1. Developing a Software Package for Conceptualizing Molecular Findings Xinghua Lu, Harry Hocheiser & Vicky Chen Dept Biomedical Informatics

2. Motivation and Goal Bioinformatics research often produce a long list of genes of potential interest, e.g., genes differentially expressed in a cancer tumor A key task is to understand what are the major functional themes of the genes – Input: a list of genes of interest – Output: divide genes in to functional groups; the functional theme of each group is to be represented by a suitable biological concept

3. Strategies Currently, gene function is annotated with specific concepts from the Gene Ontology The Gene Ontology consists of a set of concepts organized in a hierarchy—a directed acyclic graph (DAG) Given a gene list, find out their corresponding annotations on the graph Group genes whose functions are closely related to each other within the graph and search a general concept to summarize the genes Quantitatively assess the information loss and strive minimize information loss

4. Finding Coherent Modules 4

5. What are involved Learning Python programming language Object-oriented programming, graph representation, and graph algorithms Information theory Most of the functionality is already developed Need to package/organize code into a package or a tool kit – Define API – Learn the function of existing code, modify if needed – Implement API by wrapping existing code – Package into a Python module – Documentation – Submit to BioPython community.