We are the Systems Biology Research Group (SBRG) at the University of California, San Diego, led by Dr. Bernhard Palsson.
For over two decades, our lab has been at the forefront of computational biology, pioneering foundational frameworks that have shaped modern systems biology.
We developed Flux Balance Analysis (FBA) to simulate metabolism at genome scale, introduced the COBRA (COnstraint-Based Reconstruction and Analysis) approach to unify metabolic modeling, and expanded these tools into ME-models to capture the full scope of cellular function.
Our work integrates computation, omics data, and systems-level insight to build predictive models of physiology.
This web app represents the next step in that mission: making these advanced models and tools accessible, interactive, and extensible for the broader scientific community.
Get in Touch
For questions, support, feature requests, suggestions, or collaboration inquiries, please contact us at
cobrame.webapp@gmail.com.
How to Cite This Work
If you use this web application or underlying COBRAme framework in your research,
please cite the following:
COBRAme:
Lloyd CJ, et al. "COBRAme: A computational framework for genome-scale models of metabolism and gene expression." PLoS Comput Biol 14(7): e1006302 (2018). https://doi.org/10.1371/journal.pcbi.1006302
StressME:
Zhao J, Chen K, Palsson BO, Yang L "StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses."" PLoS Comput Biol 20(2): e1011865 (2024). https://doi.org/10.1371/journal.pcbi.1011865
DynamicME:
Yang, L., et al. "DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression." BMC Syst Biol 13, 2 (2019). https://doi.org/10.1186/s12918-018-0675-6
This Web Application:
Citation pending. Please check back once the associated publication is released.
