From Functional Nucleic Acids to Galaxy Training: Reflections on My Research Stay in Freiburg

I am a PhD candidate in Biochemistry at the University of Isfahan, with a research focus on the application of functional nucleic acids in medicine — both for diagnostics and for theranostics. In September 2024, I had the privilege of joining the Galaxy Europe team at the University of Freiburg as a visiting scientist under the leadership of Dr. Björn Grüning.

This experience was a turning point in my scientific journey. The Galaxy team welcomed me warmly, provided professional and technical support, and created an environment where collaboration and creativity flourished. It was also a joy and an honor to celebrate the New Year together — a moment that symbolized the spirit of community that Galaxy embodies.

Developing New Tools: CleaveRNA

During my stay, I worked on developing CleaveRNA, a tool designed to support researchers in DNAzyme design for improved target site selection. This work aims to contribute to the next generation of gene therapy applications, where careful design and reproducibility are critical for success.

I would like to express my deepest gratitude to Dr. Björn Grüning and Dr. Martin Raden, whose guidance and support were invaluable throughout the development of this tool. I am also sincerely thankful to every member of the Galaxy Europe team for their technical help, feedback, and enthusiasm that made this work possible.

In addition to CleaveRNA, I wrapped several other tools for deployment on the Galaxy platform, expanding its capabilities for both researchers and educators.

Training and Community Contributions

I actively participated in Galaxy workshops, the Galaxy Training Network (GTN), and the Imaging Hackathon, where I experienced first-hand the openness and collaborative energy of this community. I contributed to the training ecosystem by:

• Reviewing Galaxy tutorials
• Writing new workflows and training materials
• Developing a hands-on tutorial for electrophoresis gel image analysis in biochemistry applications

The electrophoresis tutorial, written in collaboration with Diana Chiang Jurado, reflects my passion for bridging molecular biology with accessible, reproducible computational tools. By combining QuPath and Galaxy imaging tools, the workflow provides an open alternative for gel quantification — a method that is widely used but often lacks transparency in analysis.

Gratitude, Memories, and Reflections

Looking back, I am deeply grateful for the chance to learn from, collaborate with, and contribute to this inspiring team. Galaxy Europe exemplifies what can happen when open-source software, scientific rigor, and human kindness intersect.

On my final day in Freiburg, we gathered for an enjoyable barbecue with the Galaxy team — a warm and memorable way to conclude my stay. The team surprised me with a beautiful wooden boat, a symbolic gift representing the city of Freiburg, signed by Galaxy members as a keepsake of friendship and collaboration. It is a memory I will always cherish.

“Science is not only about answering questions, but also about building the bridges that allow others to cross into new territories of knowledge.”

I would like to thank the Galaxy Europe team — especially Dr. Björn Grüning, Prof. Rolf Backofen, Dr. Martin Raden, Dr. Anup Kumar, Dr. Pavan Videm and all my wonderful colleagues — for their support, encouragement, and vision. It was my honor to work alongside you, to share knowledge, and to contribute in my own way to the Galaxy ecosystem. I would also like to warmly acknowledge the invaluable support of my supervisors at the University of Isfahan, Dr. Fatemeh Javadi-Zarnaghi and Dr. Fariba Dehghanian, whose scientific guidance and continuous encouragement, greatly enriched my research stay and overall academic growth.

I returned to my PhD journey at the University of Isfahan with renewed energy, inspiration, and a deep appreciation for the Galaxy community. I look forward to continuing our collaboration and to helping build tools and training that empower researchers worldwide.