In Part 1 of this post we discussed a data structure called a de Bruijn graph and covered its application to genome assembly. To summarize, a de Bruijn graph is a type of graph that represents a set of k-mers as a set of directed edges on …
Posted in Computational Biology
To provide a bit of context for a discussion of Euler paths and Euler cycles: starting around December, a group of us in the Lab for Data Intensive Biology (DIB Lab) started working through the textbook Bioinformatics Algorithms: An Active Learning Approach and the associated website, Rosalind.info.
Rosalind.info is a site that is similar in style …
A short post with some thoughts on how writing Go code has helped me learn to stop worrying and love auto-formatting tools.
Go code is terse. Not Python-terse, but terse. And unlike Java, you don't find yourself constantly resorting to the security blanket of objects - something that Python (mercifully) can go either way on.
I used Java when I taught computer science at South Seattle College, and remember telling students once that one day, students taking CSC 142/143 would be using Go instead of Java. These days, I'm not as certain of that, but given that Go's strengths are …
NOTE: These ideas are implemented in the repository charlesreid1/2019-snakemake-byok8s.
In our previous blog post, Building Snakemake Command Line Wrappers we covered some approaches to making Snakemake workflows into …
NOTE: These ideas are implemented in the repository charlesreid1/2019-snakemake-cli.
This blog post covers the implementation of an idea that was originally explored in a blog post from Titus Brown, Pydoit, snakemake, and workflows-as-applications.
That blog post implemented a basic command line wrapper around the Snakemake API to demonstrate how a Snakemake workflow could be …
Posted in Computational Biology
This is the third in a series of three blog posts describing our solution to a bioinformatics problem from Rosalind.info, Problem BA1(i) (Find most frequent words with mismatches in a string). To solve this problem and generate variations of a DNA string as required, we implemented a recursive backtracking method in the Go programming language.
Posted in Computational Biology
This is the second in a series of three blog posts describing our solution to a bioinformatics problem from Rosalind.info, Problem BA1(i) (Find most frequent words with mismatches in a string). To solve this problem and generate variations of a DNA string as required, we implemented a recursive backtracking method in the Go programming language.
Posted in Computational Biology
This is the first in a series of three blog posts describing our solution to a bioinformatics problem from Rosalind.info, Problem BA1(i) (Find most frequent words with mismatches in a string). To solve this problem and generate variations of a DNA string as required, we implemented a recursive backtracking method in the Go programming language.
Continuing with our series of blog posts on what we've been learning about Go in the process of solving problems on Rosalind.info, this post will cover how some basic data structures work in Go, and how we used each to solve problems from the Chapter 1 Rosalind problems.
The simplest way to describe a map is to say it is a structure useful for storing key-value pairs.
Before we walk through what maps look like in Go, let's talk about what a map is (in the data structure sense). And to do …
Rosalind.info is a website with programming challenges, similar in spirit to Project Euler, but with a focus on bioinformatics.
Problems in the bioinformatics track are presented grouped by chapter, with several problems per chapter. The problems are designed like a coding competition, with problems providing structured input files and expecting structured output from each calculation. Each time you solve a problem, a unique input is generated, and you have a time limit in which to run your code to solve the problem.
Go is a programming language that is …