Master's Defense

15-20 min presentation
round of questions 3x15 min
< 2 hrs in total
breadth questions: what is blast, 3 domains of GO (biology process, cellular component, molecular function)

* cellular component, the parts of a cell or its extracellular environment;
* molecular function, the elemental activities of a gene product at the molecular level, such as binding or catalysis;
* biological process, operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms.


motif - Zinc finger bind zinc ions

RDF

weeding out outliers

how will it affect biologists

reproducible research

results sound and complete?

greedy vs dynamic programming

http://www.algorito.com/algorithm/counting-coins-algorithm-greedy-vs-dynamic-programming

# The greedy method computes its solution by making its choices in a serial forward fashion, never looking back or revising previous choices. (can get stuck at local minima) (FASTER than dynamic programming)

Nevertheless, they are useful because they are quick to think up and often give good approximations to the optimum

# Dynamic programming computes its solution bottom up by synthesizing them from smaller subsolutions, and by trying many possibilities and choices before it arrives at the optimal set of choices.

In other words, a greedy algorithm never reconsiders its choices. This is the main difference from dynamic programming, which is exhaustive and is guaranteed to find the solution. After every stage, dynamic programming makes decisions based on all the decisions made in the previous stage, and may reconsider the previous stage's algorithmic path to solution.