Author: Juoko Virtanen

Testing Code: A Case Study

Reading Time: 2 minutes Testing code is essential for finding bugs before they get into production. Without automated tests it will take longer and longer to debug code as it grows in size and complexity and development will grind to a halt. I am consulting for a company that has not made it a priority to test its code. Thus, one of our early priorities was to write unit Continue Reading

Unit Testing with ScalaCheck

Reading Time: 5 minutes Unit testing is essential to writing good code. Unit testing allows us to capture bugs as they are created, not long after they are deployed. A little time spent writing unit tests can save a lot of time debugging. If unit testing is not done it can become increasing more difficult and time consuming to fix bugs as code complexity and size increases. However, in Continue Reading

A Machine Learning Case Study

Reading Time: 5 minutes This is my third blog post on MR-REX, a software package used to help determine protein structures given experimental X-ray crystallographic data, which I created while a postdoctoral fellow at the University of Michigan. You can find the other two here and here. MR-REX uses several terms to assess how well a particular placement of the protein in the unit cell reproduces the experimental X-ray Continue Reading

Maximum Likelihood

Reading Time: 7 minutes Maximum likelihood is the procedure of finding the value of some parameters for a given statistic which makes the likelihood of the the known likelihood distribution a maximum. Maximum likelihood is a method with many uses. A classic example is linear regression. If it is assumed that the errors on the x variable follow a Gaussian distribution we can compute the probability density of the Continue Reading

Storing and querying triples using Apache Rya

Reading Time: 3 minutes Apache Rya is a tool for storing and querying triples at scale. It is not used much and consequently it is poorly documented and it is difficult to get started using it. This blog post is intended to give people the information they need to get started with Rya. In order to run Apache Rya you will need Accumulo, Hadoop, Zookeeper, and of course Rya Continue Reading

Protein Structure determination aided by Stochastic Search (Replica Exchange Monte-Carlo Method)

Reading Time: 8 minutes Introduction Proteins are large molecules, which occur in abundance in every single living organism. They carry out vital functions such as transporting oxygen, converting the food you eat into energy your body can use, and many more. Proteins are long chains of linked units called amino acids. There are 20 types of amino acids. Proteins fold into different shapes depending upon their sequence of amino Continue Reading

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