Modeling in Cellucidate: Tackling Complexity, Communication and Collaboration

Ty Thomson, Plectix BioSystems

TITLE: Modeling in Cellucidate: Tackling Complexity, Communication and Collaboration

ABSTRACT: Computational models have become indispensable tools for evaluating and testing our understanding of biochemical processes in cells. In these models, researchers combine mechanistic understanding of individual components into whole system models on which simulation and analysis can be run. However, although researchers can generally express these pieces of mechanistic understanding verbally, they often have difficulty encoding their understanding into computational models because they must explicitly define the list of all possible complexes that may participate in each reaction in the model. For many complex signaling systems that are of therapeutic or academic interest, the number of possible complexes and reactions can overwhelm modeling tools and necessitate unwarranted simplifying assumptions that might bias model behavior. Additionally, such models are often comprised of long and inscrutable lists of complexes and reactions. Thus, although models are based on large amounts of facts, the models themselves are poorly positioned to communicate this information.

Cellucidate is an online software platform that enables construction and simulation of models of complex cell signaling systems via an intuitive graphical interface.

Complexity: Using a rule-based reaction framework, Cellucidate offers the capability to describe and simulate models that would otherwise require researchers to explicitly specify millions of complexes and reactions. Thus, the use of this framework enables us to build models of complex systems without making unwarranted simplifying assumptions.

Communication: The granularity of rules in Cellucidate closely mirrors the granularity of our understanding and our natural language descriptions of underlying events. Together with the intuitive graphical interface of Cellucidate, this facilitates communication by making Cellucidate models easy to read and understand. Additionally, researchers can share their models through Cellucidate with the entire research community, facilitating communication and reuse of models.

Collaboration: The web-based Cellucidate interface enables multiple researchers in different locations to collaborate seamlessly on a single model. Cellucidate also facilitates indirect collaboration by enabling users to build upon and modify models that are made available through the site.