By Joshua Havumaki
This summer Plectix had two interns with no prior systems biology experience working in our biology group. Below are their experiences using Cellucidate to recreate mathematical models of cell signaling cascades from the literature. Their cBooks will be made public in mid-September.
Elizabeth Riley is a rising senior majoring in Biology at Wheaton College and has recreated a model of the JAK/STAT signaling cascade.
At the start of my internship at Plectix BioSystems, my knowledge of biological modeling was, at most, limited. I had a basic understanding of several biological pathways and signaling mechanisms through courses in Genetics and Physiology but had never known the depth at which these pathways could be explored. I realized through modeling the JAK-STAT pathway in Cellucidate that to perceive such biological mechanisms as merely isolated stepwise reactions is limiting and inaccurate. A model can provide a more detailed view of a biological mechanism and accounts for the complexity and specifics of a system, such as the reaction rates.
Over the summer, I translated a mathematical model of the JAK-STAT pathway (Yamada et al. 2003) in Cellucidate. I found modeling this pathway in Cellucidate to be intuitive and very straightforward. I was illustrating a pathway that had only been described on paper and was able to see the dynamics of this signaling mechanism through simulating the entire model. In trying to replicate the results of the Yamada mathematical model, I learned the importance of maintaining a level of transparency in a model so that the effects of certain assumptions are known and results can be replicated. Overall, modeling the JAK-STAT pathway in Cellucidate taught me how biological and mathematical data can be applied to illuminate the dynamics and intricacies of a cell signaling mechanism.
Dima Tokar is a rising senior majoring in Finance and Microbiology at the University of Massachusetts Amherst and has recreated a model of NF-Kappa-B.
As a novice to biological modeling, I learned a lot about the systems biology approach to modeling cell signaling pathways in just the ten weeks I spent working at Plectix. Using Cellucidate as a platform, I was able to build, debug and refine two NF-kappa-B models without prior modeling experience. With the help of Plectix scientists and online resources, I was able to understand the key aspects about modeling so that I could gather information from publications and incorporate relevant parts into a model. The collaborative approach of Cellucidate made it easy to find other models to learn from as well as to get some ideas on how to interpret, translate and create stochastic models. I learned about the importance of careful documentation of the model and the importance of leaving an easy-to-follow trail for researchers who may be looking to build upon the model. Looking back at my internship, I really enjoyed working with scientists and engineers and am glad I was exposed to the exciting field of systems biology.
