Bayesian network modeling stock price change

Taking a cue from the systems biology folks, I decided to model stock price change interactions using a dynamic Bayesian network. For this analysis I focused on the members of the Dow Jones Industrial Average (DJIA) that are listed on the New York Stock Exchange (NYSE). Bayesian Networks A Bayesian network is an acyclic directed […]

gene annotation database with MongoDB

After reading Datanami’s recent post “9 Must-Have Skills to Land Top Big Data Jobs in 2015” [1], I decided to round out my NoSQL knowledge by learning MongoDB. I have previously reported NoSQL work with Neo4j on this blog, where I discussed building a gene annotation graph database [2]. Here I build a similar gene […]

iBioSim: a CAD package for genetic circuits

iBioSim is a CAD package for the design, analysis, and simulation of genetic circuits. It can also be used for modeling metabolic networks, pathways, and other biological/chemical processes [1]. The tool provides a graphical user interface (GUI) for specifying circuit design and parameters, and a GUI for running simulations on the resulting models and viewing […]

simulating RNA-seq read counts

The Challenge I want to explore the statistics of RNA sequencing (RNA-seq) on next-generation sequencing (NGS) platforms in greater detail, so I thought I’d start by simulating read counts to experiment with. This post details how I constructed a simulated set of read counts, examines its concordance with the expected negative binomial distribution of the […]

reporting negative results

Two of my recent posts have reported negative results, meaning that no meaningful effects were found during the investigations. Had these investigations been framed as hypothesis tests, we would have failed to reject the null hypotheses. Sounds boring. However there are good reasons to report these results. The first is that negative results still generate […]

GNU Octave: a free, open source MATLAB-like language for numerical computing

I tend to use Python with the Numpy, SciPy, and Matplotlib stack whenever I have to do scientific computing. For statistical computing I use R whenever this Python stack does not provide the necessary features. However, I want to draw readers’ attention to another tool for free, open-source numerical computing: GNU Octave (hereafter called “Octave”), […]

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 […]