# Building a Heap

Binary heaps are binary trees that are sorted in such a way that the parent leaf is either greater or lesser than both of its child nodes. When the root node is the greatest and each parent is greater than its children, then it's a max heap. In the opposite scenario, we have a min heap. When presented … Continue reading Building a Heap

# Testing graphs for bipartiteness

Graphs are amazing.Bipartiteness is a characteristic of certain graphs. A graph is bipartite if and only if you can color each node one of two two colors in such a way that no two adjacent nodes have the same color. Well, that's the realization of the actual definition, which can be found here. The two-color … Continue reading Testing graphs for bipartiteness

# de Brujin graphs and Velvet Optimiser

I'm working with the Velvet Assembler as part of my virus identification project. When I'm not trying to write a perl module to complement the already-bulky script files that I'm working with,  I like to do something that I usually wish most other bioinformatics scientists I've met would do as well: I like to delve … Continue reading de Brujin graphs and Velvet Optimiser

# Suboptimal Alignment Algorithm

Despite the existence of the Lalign program which could find internal duplications between two strings, I've developed my own algorithm for carrying out a similar function as part of this Rosalind problem.import distanceb="GACTCCTTTGTTTGCCTTAAATAGATACATATTTACTCTTGACTCTTTTGTTGGCCTTAAATAGATACATATTTGTGCGACTCCACGAGTGATTCGTA"a="ATGGACTCCTTTGTTTGCCTTAAATAGATACATATTCAACAAGTGTGCACTTAGCCTTGCCGACTCCTTTGTTTGCCTTAAATAGATACATATTTG"c=0da=""db=""for j in range(32,41):    for i in range(len(a)-j):        c1=0        for k in range(len(b)-j):        … Continue reading Suboptimal Alignment Algorithm

# Perl

Ever since I got to Ithaca at the Boyce Thompson Institute, I've had to learn how to program in Perl, a  less elegant version of my weapon of choice, Python.An underscore? Next, you'll be telling me to use goto and watch the world burn.My computer-esque tasks have included debugging a script that is used in … Continue reading Perl

# Any way the wind blows

Dear blog, my source of reflection,One thing that has occurred to me is that, in order to keep moving ahead in life, you need to routinely ask yourself why you are doing the things you do. For example, I've loved science since I don't even know when, but I never really ask myself why I … Continue reading Any way the wind blows