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The slides in this appendix highlight a few aspects of the software development work that I am currently leading in Dr. Julia Richards lab at the Kellogg Eye Center, University of Michigan, Ann Arbor.
Madeline is a program I developed for facilitating data management in genetic linkage studies. Linkage analysis is a technique for finding the disease-causing “needles” (genes) in the genetic “haystack” of a family.
Madeline fundamentally consists of a database engine merged with an engine that understands how people are related to one another in pedigrees. In addition to being able transform data into numerous formats and draw pedigrees used in genetic linkage analysis, the program allows one to run queries that require an understanding of the relationships between people. For example, I might ask the program to show me all of the families that have a pair of affected siblings where both parents are unaffected.
This slide highlights some of the new things we are working on for Madeline version 2 which will be a complete re-write of the program from the ground up. We are taking an object-oriented approach in redesigning the program using modern C++.
In collecting medical information on extended families, it is common to obtain only approximate information about some family members or sampled individuals. Doctors may record approximate values in medical records, and patients may not be able to recall exactly when they began having symptoms.
Most database systems simply cannot handle approximations, but in Madeline 2 we are designing classes which will be able to distinguish and record precise values, missing values, and imprecise values in the form of approximations or ranges ...