Infrastructure document was an unfortunate example of this.

Open Science and Scholarship should be about bottom-up. It should be about people, not about institutions. I want to support the community effort by working as a Board Member.

My community, OSC Eindhoven has potential to offer to the national Open Science effort. I would like to represent OSC Eindhoven by first energizing community members to speak up about Open Science. I will gather these voices and bring them to the national conversation.

At OSC Eindhoven, I am a core organizing member of the community. I closely collaborate with the community manager, Kristina Korshunova, within and beyond the community. We are doing meetups and co-teaching Open Science courses for PhD candidates.

I will leverage these engagements to represent OSC Eindhoven so that the members will feel they belong to the broader, bottom-up Open Science effort in the Netherlands and beyond.

Thank you.

Becoming a Data Steward (Speaker Notes at Social Psychology Seminar at the University of Delaware, 3 September 2025)

2025-10-15T00:00:00Z

I gave a talk at Social Psychology Seminar at the University of Delaware on 3 September 2025. I talked about my career trajectory from my PhD to becoming a Data Steward.

Below are my speaker notes that I prepared. The actual talk may have deviated from what I wrote here.

Just wanted to share. So here it goes.

Introduction to the talk #

It's great to be back at the Social Psychology Seminar.

Last time I was here, I presented about my dissertation.

First, a little bit about me. My name is Nami. My pronouns are he/him. I'm from Japan, and I live in the Netherlands.

Now, I work as a Data Steward at a university called Eindhoven University of Technology.

Data Steward? You may be wondering—what is it? The Data Steward's job is to help researchers manage their data better. More practically, I advise researchers on how to best manage data and code, and share them responsibly.

For me, it's about the way towards creating a more open and better world. The passion that I found early in my life during my undergraduate years.

I'd like to go back there and begin my story.

Philippines and feeling inequality in research and education community #

My journey to open science started back then I was in college, in the Philippines.

I was studying psychology, and I liked the subject. Just like a proper future graduate student, I used to spend a lot of time studying in the library.

The textbooks at the library described many interesting studies, mostly from developed countries, like the United States or Europe.

I was not satisfied with just reading summaries in those textbooks—I wanted to read the original published manuscript in journals, so that I know more details about the study.

One day, I learned that I could access online journals at the computers at the library. So I took notes of the published studies that I want to access. And went to the computer floor.

The floor was access controlled, so I had to leave my student ID at the desk. I got seated in front of an outdated computer, and started to search for the published articles.

But I could not find any of them in the database.

Later, I learned that my university only had money to afford journals in nursing, which was the most popular program at that time. What about psychology journals? No access.

Disappointed with the journal subscription situation at my university, I went home and started to search for the papers online.

And lo and behold, I was able to find many of the articles freely online. Many were uploaded on the researchers own website. Probably they were violating the terms with the publishers. But I liked the act of civil disobedience.

Through my experience, I realized two things. First is the power of openness. We can make the world a better place by sharing knowledge openly, especially with those who don't have access. Secondly, I realized the massive inequality between the countries in the world. Students and researchers in the rich institutions do not have any problem accessing information, but those in the Global South are deprived of access.

My journey to Open Science started that time.

Doing PhD research, pre-registration, and meeting the Netherlands #

I wanted to study in the US. The materials that I was reading often came from the US, and I thought the US was the place to be.

So after college, I went on getting my master's in psychology at Western Illinois University in Illinois.

Then, I came to the University of Delaware to work with Lisa.

Before coming to Delaware, I already had some interests in Open Science, such as uploading my conference poster to the Open Science Framework.

But it was at the UD where I grew my interest in doing open science I did. I want to thank Lisa for supporting me.

I planned preregistration studies. It was a lot of work because neither of us knew what it should be. But it was fun to figure out.

Eventually, we were able to do several pre-registration studies together.

That said, I felt like we were a bit isolated. Are there others who are also passionate about open science?

Around that time, I learned about the Society for Improvement of Psychological Science, the society whose goal is to improve how to do scholarship in psychology.

It was 2019, and the conference was in the Netherlands, in the city of Rotterdam. I only knew the Netherlands as the country of tulip and cheese at that time. I obtained funding for the summer, and traveled to the Netherlands.

Falling in love personally #

And I arrived in Amsterdam, and I was impressed right away about the independence from cars. I could ride a high-speed train from the airport to Rotterdam. Not a metro, not a tram, but an actual train people use to commute from Amsterdam to Rotterdam. How cool is that?

As a Japanese I felt a lot of affinity with the collective love and obsession with the trains

Many people already know that the Netherlands has a great bike infrastructure. And indeed, the infrastructure is great. There are protected bike paths everywhere. And remember—do not ever walk on the bike path. You will be in danger! Please don't ask how I found out.

The trains and bike paths were very impressive to see. But, at its core, it's about attention and care for people in public places. The streets have benches where people can sit. Car traffic is separated from pedestrian traffic. People see other people riding the trains, bikes, and, of course, walking around. All these designs facilitate a sense of being together in the society. In the US, we were usually stuck in our car, looking at each other as big metal objects, not as humans.

I fell in love with the country pretty quickly.

Falling in love professionally #

The public spaces in the Netherlands are great, but to be honest, I did not have much time to fully experience them because I spent time mostly at the conference venue.

But, I did not regret it because I had a great time at the conference. It was the experience that I was looking for--connecting with people who are passionate about improving how we do research.

In addition, I also liked the European academic system that treats PhD graduate students as workers, not as just students. During the lunch, I had an opportunity to speak with other graduate students. I shared that PhD graduate students in the US do not have 12-month pay and paid leaves. Many European colleagues were surprised to hear that.

The confusion and horror in their faces

All in all, it's clear to me that I want to be in this environment both personally and professionally, and I want to live in it and support it.

That's why I decided to move to the Netherlands. It was still 2019. Long before defending my dissertation.

Finishing dissertation, job search, dark times, and reclaiming my purpose #

I came back from the Netherlands, and I started to work towards my dissertation. At that time, I was aiming to graduate in 2020.

However, the COVID pandemic happened in 2020, and I had to delay my graduation to 2021.

A year later, I graduated.

But in that year, I was not ready to move to the Netherlands yet. I just graduated. The world was still in a pandemic mode. And I did not have much funding to move.

So I worked at a non-profit organization called Tech Impact for a year as a Data Science Fellow.

Toward the end of my fellowship, I was applying for jobs in the Netherlands. But I did not get any responses. I tried various kinds of jobs, from teaching positions at universities to data analyst positions at industry. But they did not go well.

Even to Booking.com. Looking back, it may not have been a wise choice.

Moving nevertheless, amid the housing crisis #

I applied to various types of jobs in the Netherlands, but I could not get an offer. Nevertheless, I decided to move. After all, it was my intention to move, rain, or shine.

Warning—not for everyone.

The first question when moving is—where to live?

I was looking into how to find housing in the Netherlands. It proved to be a difficult process. There was not been enough housing units, so the competition was (and still is) really high. To win the competition, the potential renters need to submit supporting documents, such as certificate of employment, income statements, a letter of good conduct from a previous landlord, and even a personal letter of motivation explaining the background.

Doing all of this from abroad in the US? It was an impossible task.

Around this time, I reached out to Jan, who lives in Amsterdam. Jan was a visiting PhD student at the University of Delaware, working with Mike Kuhlman. Gladly, he offered me and my wife to rent his apartment for one months, while he and his partner are on vacation.

The offer gave us courage. We had a place to stay for one month, while looking for an apartment.

In October 2022, my wife, our cat, and I are in Schiphol Airport in Amsterdam. Five suitcases. One of them was for the cat.

Still no job in the Netherlands #

I continued to apply various types of jobs in the Netherlands, but I could not get an offer.

Application after application, I was getting rejection letter.

Many people did wish me luck for future endeavors in the rejection letters!

But I was losing faith in me.

I doubted my decision--perhaps, the Netherlands was not the country for me.

I doubted myself--am I not good enough?

Without work, the balance in the bank account was decreasing.

I had only one month. No house, no work, and no one else to lean on.

I felt like I was in a dark place.

The mysterious job posting #

One chilly morning in Amsterdam, I saw a job posting. The job description was nothing like what I saw before. It talked about open science, research data management, and overall doing research better. I have never heard of data steward.

Until that point, my resume was very technical with mentions about programming languages and statistical skills. The Data Steward Job? It did not require any of that.

I thought, it’s going to require a lot of rewrite on my resume. But I saw something about this posting. Open science, doing science better—they all aligned with my values. And my origin goal of why I wanted to move to the Netherlands. This was it. I decided to overhaul my resume. And sent in my application.

And glad that I did.

Within days, I received a call from the office assistant. I was invited for the first interview, second interview, and I got an offer. It happened so quickly. It was December.

Oh and I got Covid right after. So I did not have much time to celebrate. Oh well. But it was worth job.

Data steward #

The job of a Research Data Steward is to help researchers manage research data well. It involves many things.

Data stewards can support ethics applications, especially when data come from human participants. In EU, handling personal data requires extra care thanks to General Data Protection Regulation, GDPR.

Data steward can give advice on where to best store data.

Exchanging data between collaborating universities requires data agreements. Data stewards can support along with that.

But most importantly for me, a data steward can help researchers to share their research openly, as much as possible. So that the impact of the research can go beyond the publication.

After all, the research is not all about publication. All the steps count. I'm happy that I can help people to be open to share their work. At universities, we are funded by public money. We have a responsibility to make results as accessible as possible to the world.

Things I'd do differently #

I have two things that I'd do differently.

First, I'd have spent more time focusing on finding my purpose. The time that I spent crafting resumes for travel companies (such as Booking.com) could have been spent understanding myself and what I really wanted in my life.

Two, I was reaching out to researchers in the Netherlands from the US. And most of them were really welcoming to have a conversation online. In one call, a senior researcher said that he would be happy to welcome me as a visiting researcher if I was still in the PhD program since it's a common thing to do for them. I thought I could have applied.

Continuing my journey to find my purpose #

I was not sure how to prepare for this seminar. Where to start? Should I talk about the details about the work of a data steward? Should I be the salesperson of the Netherlands? Should I follow the suit of the NWO, Dutch equivalent of NSF, to recruit academics from abroad?

One thing that I'm sure is to tell a story with a message.

And the message is this:

Nothing in my career journey makes sense, except in the light of finding my purpose, my voice.

Right now, my purpose is to advance equitable research communities from the perspective of open science.

It's a continuous struggle to listen to my voice. My voice can be sometimes very soft, also in the real life. I can barely hear it.

I'm glad that I accepted this opportunity to talk with you today. I was able to reflect, and put together the pieces. I now feel that I understand myself better.

Thank-you's #

Special thanks to Yanzi and Maggie for organizing the talk.

Thank you, Lisa, for the mentorship during my PhD journey.

And thanks to everyone who came in today.

Lastly, I want to thank Mike Kuhlman, who is no longer with us. He was the first person who keenly pointed out that I liked writing code. That affirmed my voice. I continue my journey advocating for open-source software.

The 80th End of War in Japan

2025-08-15T00:00:00Z

Eighty years ago today, many Japanese people were in front of a radio, waiting for a special announcement from Emperor Hirohito. The broadcast was announced the day before, and people were told not to miss it.

At noon, the broadcast started. The emperor announced that Japan was surrendering in the war. People realized that the war was ending at last.

My grandfather was 29 years old back then. I wonder what he thought about the broadcast.

He went to war several times as a logistics officer in China. He never mentioned his experience with war to people around him, even to his daughter who is my mother.

I wanted to hear his experience about the war. So one day, I brought my laptop with maps and asked him where he was and what his experience was. He told me that he departed from Kure in Japan and landed to Qingdao in China. But, he did not want to continue. Well, rather, he could not—because he was overwhelmed by the sadness. I don't know what he was remembering. But, I could see the scars of war through his eyes.

He passed away some years ago at the age of 104. I still ask myself, should I have asked more about his experience? That would have been emotional burden to him. But only way that I can know was from him. Who bears the emotional burden of telling stories about the war?

Today is 15 August 2025. Oji-chan, war is still happening around the world. I carry your scars with me. I want to make steps to bring peace to the world for you.

Getting Certified as a Linux System Administrator

2025-08-14T00:00:00Z

I'm now certified as a Linux System Administrator (Linux Foundation Certified System Administrator; LFCS). This certificate means that I can administer Linux systems 🐧.

I've been studying for it for 5 months. It was a long way!

Overall, it was worth my effort. Along the way, I deepened my passion for open source, especially because of its potential to create a more humane, equitable, and kinder world.

Why I took this Exam #

Professional reason: Stewarding data better #

Open source is important. As a Data Steward, I prefer recommending open-source tooling because of its transparency. When using open-source tools, the source code tells exactly how the data is treated. On the other hand, closed-source software demands trust. For example, when storing files on OneDrive, we need to trust Microsoft to treat it well. If it's open-source, we can look at the code and examine whether we can trust it.

Personal reason: Managing my data better #

I used to store my own data in cloud services, such as iCloud and Google Drive. Over the years, I've decided that this is not the right thing for me because I'm giving up ownership of my data. It's also not right for the world, because giving data to a Big Tech means letting them gain power. Some may say, "I don't have anything to hide." But it's not about that. Data is power, and we should not let big tech or anyone hoard power (no kings!).

So, I've set up a Linux home server to store data about my personal life. I use PhotoPrism to manage my photos and NextCloud to manage documents. (I'm writing this blog post using Vimwiki saved on NextCloud). In addition, I store music, movies, and TV shows on my home server so that no streaming services will track my viewing history.

Managing a home server is a lot of work. But I like it as a hobby.

Learning about Linux can be defending ourselves from Big Tech, dictators, and oligarchy. Penguins are strong.

How I studied for the exam #

First attempt #

First I followed the Linux Foundation's courses:

Linux for Cloud Technicians Essentials (LFS203)
Linux System Administration Essentials (LFS207)

I found these courses very dry and involved a lot of reading. The lab exercises were in PDF document, which is ok. But I'd have preferred to do them in a Linux shell. After all, the exam is performance-based.

I did my first exam after finishing these courses. But it was not a success. I scored 65%, just 2% short of the passing score of 67%.

Second attempt #

To prepare for the retake, I took Udemy's course Linux Foundation Certified Systems Administrator, LFCS, using a free trial. The course came with Kodekloud labs and 4 practice exams that I can use to test my skills on the browser. I liked it since I could get immediate feedback there.

I studied for 2 weeks more, and I passed the exam!

Reflections #

Childhood dreams #

After passing the exam, I remembered the time when I was 13 years old. I liked computers, and I bought a book for the "System Administrator" exam in Japan. But I remember I found the topics boring, and I ended up not taking the exam.

I got curious—why did I enjoy studying for a System Administrator exam now?

I found the previous exam questions, and I think I understand why. The exam was a multiple-choice on general knowledge about IT, but not much about Linux, the penguins.

I guess I unknowingly realized my childhood dream. I did not know about open-source software or open science. Most importantly, I did not realize the inequality that exists in the world. Being more competent in open tools is now directly tied to my life work towards creating a more kind world. So that way, I also realize my current dream. By loving penguins.

Legacy of open source #

Learning about Linux, I immersed myself in the world of open-source software. It's mind-blowing that countless people have spent their time to contribute code that support most of the IT infrastructure in the world.

Sometimes, I read the manual pages (man page). There you can see the authors. I got curious and looked up some of them. For some tools, I found that the original authors have already passed away. But their code lives on—powering the Linux machines around the world.

What's next? #

The certification exam was part of the Cloud Engineer Course that I'm following (as part of my professional development at my work). The next step is a certification for Kubernetes Administrator. I may want to create a Kubernetes cluster at home, maybe using multiple Raspberry Pi's. Stay tuned!

Survey Says: Open Science!

2025-05-22T00:00:00Z

tl;dr #

I joined the Open Science Retreat 2025 in Beatenberg, Switzerland. I went there with a little wish to create an Open Science-themed pub quiz. Little did I know what a great adventure it would be to undertake with my teammates.

Proposing to Create a Pub Quiz #

Open Science Retreat is an unconference, a conference without a set agenda. Participants propose topics on the spot. Joining this year's edition, I suggested creating a pub quiz about Open Science. We need more ways to learn about Open Science while having fun, after all. Below is the slide that I created to pitch my idea.

👋 Shoutout to Student Initiative for Open Science Amsterdam for sharing me the slide decks for their pub quiz

From a Pub Quiz to a "Family Feud" Game #

Melanie Imming, Mariana Menegon, and later Jazelle Carillo, joined the group with me. And I was not prepared for the good ride. Melanie pointed out that a pub quiz question always has a correct answer. But the world of Open Science is full of "it depends". For example, when asked about the most important value in Open Science, some may answer reproducibility, and others may say knowledge equity (Fecher & Friesike, 2014). Both of these answers are correct as being voices in the community. We wanted a game that can celebrate different perspectives and facilitate conversations about Open Science.

We found the format of Family Feud suitable. In Family Feud, the host does a survey beforehand to a group of 100 respondents (for example, "Name a house that you never want to be in"). The host uses the survey responses to make the list of popular answers. Then, the contestants try to guess the popular answers during the game (for example, "Haunted House"). We thought we can use this format to highlight different voices in the Open Science community.

Photo: Digital Research Academy

Creating Survey Says: Open Science! #

We decided to play the game on the last night of the retreat with the retreat participants. So, we only had about 2.5 days to prepare. We named the game, "Survey Says: Open Science!" and started preparing.

Creating Survey Questions #

The first task was to create survey questions. We came up with the following questions:

Open Science is driven by _________
In order to make Science more open, we need to reward _________
The most hurtful consequence of Gold Open Access is _________
I like my community to be _________
_________ is the most important value for Open Science
Please talk _________ to me!
University rankings are good for _________
Open Science, just Science _________
Citizens play the role of _________ in Science

Melanie created a Typeform survey, and we asked people to answer it:

In the short time, we received 77 responses. Thank you to those who responded to the survey!

Grouping and Coding Survey Answers #

We could not use the survey responses as-is because people can write in answers in slightly different ways. The challenge was to determine how to group answers together. We wanted to avoid having too many groups, but also making answers too generic. For example, for the question, "In order to make science more open, we need to reward __(blank)__", people answered "data sharing" and "code sharing". They are both about Open Science practices, so we grouped them into a bigger category, "OS practices (data / code sharing, preregistration)".

There is no one way to group and code survey answers. I believe if others try to code the same data, there may be other ways to group. That's an opportunity to enjoy the game with the same survey responses but different groupings.

Designing for the Day - Bidding System #

Usually, Family Feud is a game for two groups (two families) with 5 contestants each. The game begins with a face-off between the 2 groups. There were around 40 retreat attendees (excluding the Survey Says team). We wanted to let everyone in the retreat to be able to participate in the game. To achieve this goal, we divided the attendees into 8 groups with 5 members each and set up a bidding system.

At the start of the game, all groups received virtual money—90 QPF (Question Processing Fee) to use for the bidding. As the round began, the host revealed one survey question. The groups then decided how much to bid for the round. Once the bids were placed, the group with the highest bid guessed the answers to the survey question. The correct guesses were revealed on the screen, while every wrong guess received a strike. If the group got 3 strikes, their turn ended, and the team with the next highest bid got their chance to guess a popular answer. The group that guessed three answers for the survey question won the round.

Hosting the Game #

We recruited Gorka González as a host of the game, and he did a wonderful job as a host. (Thanks Gorka!). You can see how fun it was in the pictures below.

Open for Possibilities #

I did not expect developing a Family Feud game or having such fun together. Then I realized that it was an Open Science Retreat after all. We were creating a culture of openness—for new ideas, for collaborating, and for having a good time together.

Materials Available Online #

Interested in learning more? Do you want to host your own game? Check out our ResearchEquals Module for all the materials. The source code of the webapp is available on my GitHub repo.

Grant application can take over your life

2025-04-08T00:00:00Z

InfraCoalition Grant Application #

Grant writing takes a lot of time and energy. It can consume your life. Even when you are taking a much-needed break, you might feel, "You should be writing".

I have forgotten about this feeling for a while. When I was doing PhD, I felt this a lot. My challenge was to manage that feeling—that I had to convince myself that taking breaks from writing is ok. Although I've never found a way to successfully eliminate this feeling, I have learned to accept that it's ok not to work all the time.

But with a set deadline, it was hard not to feel that way.

In the past weeks, I found my life consumed by the grant application. I wanted to write about my learning.

InfraCoalition View #

The grant proposal is called InfraCoalition. The proposal is for the Open Science Netherlands Infrastructure Call. In the proposal, we the applicants want to transform an existing publishing platform (ResearchEquals) to an open infrastructure that does not depend on Big Tech, bringing power back to the research communities.

The current research infrastructures are mostly centralized. The business models of Pure, Scopus, and most publishers focus on bringing researchers to one place to their platform. Scientific power is being centralized. Worse, they will track your behavior on the platform and sell them for extra profit.

The centralization is problematic since it does not reflect the decentralized nature of academia. The academia is inherently decentralized and federated. Universities are independent. But, they collectively advance the human knowledge together.

It's time for the research communities to reclaim autonomy in the research infrastructure. I believe InfraCoalition can help with that.

Writing Process and Learning #

The writing process of the grant is always hard, and InfraCoalition is not an exception.

We started with a great pre-proposal spearheaded by Chris Hartgerink. The proposal was received well, reviewers gave positive advice to submit a full proposal.

In the main proposal writing phase, I took the main driver's seat. It was my first time to coordinate a coalition of a six.

Chris helped me a lot on this. Below were some points of learning for me.

1. Trust that everyone is there to help you #

In the first meeting, I was too focused on leading a perfect meeting as a chair. My focus was controlling the meeting, by keeping the agenda and timeline. But the reality is that everyone is there to help you during the meeting. In the end, everyone wants a successful meeting.

Of course, keeping the discussion on track is important. But the more important task is to make it easy for members to contribute. One way to do so is to state your opinion as a chair.

2. Use your position as a starting point #

In one meeting, I wanted our group to decide whether to welcome a new member. I thought there was no issue in doing so. But, I did not want to bias anyone in the room. So, I introduced the topic neutrally without my position and asked the members for their opinions.

I think that may have created a moment of confusion, whether I had doubts, and what reasons. Also, being the first one to express an opinion in a group is scary. As a chair, I could have taken the bullet and lifted the burden from others.

Sometimes, my Japanese background can get in the way of stating my opinion directly and clearly. But, clarity is important in cross-cultural communication. After all, no one can read my mind (I hope).

3. Propose a due date when requesting an action #

When requesting information or action (for example, to review something), it's better to ask for a date. (Can you do this by Date X?) This is not for micromanaging. Rather, asking for a timeline helps the mutual planning. The person who will be completing the task may realize that the timeline is too tight. Often, we think that we have all the time in the world, especially working on an exciting project. If I have a clear due date, I can evaluate whether it works with my other obligations.

When asking for a date, it's best to be specific. Hearing "by 10 a.m. on Friday", I know exactly by when I need to do the task. If I hear "by the next week", I'm confused if the task should be completed by next Monday, or by 5 p.m. next Friday.

4. Focus on co-creation #

Working on a material together is a challenge. You may create something. And someone else will completely re-write it. For example, a PhD supervisor can re-write paragraphs in the PhD candidate's work.

Having your writing overwritten by your collaborator may make you feel like you wasted your time. The important thing here is that we should separate the text and the idea in it. The text may be deleted or altered. But, the idea you expressed in the text could have helped your collaborator to come up with the re-write. That way, both parties are co-creating.

5. Call for a vote to check the opinion as a group #

In a group meeting, it's often unclear whether everyone agrees on a topic. I once asked in the room, "Does everyone agree with this?". Some reacted by nodding, others via Teams Emoji, another said something, but it was still hard for me to know if we reached a consensus. In cases like this, I could have called a vote by raising hands. For example, I could have said, "I want to take a vote to check our position on this topic as a group. Can you raise your hand if you agree?".

6. Make sure that everyone's voices are included #

The beauty of working as a group is that we have different people with different ideas, backgrounds, and personalities. So, we will always have differences in speaking time—some members talk more than others. The chair's responsibility here is to make sure that everyone had a chance to express their opinion. The chair can say something like, "I want to make sure that everyone had a chance to express their opinion. Is there anyone who hasn't spoken up and wants to contribute?"

Proposal submitted #

Overall, it was a good learning experience for me to lead the group. I thank all the InfraCoalition members for staying with the ride. Also, special thanks to Chris for coaching me throughout the process.

We submitted our proposal on 11 April 2025. I'm looking forward to receiving feedback from the reviewers (hopefully in August or so)!

Join a Union to Fight Against Fascism

2025-03-12T00:00:00Z

Education is a prerequisite for democracy. Without education, we are ill-equipped to analyze social issues and make informed decisions. In the end, we become blind followers, which benefits fascists, oligarchs, and exploiters.

I'm infuriated to see the systematic attack on education around the world. In the Netherlands, the government is once again cutting education budgets. People are losing jobs: The University of Twente laid off more than 40 employees, and University College Roosevelt, 20 employees. And that's just the beginning, NL Times reports.

Unions are pushing back against the budget cuts. My identity as a unionist is emerging. But, I find it difficult to find fellow unionists. Most of my colleagues are, as far as I know, not a member of a union. Indeed, trade union membership in the Netherlands is decreasing over the years (CBS: Statistics Netherlands).

Sometimes, I feel a bit lonely.

When I was a PhD student in the US, I saw many colleagues being taken advantage of. Their passion was used as a justification for poor working conditions, such as low wages, longer working hours, and no paid leave. An unwritten rule was, "You should not complain and just be grateful for being able to pursue your love for science." I disagreed, and I wanted a change. So, I joined a movement to start a union. The movement did not succeed. But, I renewed my conviction to support a unionized workforce, which was a part of my drive to migrate to the Netherlands.

In 2022, I migrated to the Netherlands. As soon as I started working at a university, I joined a union (AOb: General Education Union).

Many people don't know about unions or what they do. I believe it's because workers are generally happy, unlike the situation in the US. If we don't have serious labor problems, we tend not to think about unions.

I'm a bit worried about the current situation. A union that does not continuously get new members will lose organizing power, and the leverage to make a change. For now, we have some leverage. But with the decreasing union membership, I'm not sure for how long.

The fight against fascism and labor exploitation is a continuous process. If unionists stop fighting, exploiters will prevail. Fascists and exploiters will always emerge. The important thing is that we keep holding the line.

Join a union to fight against fascism and exploitation.

Unions to join #

If you are working at a university, I'd recommend joining one of the following unions:

FNV (Federation of Dutch Trade Unions) - The largest union in the Netherlands covering various sectors
AOb (General Education Union) - A union for workers in education and research

If you are not working at a university, I'd recommend checking out FNV.

Union membership costs a fee. Your employer will reimburse the 40% of it.

Defending the University from Budget Cuts

2025-03-12T00:00:00Z

Last week, I came across with this livestreaming event on LinkedIn:

After the event, I posted on socials (Mastodon, Bluesky, LinkedIn). And, I wanted to post it here on my blog:

What an inspirational livestream! As a former graduate student in the US who was involved in an unionizing movement, I resonated with many points. Below are my takeaways from the lecture:

Cultivate your identity as a worker. You provide valuable work, and you can use that as your leverage to make a positive change.
Don't keep hoping things will get better. Stop being on the sidelines. Now is the time to act.
Don't go alone. You cannot affect decision-makers yourself. When you combine and coordinate actions with others, you have a leverage to negotiate.
Use a democratic process to start organizing. Talk about what the problems are, what solutions would be, and what steps can be taken. The goal is to make an actionable plan to present to decision-makers. "We unionists don't hope. We plan."
Look for the leverage that does two things at the same time: (1) defend the position that we still have, and (2) undermine the opponent of the strategy and their own survival. One way to do so is by partnering with civil society actors (e.g., associations, churches, NGO's, patient organizations). By doing so, you can undermine the narrative that the university is useless. Communicate the value of university education clearly.

Thank you, Daniel Gutiérrez and FNV Universiteiten for the event!

The livestream of the event is available on The University of Twente's website:

I will follow up this post to reflect more on (1) my attempt to start a union in the US as a PhD student, (2) my move to the Netherlands to finally join one, and (3) my worries about unions in the Netherlands. 👋

Revisiting my PhD dissertation after 4 years

2025-02-25T00:00:00Z

I wrote my PhD dissertation openly on GitHub repo, starting 2020. After 4 years, I found that many things were broken. I also learned many things over time. In this blog post, I share my story of revising my dissertation, finding issues, and fixing them.

Why I wanted to make my dissertation reproducible #

Trying to say goodbye to Google Doc #

I made the first commit to the repository in December 2020. It was after my proposal defense.

Before that, I was using Google Doc for my dissertation. It was available, easy, and sharable: an important feature to get feedback from my advisor and committee members.

But, I was not completely happy. I was passionate about Open Science, and I wanted to do my dissertation in an open manner. After all, a mortal like me can only do one dissertation in a lifetime. I got one shot, and I wanted to have a good one.

Saving myself from death by a thousand copy-pastes #

I was using R to analyze data and Google Docs to write texts. This setup meant that whenever I had updates on analysis from R, I had to copy-paste those outputs to Google Doc. Oh, and I had to follow the APA format for reporting. Like: (r(235) = -0.05, p = .466, 95%CI [-0.17, 0.08]), with the italicized letters r and p. If anything changed in the analysis, I had to redo the formatting again.

The process was error-prone and tedious. Creating a reproducible manuscript meant that these numbers should automatically be updated if there were any changes. No more death by a thousand copy-pastes.

Working toward Open Science #

Open Science was, and is, core to what I do. By making a self-reproducing dissertation, I share my research process openly, working towards to my passion.

Starting a GitHub repo #

I started my GitHub repo, and I looked for options to create a reproducible thesis.

I first tried WORCS (Workflow for Open Reproducible Code in Science). You can see that in the first commit, which is the template Markdown file from WORCS.

But I quickly realized that WORCS was not best for my use case. WORCS was more suited for creating a shorter, article-length publication while I needed a solution to render a dissertation, which is more like a book.

So, I switched to use the combination of R Markdown and Bookdown. Using this setup, I was able to combine the code and writing using the same place, in R.

Regret 1: Not starting early and small #

At this point, I already had my proposal written up. That meant that I already had a good amount of writing in Google Doc. I had to manually import them, and by doing so, I lost the history of the changes in the proposal.

Starting early would have also allowed me more time to develop my muscles to use git, GitHub, and Bookdown to practice the flow. As I mention later, my earlier commit messages are cryptic, and I in the present cannot decode the meaning anymore.

If I had started the repo earlier, I could have started the project smaller in scope. In my case, my entire proposal was ready, and thus came with the dependencies of citations and formatting, which I had to fix while importing. By starting small and early, I could have avoided those issues.

Regret 2: Not storing data in a data repository #

My usual research workflow that time was to store data somewhere in the project directory. So, I created a data folder under the repository, which meant that the data was checked in the git repository.

At that time, I did not think much about it. But, right now, I regret doing so for the following reasons:

The data is hidden behind the project, not having a unique identifier (e.g., DOI). The data is not easily findable, and thus not very FAIR (And my Data Steward self is not proud of it.)
My data files were in binary (the R Data Serialization format in Rds). Any update to the dataset file caused the replacement of the file, which bloated the repo size.
By using a data repository, I could have easily tracked the different versions of the data (e.g., on Zenodo to manage versions).

Regret 3: Not committing with meaningful commit messages #

The first few commits of the repo are confusing. Below, you see 3 commits both commented as, "prereg":

I may have had some ideas of what these messages meant in 2021. Now, they are lost forever.

I regret not leaving meaning commit messages.

Nowadays, I try to follow Conventional Commits for commit messages (e.g., feat: add a boxplot for Study 1a). But, any consistency and additional information can help.

💡 During the presentation, my colleague Niek pointed out that it's possible to enforce Conventional Commits messages using pre-commit hooks. I found conventional-pre-commit (Python) and @commitlint/config-conventional (JavaScript)

Dissertation 'done' #

Nevertheless, I was able to finish my dissertation, and I defended it in June 2021. I was done with a PhD, and I thought I'd never look at my dissertation again.

Dissertation strikes back #

In 2024, I was at a meeting about a software management plan. The moderator asked whether anyone had written a research software.

At first, I thought, "I have never done that before." But then, I remembered my dissertation is essentially a software.

I got curious to revisit my dissertation. It's been a long time. But, it should be reproducible.

I cloned my GitHub repo and tried to run my dissertation.

Did it run? Of course not!

Let's see what problems that I had.

Regret 4: Git-ignoring randomly #

When I first tried to run the dissertation, I got an error for missing files. "How is that possible?", I thought. I looked at the gitignore file, and found that I ignored the .csv and .tex files—both of which were used in the project.

"Oh, no... Did I lose data for my project?"

Fortunately, I saved all study-related data in the Rds format, which was not ignored. So, no critical data for my dissertation was lost. The missing .csv file was for rendering the list of measures. And the missing .tex files were for the page for the signature and the layout. I added back the .csv file (commit), and fixed issues for the .tex files (commit & commit; pull request).

Moral of the story: Don't git-ignore files randomly. Think through the consequences and limit the scope of ignoring, such as ignoring files under certain directories.

Regret 5: Not keeping track of dependencies #

When I was trying to re-run my dissertation, I got errors for missing packages. I wondered, how many package dependencies my dissertation had.

So, I set up the pak package & renv, and counted dependencies involved, including secondary dependencies.

In total, I had 242 packages. Well, that was a lot.

Dependencies are not only about the R packages. Some R packages require certain software to be installed on the OS, which are called system requirements. For example, the ggplot2 package requires clang++ (C++ compiler), which usually comes with an operating system. The situation gets complex when installing a package with multiple package dependencies that require different system tools. For example, installing the kableExtra package requires the svgLite and xml2 packages that require libpng and libxml2 as system requirements, respectively. So, I had to deal with the system requirements of the 240+ packages in addition to installing those packages. The process was time-consuming.

Also, don't forget about the R and RStudio versions and the OS environment itself—these are all dependencies, creating a pyramid of dependencies.

To solve this situation of system requirements, I created a Docker image based on the RStudio image from rocker and installed dependencies (Dockerfile).

Regret 6: Not using Docker earlier #

Lastly, I regret that I was not using Docker earlier. As I mentioned, I could have avoided many issues by taking a snapshot of the OS environment, system dependencies, R packages, and the R and RStudio itself.

In the end, I also set up a GitHub action to create and publish a Docker image on GitHub. So, my repo has a CI/CD pipeline after many years. Better late than never.

Dissertation now #

After working on these issues, I feel happy with the state of the dissertation.

Along the way, I also converted from using RMarkdown and Bookdown to using Quarto, which further simplified the dependencies (FAQ for R Markdown Users).

I'm most proud that my dissertation replicates simple, 3 lines of code:

git clone https://github.com/nsunami/dissertation.git
cd dissertation
docker compose up

Summary #

In summary, I had 6 regrets:

Not starting early & small
Not using a data repository
Using bad commit practices
Git-ignoring willy-nilly
Letting 240+ dependencies run wild
Not using Docker earlier

Hope you won't have these regrets!

If you are curious to check out the code, the GitHub repo for my dissertation is nsunami/dissertation in HTML & PDF.

I presented about my dissertation journey at a meet-up of Open Science Community Eindhoven (OSC/e) on 28 January. The presentation slides are available at 10.53962/x4b0-jtqj. You can also see them below:

Unable to display the PDF file. Download instead.

Why I Migrated to the Netherlands from the US

2025-01-03T00:00:00Z

I migrated to the Netherlands from the US in 2022. I'm often asked why I did so. To answer those questions well, regardless of whether I had coffee in the morning, I wanted to write down here why and how I migrated to the Netherlands here.

Living in the US #

In 2019, I was living in the US doing my PhD at the University of Delaware. At that point, I had been in the US for 6 years. I was studying social psychology, with my mentor, Lisa Jaremka.

Among social psychologists like myself, there was a big debate about whether we were doing science right. A prominent social psychologist (Diederik Stapel) was caught fabricating data. Concerned, researchers in psychology came together, selected 100 old studies, and tried to re-do them, hoping that they will get the same results. The researchers found shocking results—they could only replicate 2 in every 5 studies. Researchers called the finding a "replication crisis".

Learning about a conference in Rotterdam #

I was also concerned about the replication crisis, and I learned about Society of Improvement of Psychological Science (SIPS), a scientific group whose aim is to improve psychological science. Their annual conference was in Rotterdam, The Netherlands.

At that time, I barely knew about the city and the country. The location was also a bit too far to travel. Nevertheless, I was very eager to go. So, I conjured up funding from my university to go there.

Experience in the Netherlands & Falling in Love #

In July 2019, my wife and I landed to Schiphol Airport, and took a train to Rotterdam. We still did not know that we would fall in love with the country in the next several days.

Looking back, I think of three reasons that I fell in love with the Netherlands, namely (1) its public spaces designed with care for people, (2) its protection of labor workers' rights, and (3) the drive towards Open Science.

Reason 1: Public Spaces Designed with Care for People #

The architecture of the Rotterdam Central station is beautiful. The whole building looks like a wedge diagonally pointing up to the sky. It also looks like a symbol of resilience for the city that was razed by Nazi Germany during World War 2.

Arriving at the station and walking towards the entrance of the building, I had a very strange feeling—I felt welcomed. But, I was just with my wife. Nobody welcomed me or greeted me personally. I looked around and wondered why I felt that way.

The entrance of the station was designed so that it widens towards the exit. The ceiling also gradually gets higher as you'd walk towards the main entrance. I saw people coming in and out freely. There was an ample room for people to gather, but also a feeling of nudge for people to go and explore the city, as if I'm gently escorted towards the exit. It was as if the space were telling me, "Welcome to the city, here you will find wonderful things." That was a good feeling.

There must be a lot of thought that went into this, I thought.

It happens that the Rotterdam Central station was not the only space designed with thought and care for people. During my stay, I learned that many infrastructures for pedestrians, bikes, and trains were not only readily available, but crafted with thought.

In my experience in the US, walkers, bikers, and train-riders were, I felt, second-class citizens. Most public spaces were centered around cars—roads were wide for cars, but sidewalks and bike lanes were narrow and often nonexistent. The Dutch public spaces blew my mind, at the same time I felt like I belong. And strangely, I felt like I was cared by the city and the environment. Not as a driver, but as a person.

Reason 2: Better Workers' Rights, even for Graduate Students #

During the conference, I wanted to get to know other fellow graduate students. After several years of being a graduate student, I knew what bonds graduate students together—that was, to gripe about how hard the life of a graduate student was to each other.

In the US, PhD graduate students are treated as students who are fortunate to get paid to study. After all, students are usually not paid to study. A university is very generous to pay students to pursue their passion as a form of stipend, even if it's 9 months per year. The rest 3 months? Don't be ungrateful, figure out by yourself. Paid vacation days? Don't act like you are employed—you are only a student, and thus you get none.

Life as a PhD student in the US was tough.

With my gripes, I approached my fellow PhD student attendees, who are coming from the Netherlands or other European countries. But, instead of approving and empathic nods of "me too", I got expressions of horror and disbelief: "Are you serious? You are not getting paid full year—let alone having no paid vacation?"

In return, I was shocked too—that they get benefits such as full-time contract and paid leaves, and overall being treated like an employee.

At the same time, I felt sick and disgusted. I realized that the US system exploited many PhD students unfairly. The system tells them that they are fortunate enough to continue what they want to do. As such, PhDs are not worthy of being treated as employees.

I learned that it's possible to imagine a system of care that treats PhDs as employees. I wanted to support that. Not the system of exploitation.

Side Note: I was fortunate to have a great mentor (Lisa Jaremka) who supported me through my education journey via summer funding and prioritizing work-life balance. But, I think my experience was an outlier.

Reason 3: Drive towards Open Science #

I care about Open Science—for me, it's about opening mind and heart, and advocating for it is to fight against global inequality (my LinkedIn post & ResearchEquals Interview).

When I was working towards a PhD in the US, I was doing practices in Open Science, such as writing hypotheses before I did a study (preregistration), and asking for reviewers to review my study proposal before data collection (registered report). I also posted actively on Open Science Framework to share my research and teaching materials.

But, I sometimes felt like it was a bit of lonely effort. Of course, my advisor was supportive of it, but shouldn't we be encouraged to do open science practices by the department, university, and the government? I felt like a coordinated support and initiative was lacking at that time in the US.

Learning about the Netherlands' Open Science landscape at the conference in Rotterdam, I felt like the country had a fertile ground for Open Science efforts to grow. Especially in terms of (a) the legal landscape and (b) the community.

One challenge that I faced in sharing a publication is how to deal with the copyright with the publishers. Usually, when a researcher writes a paper for a publication, they cannot simply post it on public. The publishers will try to stop researchers from doing so, since they want to keep the article behind "paywall" and allow only people with subscriptions to access it with fee (or paid for by universities). This greed of the publishers locks up the information, and people without subscriptions will have a hard time accessing it. I experienced this problem first-hand when I was studying at a university in the Philippines. Being in a global South country, my university did not have money to pay subscriptions, and thus I could not access most publications—that is, officially speaking.

Unofficially, though, I did manage to get access to many publications thanks to many researchers posting their articles online "illegally", the act of civil disobedience for the value of openness. But, the publishers were obviously not happy about this, and they were threatening researchers, sending takedown notices to universities.

Now that I have something to share as a PhD student, I wanted to share articles freely, but I was also afraid of legal actions.

In the Netherlands, one did not have to worry. During the conference in Rotterdam, I learned that Dutch researchers have protection from the government. Because of the Taverne Amendment (Article 25fa of the Dutch Copyright Law), researchers can share their publications freely, even if the publisher prohibits authors to do so.

Having such a legal protection meant to me that the Dutch society was concerned about this problem, and working to solve it. I wanted to contribute to that kind of society.

Community building for Open Science #

Open Science cannot continue without support from peers. When I was doing a PhD, I felt a bit alone for doing Open Science practices. Sure, it felt a little good because I felt like I and my advisor were doing a special thing. But looking back, I was looking for other people who can share the passion with me.

In the Netherlands, I learned that there were efforts to create communities for Open Science (Open Science Community Netherlands, OSCNL). "Our Community is Open" is the slogan of the Open Science Communities.

At the SIPS conference, I had a taste of being surrounded by open-minded people who connect in Open Science values. I wanted to continue that feeling, and I saw the Netherlands as the place to be.

Deciding to Migrate and Next Steps #

At the end of our stay in the Netherlands, my wife and I were in love with the country. After coming back to the US, we reflected on our experience in the US, and we asked where we would be happier living in. We listed things that we like and dislike about the Netherlands vs. the US. For the list of likes, we had a longer list for the Netherlands, and for the dislikes, the US. Our answer was obvious: the Netherlands.

Oh, our cat did not get to make a list, but we decided to ask for her forgiveness later.

Then, we wondered how we can migrate to the Netherlands. What kind of visas do we need? Where will we be living? How about work? I plan to write about these in a separate post.