SBML4Humans GSoC 2021 Project

This project focuses on developing an interactive report interface for presenting SBML model information. This requires a strong base in understanding the current state of the SBML report and the code that helps in generating the reports. This week’s exercises were centred around understanding the reports module and tests.  The second week of preparation taught me many new things related to SBML report generation and rendering of the report. I learnt about reading (parsing) SBML model documents, creating structured and formatted document trees from the parsed models, and presenting them in pretty-printed and HTML formats. During this period, I have studied the following resources: Overview and test examples of the SBML report generation process from the documentation ( https://sbmlutils.readthedocs.io/en/latest/notebooks/sbml_report.html ) Code of the reports module from the repository ( https://github.com/matthiaskoenig/sbmlutils/tree/develop/src/sbmlutils/report ) Code of related...

The Systems Biology Markup Language (SBML) is a standard language to represent biological models in a computer readable and exchangeable format. The goal of this project is to create a human-readable, reactive and navigable web-based interface for easy visualization of these SBML models. More information about the project can be found on the Github issue ( https://github.com/nrnb/GoogleSummerOfCode/issues/164 ). I am preparing myself for this project and am being mentored by Dr. Matthias König . The first week of learning taught me some great things, some new and some known (e.g. the SBML 3 structure, history, abstract and core ideas). I have gone through the following resources have reached a good understanding of the core ideas: The SBML Homepage ( http://sbml.org/Main_Page ) The SBML 3 abstract and overview in the following publication https://www.embopress.org/doi/full/10.15252/msb.20199110 Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gill...