Understanding how cells orchestrate their behavior to construct a complex functional organ or an entire organism is an important scientific problem, which despite the tremendous progress in molecular and cell biology poses many open questions (e.g., how are stem cell population dynamics regulated to build and maintain organs.) Computational methods and modelling are beginning to play an important role in understanding developmental processes, by allowing the construction of mechanistic models of the underlying systems, performing in-silico experiments and suggesting new directions for experimental investigation. However, many of the existing computational methods and tools are not accessible to experimental biologists (e.g., large sets of differential equations or complex software code), thus it is difficult for the experts in the field to ensure the hypotheses and assumptions incorporated in the model are reasonable, and that models keep up to date with the latest experimental findings.
To alleviate this problem, we have developed Biocharts, a tool supporting a visual language to model complex dynamics, in an intuitive and more accessible way for the wider scientific community. Biological assumptions and experimental results can be encoded within a common framework, using scenarios and states. Models can be interactively explored by the user to ensure they capture the intended behaviour, visualizing model execution using the same language the model is developed in. We are currently applying the tool in developmental biology and stem cell research.
The following modeling examples are described in more detail in our documentation
For more biological examples download the tool and related documentation.
Former Interns that have done research related to the tool and methodology: Chris McEwan, Aleks Milicevic, Antti Larjo, Itai Segall.
Biocharts uses Dynamic Data Display for visualising simulation plots and spatial behavior.