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miRprimer designs primers for PCR amplification of microRNAs as described (Busk (2014). A tool for design of primers for microRNA-specific quantitative RT-qPCR. BMC Bioinformatics. 15, 29) for use with the method miR-specific RT-qPCR (Cirera, S., and Busk, P.K. (2014). Quantification of miRNAs by a simple and specific qPCR method. Methods in Molecular Biology. 1182, 73-81.). The program was written in Ruby and is available as source code for developers and as an .exe file for easy use.

Tab2MAGE uses a flexible spreadsheet format for MIAME annotation of microarray experiments. Tab2MAGE spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.

Open source code base for enabling software innovation in imaging. The extensible and robust platform includes viewing, archiving, management, workflow and distribution of images as well as an open architecture for core competency tool development.

Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.

Ruby Research Wiki (RRiki) can be used to keep notes and organize references for research. It uses a browser interface, an intuitive plain text formatting language (markdown), and facilities to cross-reference and hierarchically organize notes

Simulator of virtual animals made up of biological neural networks for research in the Computational Neuroscience field.

CompLearn is a general-purpose compression-based machine learning system that uses data compression to learn or data mine patterns in arbitrary data.

Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.

EPTable is a simple web-based tool to analyze microarray gene expression profiles with additional gene profiles.

A client side browser implementation of Tom Ray's Tierra Artificial Life simulator (http://en.wikipedia.org/wiki/Tierra_(computer_simulation)).