What I’m developing at the moment, my contributions in research groups, and some side projects.
A ready-to-use virtual machine for teaching and learning Bioinformatics.
I have built Docker images for the following software when required in the research group or as a learning exercise — VIGA, QIIME 11, PyFBA, and DADA 2.
These images include programs and their dependencies pre-installed. In some cases, there are wrapper scripts in Bash, that will help users run containers easily, without needing root privileges. You can get these scripts and Dockerfiles from GitLab.
Related blog post
Docker images for Bioinformatics software
These are projects I worked in the past and are not currently in development. If there is an important issue that needs to be fixed, please get in touch with me.
The following projects in this list were developed in research groups as part of a team — RiboPlot, riboSeqR wrapper for Galaxy, IT Query and IT CRISPR. These were all written in Python 2 and are not currently being developed. Python 2 is not supported as of January 2020.
A Python program to plot and output Ribo-Seq read counts from BAM format alignment files.
This program and the riboSeqR Galaxy wrapper discussed below, were developed under the supervision of Dr. Audrey Michel and Dr. Pasha Baranov at LAPTI, UCC in 2015.
Documentation is available here.
Galaxy wrapper for riboSeqR
Using the inclued tools, you can prepare input files for riboSeqR from SAM format alignment files, calculate triplet periodicity, perform metagene analysis, plot ribosome profiles, and perform differential translation analysis using baySeq.
You can install
riboseqr_wrapper from Galaxy tool shed.
Source code is available on GitHub.
BioNumerics 6 GUIs and scripts
These programs were written using Python 2 and PyQt 4 and were developed in collaboration with members in the Microbial Phylogeography group at Environmental Research Institute, UCC during 2007-2012 under the supervision of Prof. Mark Achtman.
You can get these programs and scripts from GitLab.
GWIPS tools — download genome annotations from UCSC
A live Linux CD with Bioinformatics software pre-installed2.
Sphinx theme using the Solarized colour scheme (GitLab).