Software

BioVM

An open, customisable, virtual machine based on Ubuntu Linux for teaching and learning Bioinformatics.

Links
GitLab (source code) • SourceForge (download) • Documentation

BioVM Desktop

Go!

An Android app that displays motivational quotes from Reddit r/GetMotivated. It is written in Dart and Flutter and uses the Reddit API to retrieve quotes in JSON.

Available on Google Play Store

Go! for Reddit

Scientific software developed in research groups as part of a team

RiboPlot

A Python program to plot and output Ribo-Seq read counts from BAM format alignment files. This program and the riboSeqR Galaxy wrapper were developed under the supervision of Dr. Audrey Michel and Dr. Pasha Baranov at LAPTI, UCC in 2015.

The main program is written in Python 2 and uses the pysam module for working with FASTA and BAM format alignment files. Matplotlib is used for generating plots. HTML output is generated using the Skeleton CSS framework and the Tablesorter JavaScript library is used for sorting the HTML table produced from Ribocount.

Sample plot from Riboplot

RiboPlot is available on:
PyPIAnacondaGalaxy toolshedGitHub Documentation

Galaxy wrapper for riboSeqR

This is an XML wrapper for integrating the R package riboSeqR in RiboGalaxy and Galaxy.

Features implemented include preparation of riboSeqR input from SAM format alignment files, triplet periodicity, metagene analysis, plotting ribosome profiles and differential translation analysis using baySeq.

riboSeqR wrapper is available on GitHub.

BioNumerics 6 scripts and GUIs

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.

Main window of IT Query IT Query is used for visualizing and managing data from ItemTracker LIMS system.

Main window of IT CRISPR IT CRISPR is used for assembling and tracking the progress of CRISPR sequence experiments.

BioNumerics scripts can be obtained from GitLab.

Docker images

For VIGA, QIIME 1, PyFBA, and DADA 2 programs with dependencies pre-installed. Docker images and corresponding Dockerfiles can be obtained from Docker Hub and GitLab.

GWIPS tools

Python scripts for automated download of genome annotations and reference sequences from UCSC. GWIPS tools can be obtained from GitHub.

Other projects

Themes for Pelican and Sphinx

pelican-attila-x

A theme for the Pelican static site generator based on the Ghost blogging engine’s Attila theme. This is a work in progress. A release will be made when theme is feature complete.

susty-pelican

The Wordpress susty theme ported to Pelican (repository).

Solar theme for Sphinx

Theme for Sphinx documentation projects based on the Solarized color scheme (repository).

VLinux

VLinux was a live Linux CD with Bioinformatics software pre-installed.
Note: Development has been discontinued. Please consider using BioVM instead.

VLinux Desktop