Smart VCell
Model Explorer
A comprehensive collection of references, papers, and data sources that power our biological modeling platform.
Research Papers
Leveraging public AI tools to explore systems biology resources in mathematical modeling
Meera Kannan, Gabrielle Bridgewater, Ming Zhang & Michael L. Blinov
Virtual cell modeling and simulation software
I.I. Moraru, J.C. Schaff, B.M. Slepchenko, M.L. Blinov, F. Morgan, A. Lakshminarayana, F. Gao, Y. Li, and L.M. Loew
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks
Adrien Rougny , Vasundra Touré , John Albanese , Dagmar Waltemath , Denis Shirshov , Anatoly Sorokin , Gary D Bader , Michael L Blinov , Alexander Mazein
Attention Is All You Need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N. Gomez, Lukasz Kaiser, Illia Polosukhin
bnglViz: online visualization of rule-based models
Noah Liguori-Bills, Michael L Blinov
Bioinformatics, Volume 40, Issue 6, June 2024, btae351, 2024
DOI: 10.1093/bioinformatics/btae351
Data Sources & Other Tools
VCell Database
The Virtual Cell Database repository stores all the models created using the Virtual Cell software.
Visit SourceBioNetGenLanguage (BNGL) code visualizer
BioNetGen is software designed for modular, structure-based modeling of biochemical reaction networks.
Visit SourceGitHub Repositories
vcell-demo
Backend and API for the VCell Model Explorer demo.
Technologies: Python, Streamlit, Ollama, Groq, VCell API
View Repositoryvcell-front-demo
Frontend application for the VCell Model Explorer.
Technologies: React, Next.js, TypeScript, Tailwind CSS, ShadCN
View Repository