Despite their importance, we do not yet have comprehensive and accurate models that can guide medicine and bioengineering. Model building is one of the major bottlenecks to predictive models. In particular, model building is still a labor-intensive, ad hoc process. This inhibits researchers from building comprehensive models, and creates models that are hard to understand, reuse, and extend.
We are developing the first tools for systematically, scalably, and reproducibly building models of intracellular pathways. This includes tools for scalably aggregating data for modeling, organizing this data for model design, and systematically designing models from this data. These tools will make model building reproducible by tracking the data sources and assumptions used to build models.
We are using cell models as a test bed for developing broadly-applicable methods for scalable model construction. This allows us to concretely test our ideas. However, our tool will be modular and extensible to enable future support for additional domains.
To ensure our tools advance biomodeling, we are developing our tools in conjunction with several driving projects which aim to develop whole-cell models of bacteria and human cells.
We anticipate that our tools will help researchers build more predictive models, and we anticipate that these models will help advance science, medicine, and bioengineering.