Building a Virtual Model

Focus on the Biological Mechanism of Interest

Our mission is to emulate the development of life by simulating its biological building blocks and their interactions.

This focus is on the living cell and its immediate environment. Typically, we are not concerned with everything inside a cell’s wall, but only on those critical elements of its biological architecture that relate to, and impact, a specific path or mechanism of interest.

The goal is to achieve relational clarity between critical biological events within a cell and its environment; to transform an otherwise static snapshot of a biological mechanism into a dynamic and actionable virtual network of manageable events.

That is to say, we bring virtual life to a static understanding of a given biological mechanism.

Although CellSim™ is capable of creating basic, virtual biological mechanisms from the ground up, we generally start with a framework of information that is considered to be well understood.

For example, starting from existing knowledge, mechanisms of methotrexate (MTX)-induced stress pathways in the hepatocyte are shown below as a diagram of related biological events.

Ezhilarasan D. Toxicology. 2021. doi: 10.1016/j.tox.2021.152840

By creating an interactive baseline model of the above, outlined in red, one which is known to correspond to in vitro or in vivo observations, it then becomes possible to conduct any number of virtual experiments within this virtually alive and dynamic framework.

The adjacent Metabolic Network diagram describes critical and constitutive parts of the mechanisms depicted in the above starting diagram.

Like the originating diagram, our Metabolic Network diagram is also abstracted so as to focus on the critical elements necessary for an initial and working relationship between the constitutive parts of this biological mechanism.

This Metabolic Network is but one facet of a highly dynamic and actionable virtual environment, comprising a comprehensive, virtual cell biology laboratory – a snapshot shown below.

It is intended to work hand in glove with the wet lab; typically in an iterative and interactive manner during the pursuit of greater insight into possibly undiscovered relationships among known as well as yet unknown, biological elements.

This abstract baseline model is only the beginning. You then iteratively build more details and granularity into the model or expand it to model and simulate ever more complex, non-linear and emerging properties, including cell growth, divison, movement or death.

Going from abstract to ever more detailed and actionable models.

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