denbi-modsim.github.io

Advanced Modelling with COPASI

Abstract:

COPASI is a widely used software tool for modeling, simulation, and analysis of biochemical reaction networks. Compatible with all major operating systems, it supports a wide range of computational methods—including deterministic and stochastic simulations, steady state analysis, optimization, sensitivity analysis, and more.

This workshop focuses on advanced techniques in parameter estimation, including:

• Integration of heterogeneous data from time course and steady-state experiments
• Identifiability assessments to determine meaningful parameters
• Implementation of constraints and weighting strategies to refine models

Participants will also learn how to automate and customize analyses through scripting with COPASI, expanding their modeling capabilities beyond the graphical user interface.

In the afternoon, participants are encouraged to bring their own models or parameter estimation challenges for a collaborative, hands-on session guided by experts.

Educators:

Frank Bergmann (Heidelberg University), Stefan Hoops (University of Virginia), Ursula Kummer (Heidelberg University), Pedro Mendes (University of Connecticut), Jürgen Pahle (Heidelberg University), Sven Sahle (Heidelberg University)

Date:

Oct 10, 2025, 9:30a - 4p (CEST / UTC+2)

Location:

BioQUANT, Im Neuenheimer Feld 267, 69120 Heidelberg

Prerequisites:

Participants should have the latest version of COPASI installed.

This workshop is intended for experienced modellers with a solid grasp of COPASI. It builds on foundational skills and explores advanced strategies for analyzing complex biochemical models.

Registration:

Registration is free but required and limited to 30 participants.

Registration Form

How to get to the workshop

The workshop will take place in Seminar room 42 of the BioQuant (INF 267, 69120 Heidelberg)

By car:

Coming from the motorway (A 656)

• Turn left towards “Chirurgie” at the end of the Autobahn. Having crossed the Neckar on Ernst-Waltz-Brücke follow Berliner Straße. At the 2nd traffic light (“Shell” gas station & “Bunsengymnasium”) turn left towards Neuenheimer Feld (BioQuant 267).

By public transport:

From main railway station (Hauptbahnhof):

• Take either the tram number 24 (direction Handschuhsheim) or the number 21 (direction Technologiepark) and get off at the “Bunsengymnasium” stop.

From Heidelberg downtown (Bismarckplatz):

• Take the bus number 31 towards “Neuenheim, Chirurgische Klinik” and get off at the “Bunsengymnasium” bus stop.

This workshop is part of the de.NBI SysBio Workshop series 2025. more information