fuzzy logic toolkit in C++

I recently came across some old C++ code I wrote about 10 years ago to assist fuzzy logic reasoning. This program is now posted on GitHub at https://github.com/badassdatascience/fuzzy-logic-toolkit and is described below. An example of the tool in action (with code) follows the description. Fuzzy Logic Suppose we have a numerical value for distance to […]

synthetic biology: an emerging engineering discipline

In the last decade a new engineering disciple called “synthetic biology” has emerged. It differs from the science of biology in that it applies engineering strategies to the creation of cells that perform a desired task, such as the production of drugs or biofuels. It also differs from previous genetic engineering approaches by stressing the […]

building a web-enabled temperature logger

Not wanting to miss out on the “Internet of Things”, I decided to learn some of its foundational technology, namely microprocessor programming. Actually, I used a Raspberry Pi in this project instead of a classic microprocessor, but the idea is the same. Here I describe building a web-enabled temperature logger, complete with a web application […]

rapidly extracting a subsequence from chromosome sequence data in Java

The Challenge We have a text file containing the nucleotides of a chromosome, say human chromosome 11, and need to be able to quickly extract a subsequence from the chromosome text given a nucleotide position and number of subsequent nucleotides to include. The problem is that chromosome files are huge, e.g. 135 megabytes for chromosome […]

engineer moves into an RV

I recently moved into a travel trailer to lessen the southern California cost of living (and because I like the idea of portable structures as an answer to housing scarcity). This living arrangement sparks my engineering creativity, which is the motivation for this post. Here I discuss RV living from a mechanical and software engineer’s […]

pyDome updates: tangential and spoke angles

In a previous post, I introduced pyDome, a Python program for calculating geodesic dome vertices, chords, and faces. I have since added two hub angle computations to the program, and report on that progress here. Face angle calculations still need to be implemented. Angles Between Chords and the Hub Tangent Plane The angle between a […]

building a forecasting application with AngularJS

Lately I’ve been working on an application that forecasts Amazon EC2 spot instance prices. (The forecasting element of this application will be described in a forthcoming blog post once I finalize the forecasting method). The tool needed a user interface, and I decided to write it with AngularJS as a learning exercise. This post describes […]

proportional-integral (PI) controller in Vensim

In my last post, I discussed an attempt at designing a PID controller using the Kepler Scientific Workflow system. Here I report on a similar (yet successful) development of a proportional-integral (PI) controller in Vensim PLE. Vensim is a software package for describing and simulating dynamic models, particularly those involving feedback. I’ve often described it […]

chaining map operations in Hadoop

Suppose we have a list of RNA sequences (pictured below), and we want to calculate both the “GC” nucleotide content and the RNA folding energy for each sequence using Hadoop 2.2.0. Furthermore, we want to chain the two operations so that each GC content result is fed to the corresponding sequence’s dG calculation. We also […]