SC2ODE: Single-Cell data to Ordinary Differential Equation-based mechanistic modelling 

Date: 5th & 6th November 2025, Time: 08:30-19:00

Location: Hamburg Center for Translational Immunology (HCTI), Building N25, UKE

Description: Single-cell (SC) data are massively enriching our view of dynamic cellular systems, yet most analyses remain descriptive. This workshop introduces ordinary differential-equation (ODE) modelling as a quantitative extension of SC studies. Participants will learn to integrate cell-state frequency trajectories into mechanistic models using the open-source R packages. Guided practicals will cover data integration, parameter estimation, identifiability analysis and visualisation of results. The programme combines brief theory capsules with extended hacking sessions, enabling each participant to generate preliminary kinetic parameters – either for their own dataset or for benchmark data supplied by the organisers. The course builds on a published conceptual framework.

Organisation & Funding: The activity is organised by the Department of International Affairs at the University of Hamburg and the Center for Biomedical AI at the University Medical Center Hamburg-Eppendorf, with funding from the German Federal Ministry of Research, Technology and Space. Travel and accomodation costs will be covered for participants from EUGLOH member universites.

Target group: Natural/ Life science PhD students & postdocs with advanced R and single-cell analysis experience, enrolled at one of the nine EUGLOH member universities or affiliated partner institutions (at own costs).

How to Apply: Complete the homework for self-assessment and submit your three sentence motivation statement why we must select you together with your CV via the online registration form by August 30.

Note: Priority will be given to applicants who have not participated in EUGLOH events previously.

Preliminary programme

Day 1

  • Welcome
  • Short introduction into key concepts behind SC data and ODE-based modelling
  • Setup of dMod framework, read-in data, run simulations (1.5h)
  • Model selection (1.5h)
  • Dinner

Day 2

  • Soft skill tips and tricks (feat. EU office)
  • Short introduction into parameter estimation
  • Identification analysis (4h)
  • Wrap-up and summary of lessons learned
  • Networking closure: local PIs present themselves to the international guests