To assist with a project I’m working on, I recently implemented a substantial portion of DisGeNET as a graph database. Furthermore, I added MeSH, OMIM, Entrez, and GO into the database to facilitate linking of data between these sources. Here I briefly describe these data sources, describe graph databases, and then show how use of […]

# Category: science

## the science of gender identity (part 2: brain anatomy)

This is the second post in a mult-part series surveying the current science of gender identity, particularly with regard to the transgendered population. In my previous post I discussed the proposed genetic associations and corresponding research. A future post, if I can find sufficient data, will address neuropsychology research related to the transgender experience. Here […]

## the science of gender identity (part 1: genetics)

This is the first in a multi-part series surveying the current science of gender identity, particularly with regard to the transgendered population. I intend to discuss the genetic, brain anatomic, and neuropsychological findings of recent studies on the matter. As always, I will incorporate my own statistical analysis of raw study data wherever possible. Here […]

## fast genomic coordinate comparison using PostgreSQL’s geometric operators

PostgreSQL provides operators for comparing geometric data types, for example for computing whether two boxes overlap or whether one box contains another. Such operators are quick compared to similar calculations implemented using normal comparison operators, which I’ll demonstrate below. Here I show use of such geometric data types and operators for determining whether one segment […]

## 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 […]

## Kaplan-Meier estimator in Python

The following Python class computes and draws Kaplan-Meier product limit estimators for given data. An example of how to use the class follows the code. Code Usage Example

## 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”), […]