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Clinical Practice Guidelines (CPGs) guide optimal utilization of clinical delivery of health care through evidence-based medicine, where care procedures are rigorously evaluated and improved through the examination of evidence. Care mapping is the technique of using flowcharts to graphically capture CPGs as discrete, actionable steps. Health professionals can create and use care maps to expedite and ensure excellence in optimal process workflow in patient care. Analysis of care maps would provide insight into similarities and differences in care procedures. However, quantitative analysis of care maps is difficult to perform manually, and becomes impossible as the set of care maps for comparison increases. Computational methods could be employed to obtain the required quantitative data, but current document standards for developing, sharing and visualizing care maps are not rigorous enough for computational analysis to take place. By using Bioinformatics approaches, we can solve these problems. Firstly, we can develop a standard care map file format for electronic storage. Systems Biology Markup Language (SBML), a document format used to describe biological pathways, can be used to develop the required file format. This method works because care maps are notionally very similar to biological pathways. It allows use of multiple alignment algorithms (traditionally used to align and cluster biological pathways) with these transformed care maps in order to derive quantitative data.This project involved the development of a software suite that is able to generate care maps in the SBML format and align them using an existing global multiple pathway alignment algorithm. It is part of a larger project that examines efficacy of CPGs. This would allow for two important studies to be conducted: a breadth study across multiple EDs and a longitudinal study over time within a single ED to see how it has been able to implement and adapt to the CPGs. By utilizing Bioinformatics approaches in care mapping, two important objectives were realized: the creation of a document standard for care maps, and computational comparison and contrast of CPGs. This opens up the exciting new field of Translational Informatics, which applies existing Bioinformatics concepts to e-Health, e-Medicine and Health Informatics.