Starting Google Summer of Code 2025

 

Hi,

I am Jiahui Hu, 2nd year CSE student at the Northeastern University, Roorkee, India. I am incredibly excited to share that I was selected in the Google Summer of Code (GSoC) this year with the National Resource for Network Biology (NRNB) as a mentoring organization. I will be working on the project "Optimization of SBOannotator for Dynamic Term Integration and AI Enhancement" in this program. I am incredibly thankful to the wonderful mentors, namely Dr Nantia Leonidou，Dr. Andreas Dräger, who helped me to get selected and will guide me throughout this project.

This blog series is dedicated mainly to share my progress for the project. The official coding period started from 23nd June, and the community bonding period begun from 8th May. In this period, I will be exploring the codebase with solving some small issues and will discuss the implementation details with the mentors and finalize them.


What is NRNB?



The National Resource for Network Biology (NRNB, https://www.nrnb.org) organizes the development of free, open-source software technologies to enable network-based visualization, analysis, and biomedical discovery. Biomedical research is increasingly dependent on knowledge expressed in terms of networks, including gene, protein and drug interactions, cell-cell and viral-host communication, and vast social networks. Their technologies enable researchers to assemble and analyze these networks and to use them to better understand biological systems and, in particular, how they fail in disease.


About the Project - SBO Annotator


My GSoC project is based on issue #261, and the repository is currently present at this link.


SBOannotator is the first standalone tool that automatically assigns SBO terms to multiple entities of a given SBML model. The main focus lies on the reactions, as the correct assignment of precise SBO annotations requires their extensive classification. Our implementation does not consider only top-level terms but examines the functionality of the underlying enzymes to allocate precise and highly specific ontology terms to biochemical reactions. Transport reactions are examined separately and are classified based on the mechanism of molecule transport. Pseudo-reactions that serve modeling purposes are given reasonable terms to distinguish between biomass production and the import or export of metabolites. Finally, other model entities, such as metabolites and genes, are annotated with appropriate terms. Including SBO annotations in the models will enhance the reproducibility, usability, and analysis of biochemical networks.


Web application hosted at TueVis is accessible and ready to use at sbo-annotator-tuevis.cs.uni-tuebingen.de/



This proposal aims to transform SBOannotator from a static, hard-coded tool into a dynamic, intelligent system for annotating SBML models with Systems Biology Ontology terms.

By implementing real-time SBO term retrieval, integrating multiple enzymatic data sources, and incorporating LLM-based annotation assistance, this project will significantly enhance both the accuracy and usability of SBOannotator while maintaining its core classification strengths. The addition of a standalone desktop GUI with interactive visualizations will make these powerful annotation capabilities accessible to a broader range of systems biology researchers.

The complete details about my project can be found in my project proposal.


For any discussions, please contact me here:

E-Mail: lareinahuwork@gmail.com


Regards!




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