INCOME Hackathon 2023
Mathematical models are essential tools in systems biology and systems medicine. They contribute to an understanding of structure and dynamics of cellular and tissue dynamics far beyond their isolated parts, as well as to the prevention, diagnosis and therapy of diseases. Yet, model topology as well as model parameters are often unknown and need to be inferred from experimental data. Over the last years, there was substantial progress in the development of standardized model selection and parameter estimation pipelines. Furthermore, optimization and sampling methods have been improved, and novel concepts introduced (e.g., at the interface of mechanistic modelling and machine learning).
In the scientific track on Integrative Pathway Modelling of Bonn Conference on Mathematical Life Sciences, state-of-the-art methods and software tools will be discussed and applications will be presented. To complement this, we offer a 2-day hackathon.
The hackathon will provide participants with time and space to work on methods and software tools applicable in systems biology and systems medicine. Complimentary, help with the use of methods and software tools will be provided. The hackathon is intended to be a space to technically improve both models and tools. The aim is to work jointly on open problems related to integrative pathway modelling in systems biology and systems medicine. To achieve this, we will address the following topics at the hackathon:
Topic 1: Extension and refinement of the PEtab standard and supporting tool
This will include the extension of PEtab standard towards model selection and complex time series. Furthermore, we will speak about further annotation possibilities, e.g. for the integration of PEtab in clinical workflows.
Topic 2: Extension of model and data repository
To improve the reuse of models and datasets, we want to extend our benchmark model repository. The benchmark collection was published in 2018 and collects 20 benchmark models. Additional published models should be included. For this the SBML files and the data have to be parsed into a specific format.
Beyond these predefined topics, there is the room for more. This will also include the support of new users and tool developers in applying the methods and using community standards.
Thursday, April 20
| 15.00 - 15.15 | Welcome and brief introduction (Jan Hasenauer, 15 min) |
| 15.15 - 15.30 | Presentation of topics |
| 15.30 - 16.30 | Hacking |
| 16.30 - 17.00 | Break |
| 17.00 - 18.30 | Hacking |
Friday, April 21
| 9.00 - 10.30 | Hacking |
| 10.30 - 11.00 | Break |
| 11.00 - 12.00 | Hacking |
| 12.00 - 12.30 | Presentation of results and concluding remarks |
Jan Hasenauer ([email protected])
Alte Sternwarte in Bonn
Poppelsdorfer Allee 47
53113 Bonn
Rooms "Kassiopeia" (EG) and "Lyra" (1. OG)
Remark: As this is a satellite event to the Bonn Conference for Mathematical Life Sciences 2023.
The topics covered by the hackathon are broad and allow for the contribution of persons with different backgrounds. Ideally, participants have programming experience (MATLAB, Python, R, etc.) or experience with mechanistic modeling. Furthermore, we invite users of the different software tools for the testing of the functionalities, the contribution of models to the model and data repository, and development of the comprehensive model of the cellular processes.
