Topics and projects

The key goal of systems biology is to achieve a system-level understanding of complex biological processes. The BMBF-funded project INCOME contributes to this by providing tools and workflows for a modular approach to understand cellular processes. Together, we aim at harmonizing and integrating models contributed by a variety of research groups into one comprehensive model. To achieve this, we address the following topics at the hackathon:

Topic 1: Implementation of import functionality for modeling tools

For the benchmark collection a combined model and dataset format has been established which provides all required information for model simulation, parameter estimation and uncertainty analysis. The benchmark collection was published in 2018 and collects 20 benchmark models. The format simplifies the communication of models and dataset and the evaluation of methods. To spread the format, we want to establish import functions for established modelling tools, e.g.

Topic 2: Development of a format validation tool

For the streaming of the modeling process, it would be important to have a format validator. A first version has been implemented at the first hackathon. Here, we want to extend it, e.g. by adopting ISA Tools, and improve it further.

Topic 3: 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.

Topic 4: Evaluation of supervised model merging

The model merging tool developed within INCOME will be evaluated on the models in the benchmark collection and additional models provided by  participants.