Hackathon in Februrary 2020

Integrative pathway modeling in systems biology and systems medicine

February 5-7, 2020

Bonn, Germany

Mathematical models of cellular pathways are essential tools in systems biology and systems medicine. They contribute to an understanding of structure and dynamics of cellular processes far beyond their isolated parts, as well as the prevention, diagnosis and therapy of diseases. Yet, there are a variety of challenges.

The 3rd Hackathon on Integrative Pathway Modelling in Systems Biology and Systems Medicine will gather experts in pathway modeling to improve existing tools for:

   - Modeling and simulation

   - Parameter estimation

   - Model and data standards

   - Model reuse, extension and integration

The projects will focus on dynamical models, including Ordinary Differential Equation (ODE) models and multi-cellular models. Information about the specific goals and the considered tools are available in the topics list. Please feel free to submit additional topic to: contactnoSp@m@integrative-pathway-models.de

As part of the hackathon, the domain experts David Nickerson, Jens Timmer and Jordi Garcia-Ojalvo will provide an a comprehensive tutorial on reproducible modelling. The aim is to inform students about current standards and to assist them with the implementation of the standards in their project

As reproducibility of modelling results is essential in systems biology and systems medicine and the basis for reuse and refinement of virtual experiments, the Hackathon offers a tutorial on "How to make your model beautiful”. This includes instructions for the export of models into standard formats (SBML, CellML, BioPAX), visual representation of models in SBGN, export of simulations in SED-ML, and semantic annotation of models with Bio-Ontologies.

Up to 15 travel grants are offered to PhD-candidates and PostDocs who wish to get some hands-on experience in the standardisation of models. Apply with a model of choice (published or about-to-be published) to receive travel support and supervision in polishing your model throughout the hackathon.

The hackathon is this time co-organised with the Workshop on Computational Models in Biology and Medicine 2020, February 4 & 5, in Bonn.

Hackathon funded by the German Ministry for Education and Research (BMBF) via the e:Med Project INCOME.


Confirmed keynote speakers:

Jens Timmer, University of Freiburg

David Nickerson, University of Auckland

Jordi Garcia-Ojalvo, University of Pampeu Fabra