Date and time:
15 October 2025 at 15:30 pm
Place:
Sano Centre for Computational Medicine
3rd floor in CE building, entrance C5
Czarnowiejska 36, Kraków
Maximum number of participants: 10
Duration: 3h
Jan K. Argasiński1, Cemal Koba1, Rosmary Blanco1, Monika Pytlarz1
1Sano - Centre for Computational Medicine, Czarnowiejska 36, 30-054 Kraków, Poland
j.argasinski, c.koba, r.blanco, m.pytlarz@sanoscience.org
Keywords: Computational neuroscience, brain-gut axis, methodology, study design
1. Introduction
The brain–gut axis, a bidirectional communication network linking the central nervous system and the gastrointestinal tract, is emerging as a interesting domain in understanding neurological, metabolic, and psychiatric disorders. Despite growing biological and clinical interest, computational approaches to studying the brain–gut axis remain basic. This tutorial responds to the need for a methodological framework for researchers aiming to explore the brain–gut axis from a computational neuroscience perspective. Focusing on scientific literature as both a source of knowledge and a foundation for study design, the session will introduce participants to modern tools and strategies for initiating research in this field.
2. Description of the tutorial
This 3-hour tutorial serves as both a literature deep-dive and a methodology primer. Participants will work in a guided exploration of the latest scientific publications on the brain–gut axis, with a particular focus on computationally relevant research.
The session is divided into three components:
Literature Exploration and Mapping:
Participants will learn systematic methods for identifying, filtering, and categorizing relevant literature using tools like PubMed, Scopus, and AI-powered search engines (e.g., Semantic Scholar, Connected Papers). Emphasis will be placed on extracting methodological content, modeling approaches, and data sources.
Scientific Methodology for Study Planning:
We will demonstrate how to analyze existing studies to extract assumptions, computational models, and data modalities (EEG, fMRI, microbiome profiles, behavioral markers). Participants will collaboratively map gaps and research opportunities, developing hypotheses based on the current state of the field.
Pipeline Prototyping for Brain–Gut Studies:
The final part of the session will be a walkthrough of how to draft a computational research pipeline. This includes defining input data, identifying possible modeling techniques (e.g., neural networks, graph-based models, Bayesian inference), and conceptualizing evaluation strategies.
The goal is to help participants move from reading to research planning.
The format includes short lectures, guided group work, and discussion.
3. Knowledge and skills to be gained
By the end of the tutorial, participants will be informed on how to:
- Conduct literature reviews focused on computational neuroscience topics.
- Identify and extract methodological insights from scientific publications.
- Recognize and categorize computational approaches applicable to brain–gut research.
- Formulate basic study designs for modeling the brain–gut axis.
- Draft conceptual pipelines for computational experiments, including data selection, modeling strategies, and analysis plans.
- Understand the interdisciplinary landscape of brain–gut research and the role of computational tools within it.
Acknowledgements: This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 857533 and from the International Research Agendas Programme of the Foundation for Polish Science No MAB PLUS/2019/13. The tutorial was created within the project of the Minister of Science and Higher Education "Support for the activity of Centers of Excellence established in Poland under Horizon 2020" on the basis of the contract number MEiN/2023/DIR/3796. We gratefully acknowledge Poland's high-performance Infrastructure PLGrid ACC Cyfronet AGH for providing computer facilities and support within computational grant no. PLG/2025/018289.
References:
- Mayer, E. A., Nance, K., & Chen, S. (2022). The gut–brain axis. Annual review of medicine, 73(1) 439-453.
- Mayer, E. A., Naliboff, B. D., & Craig, A. B. (2006). Neuroimaging of the brain-gut axis: from basic understanding to treatment of functional GI disorders. Gastroenterology, 131(6), 1925-1942.
- Burns, J. L. (2009). The Scientific Method through the Lens of Neuroscience; From Willis to Broad. In Forum on Public Policy Online (Vol. 2009, No. 2). Oxford Round Table. 406 West Florida Avenue, Urbana, IL 61801.
