Modeling Biology

What exactly does WayFarer do?  WayFarer is a modeling tool that enables scientists to capture their own mental models.  WayFarer provides an intuitive, graphical environment to map out and display ideas that will stimulate the creative process.

The figure below represents three levels of abstraction in the modeling hierarchy. At the top, M2, level is a Modeling Description Language (MDL).  This can be the Unified Modeling Language (UML), Web Ontology Language (OWL), or Java; any language that can be used to build the underlying modeling tools.  The M1 level is the level of modeling tools; the resource that encompasses general scientific knowledge that can be used to describe more specific knowledge.  At this level scientists often use the Gene Ontology (GO) as well as other ontologies, Systems Biology Markup Language (SBML) and WayFarer. 

The M0 level is the level at which the actual biology is represented; the level at which a scientist describes the results from her lab experiment or develops a hypothesis about what processes may be at work.  A scientist may want to represent an apoptotic pathway, how a particular siRNA may activate a gene or the numerous mutations of the p53 protein and how they may interact with other proteins.  The scientist may be focused on the pathways involved with a disease process such as Muscular Dystrophy or how a particular SNP may affect a therapy. 

The value of using a high quality modeling tool lies in its ability to:

WayCraft has developed WayFarer with aim of meeting the needs of the biological researcher, providing a semantically rich framework in which to capture and retain their ideas and results. The integrated environment enables the sharing of ideas between researchers, lab groups and across entire organizations.


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