Workshop

Young Developmental Biologist Workshop (4^th to 5^th September 2025)

As part of the V4SDB Meeting 2025, we invite early-career scientists to join the Young Developmental Biologist Workshop, designed to equip students and postdocs with essential skills for their research journey.

The workshop will feature

• Chalk Talk Session
  This session offers participants a chance to introduce themselves and present their research in a casual, interactive format. Each participant will have the opportunity to share their work, ask for feedback, and engage in discussions with their peers and mentors. The chalk talk format encourages collaboration and idea exchange, helping participants refine their research concepts while also building valuable connections with others in the field.

• How to Write an Effective Abstract
  This course aims to introduce participants to the best practices for writing an abstract.  It may seem like a small detail, but the abstract is the key showcase of your research, and great attention must be given to its writing.  This workshop is not just about theory – it is hands-on!  Each participant will leave with a well-crafted abstract and title for their own research.

• Introduction to Proteomics Analysis
  This workshop provides a comprehensive introduction to LC-MS/MS proteomics. In the first part, participants will learn the fundamental principles of proteomics, the current technical possibilities, and the basics of experimental design. The second part of the session is hands-on: Participants will analyze a sample dataset in R.

• Micro-CT Data Analysis
  This workshop focuses on the image analysis of 3D imaging data obtained via micro X-ray computed tomography, with an emphasis on biological samples. Participants will explore the analysis of both hard and soft tissues, covering essential pre-processing techniques like contrasting and denoising to improve data quality. Key segmentation methods will be introduced to isolate structures of interest, followed by morphological analysis to quantify selected regions across entire sample volumes. This approach allows for identifying structural changes that may not be visible in 2D imaging. The session will provide hands-on experience using both open-source tools like Fiji and professional image analysis software, ensuring participants gain practical skills applicable to micro-CT and other 3D/2D imaging datasets.

• Time-Lapse Microscopy Analysis of Live Mouse Oocytes and Early Embryos
  This session will provide a practical demonstration of both qualitative and quantitative analysis of imaging data from time-lapse microscopy (obtained by confocal as well as light-sheet microscopy) of live mouse oocytes and early embryos. The session begins with a brief lecture on the principles of live oocyte and early embryo microscopy. Then, participants will engage in hands-on activities, which include processing raw microscopy data, preparing high-quality images and videos for publication, and conducting basic analyses of meiotic events such as resumption, anaphase entry, and chromosome segregation. Additionally, participants will explore qualitative image analysis, including measuring spindle volume at various time intervals and tracking signal intensity during meiotic maturation.

• Introduction to Single-Cell RNA Sequencing Analysis
  This workshop provides an overview of best practices for single-cell RNA sequencing, from sample preparation to data analysis. Participants will learn key steps in sample processing to ensure high-quality data, followed by essential data processing techniques. The session covers quality control checks, removal of doublets, cell clustering, and differential expression analysis between samples or individual cell clusters. Through hands-on practice, participants will gain practical experience in interpreting and analyzing single-cell transcriptomic data.

• Protein Structure Prediction with AlphaFold
  This session introduces the fundamentals of protein structure prediction using AlphaFold. Participants will learn best practices for preparing input sequences, running predictions, and interpreting results. The session covers quality assessment of predicted structures, limitations of the method, and practical applications in research. Hands-on exercises will guide participants through analyzing structural confidence scores, identifying functional regions, and integrating AlphaFold predictions with experimental data. This workshop provides essential skills for leveraging AlphaFold in structural biology studies.

• Round table discussion: The Use of Artificial Intelligence in Research
  A strictly informal “pub hall” discussion about the use of ever present LLMs in research. What are the clear advantages, what are the clear threats? How can we exploit the former and guard ourselves from the latter? Bring your own beer or we’ll try to provide some.

The number of workshop participants is limited. Selected participants will be contacted to confirm their acceptance to the workshop and to choose their preferred sessions from the available parallel sessions and receive further details.

Programme

Day 1
08:00-08:30	Registration
08:30-10:00	Chalk talks, part 1
10:00-10:20	Coffee break
10:20-12:00	Chalk talks, part 2
12:00-13:00	Lunch
13:00-17:00	Introduction to Proteomics Analysis Petr Vodička, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences
13:00-17:00	Time-Lapse Microscopy Analysis of Live Mouse Oocytes and Early Embryos David Drutovič, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences
17:00-17:30	Coffee break
17:30-19:30	How to Write an Effective Abstract Jakub Harnoš, Masaryk University
17:30-20:00	Micro-CT Data Analysis Viktória Parobková, CEITEC Brno University of Technology
20:00-23:00	Bites & Banter
20:30-21:30	Round table discussion: The Use of Artificial Intelligence in Research Moderator: Máté Varga, ELTE Eötvös Loránd University

Day 2
08:00-11:00	Introduction to Single-Cell RNA Sequencing Analysis Irina Poverennaya, Medical University of Vienna
08:00-11:00	Protein Structure Prediction with AlphaFold Pavel Kohout, Masaryk University