The center aims to enable larger and more accurate systems biology models, as well as their applications to science, bioengineering, and medicine, by enhancing their understandability, reusability, and reproducibility.



Model building

We are developing tools for systematically building models, including comprehensive whole-cell models. This includes tools for aggregating data for modeling and for designing models from large datasets. The development of these tools is being driven by several scientific projects which aim to develop sophisticated models of bacteria and human cells and use the models to understand cell growth and design genomes.

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Model & simulation annotation

We are developing technology and methods to help scientists retrieve, understand, visualize, and then augment and merge models to model additional aspects of pathophysiology and test new hypotheses. Specifically, we are (a) developing and improving tools for model annotation, and (b) developing and testing tools for model visualization and integration.

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Simulation and visualization

We are developing fast browser-based simulation and visualization tools to enable interactive evaluation of model behavior within webpages, including with journal websites next to articles which report models and/or simulation results. This will include a browser-based simulator and a browser-based plotting engine that are capable of simulating models and simulations encoded in SBML and SED-ML.  These tools will provide near real-time data for interactive model exploration.

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Collaborative projects

To ensure the center develops technologies that enable more predictive and more reusable models, the center is collaborating with several researchers to test these technologies on several basic science, bioengineering, and medicine projects.

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To help researchers conduct modeling systematically, scalably, and reproducibly, the center provides several services to help researchers build and disseminate high-quality, reusable models.

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Training and dissemination

To help researchers develop better and more reusable models, the center provides training in scalable model building, model annotation, model verification, and reproducible modeling.

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The Center for Reproducible Biomedical Modeling is led by an international team of investigators with expertise in all aspects of systems biology modeling including model building, representation, calibration, simulation, analysis, and visualization.

Herbert Sauro
Herbert SauroDirector
University of Washington
John Gennari
John GennariCo-Director
University of Washington
Jonathan Karr
Jonathan KarrProject Director: Model Building
Icahn School of Medicine at Mount Sinai
Ion Moraru
Ion MoraruProject Director: Simulation & Viz
University of Connecticut Health Center
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