End of (5) Year(s) Reflections

Molecules are everywhere around us - and I am intrigued by unraveling the magic of their mechanisms. There are so many structures, each of them specialized to serve as a messenger, weapon, or nutrient. With my team, we are developing tools to find out what they look like and what they do.?

Caption top picture: Meandering sand and water under the UCSD Scripps Pier - March 2024 - Picture by: Justin van der Hooft

As autumn and the festive break bring moments of reflection, let me look back at my first five years of being a PI or better phrased: a team lead of a fanatic group of enthousiastic, competent, and committed students and postdocs ??.

At the start, I had some idea of what PI life would be like, but every so often, I felt more like a "Feather on the Clyde": The river feels so wide, and I don't know how to make it to the other side (Song text by Passenger – the River Clyde flows through Glasgow, Scotland)

Becoming a teacher, becoming a supervisor, becoming a team lead - all these roles ask different personal traits and qualities to step forward and develop. At the start of my journey, I still had to discover hidden traits and learn skills to lecture, supervise, and lead. With huge thanks to my team members, colleagues, course instructors, and others that allowed me to make mistakes and learn from them, I could grow from a one-person-band to a team lead of an international & diverse team doing great research and helping each other out. I could mention quite a few names here, but you know who you are ??. In the picture, I, in the form of my silhouet, feel the support by all of you out there that are standing behind me and encourage me in many different ways and I do recognize your reflections in the water. Thank you so much ??!

As said, making mistakes is important as it allows you to learn and grow from them, but even so, being told you are doing well with concrete examples is also important as it reinforces good practice. During my teaching, supervision, and leadership journey, I have been fortunate with so many of you that gave me honest feedback on how my actions and behaviour affected them. I have realised that I care a lot about the people around me, and I know I sometimes care so much that I forget I should also care about myself and be forgiving to myself: after all, I am doing my best and that is all I can do. And to all of you: do not forget to tell the people you care about how they affect you in a positive way....

More often than not, the answer to your issue is hidden in plain side.... however, you have to see it to understand it, or to understand it to see it....(paraphrasing Johan Cruijf here). Just like in my work, where we aim to find the hidden patterns in the data, in the puzzling picture above, there is a hidden reflection....the coloured patches on the dark river background are of a colourful passenger bridge linking the two sides of the Clyde. Let the colors represent the diversity of people and expertise needed, then I am building bridges between people, disciplines, and tools to further science. A recent example of this is our team review on metabolomics and visualization: most of our team members did join in this effort, also including several close collaborators ??! In this review, we combine various expertise and argue how important it is to keep the human in the loop when analyzing large datasets. With tools like SpecXplore, msFeaST, MS2LDA, MS2Query, and FERMO, we are working on guiding the users through the key steps to let them answer their research questions with their metabolomics data. Furthermore, the matchms Python framework and NPLinker code base and visualization app will facilitate mass spectral data handling and paired omics analyses.

DOI of publication: https://doi.org/10.1039/D4NP00039K

Code base: https://github.com/matchms/matchms

Code base: https://github.com/NPLinker/nplinker

With our team, we lead and contribute to community efforts in creating standards and resources for the metabolomics and multi-omics fields. These are usually also Open Science initiatives that generate Open Source software or Open Access databases. I believe that such team endeavours are key for the metabolomics and multi-omics fields, as they bring scientists from various (sub-)disciplines together and let them learn each others' jargon and agree on a "shared language". Is it always easy to communicate in an internationally diverse setting? Well, for me, it comes with its challenges and frustrations; yet, there is so much creativity and joy that it is worth the efforts it takes to build bridges between cultures and communication styles. Over the last years, our team has substantially grown, and I have worked on my team building skills and on creating and maintaining an open, fair, and welcoming atmosphere. It is an honor and my pleasure that so many early career talents have joined my team to collaboratively build expertise in computational metabolomics and integrative omics mining. Could I imagine this 5 years ago? Certainly not.... Did I dream of it? Perhaps....and it is great to see nice dreams come true!

Over the last year, I have also come to realise more and more that no matter how well we plan the route ahead, life always finds ways to throw you off-guard. Instead of resisting that, I think that allowing yourself the time to respond and reflect will let you appreciate the nice things that may come out of these moments….just like the pier at La Jolla in the top picture: sticking out straight ahead into the ocean, yet allowing for the sand and water (i.e., life) to fluctuate and find its path in between the pier (i.e., the planned path forward). Let us embrace the beautiful patterns that can emerge out of chaos!

Over the last 5 years (and before), I have also organized several workshops and joined workshops and schools as an instructor, on the European continent, across the pond, and the globe. It has been a privilige to connect with the participants and fellow instructors to shape a thriving computational metabolomics ecosystem, nowadays used by both academia and industry. I think the nice interactions between both the tools and humans behind the tools facilitate the uptake of the processing, analysis, and annotation tools throughout the metabolomics community. Let us keep doing this together ??!

Looking into the future of my field, I expect the omics datasets to become larger, more multi-layered, and more complex, and I expect increasingly important roles for networking-based and AI-based tools to capture (bio)chemical meaning from the many signals that metabolomics datasets generate. There is still so much to discover and appreciate from microbial, plant, and human metabolism ??! I believe we can only tackle the challenges that come along with entering the truly Big Data Era if we work as a team and connect expertise by making efforts to speak each other's language. It is then, that we can gain more insights in the chemical language spoken all around us: by molecules!

What will be here in the next year? There is plenty to look forward to ??! Two new members will join, with shared postdoctoral contracts with Utrecht and Leiden, thus also starting new collaborations that will open up new scientific possibilities. There will be several work travels, including a visit to Johannesburg, South Africa, to give lectures in my role as a Visiting Professor there. By inviting and hosting paired omics miners to Wageningen for a workshop in March, I will have the opportunity to celebrate ?? 5 years of computational metabolomics & metabolome mining in Wageningen during a symposium. We will also visit Metabolomics 2025 in Prague, Czech Republic, with a large delegation of my team - this will be another chance to celebrate our lustrum!

In the past years, some team members have joined and left our team to find their next role, for example as research software engineer. The next years will see the first team members finalizing their PhDs, graduating, and leaving our team to find different roles elsewhere. It will be strange to see you leaving, but I am looking forward to following and supporting your future careers.

For now, I wish you all a restful, peaceful, and fulfilling festive break, and, above all, a healthy, but also colourful, creative, and collaborative 2025!?

May you see many colourful flowers and meet colourful, creative, and considerate people! :-)