Software

A list of software I had developed or contributed towards in the last few years. Most of the code is available on Github under an open source license.

2015

RiboPlot - a Python program to plot and output Ribo-Seq read counts from BAM format alignment files. Available online at RiboGalaxy, from PyPI and as a Galaxy wrapper.

Related publication: RiboGalaxy: a browser based platform for the alignment, analysis and visualization of ribosome profiling data. PubMed, NCBI.

Sample plot from RiboPlot

gwips_tools - a Python program for automated download of genome annotations and reference sequences from UCSC.

Contributed a patch to fix an issue with exporting history items in Galaxy.

2014

ScienceFormat (now discontinued, page on Facebook) - an online manuscript preparation system for Researchers.

Screenshot of ScienceFormat manuscript editing page

Implemented the functionality of importing tasks and task lists from Microsoft Excel files on Teamwork.

2012

IT Query - A graphical user interface written in PyQt for visualizing and managing data from the ItemTracker LIMS system in BioNumerics.

Related publication: Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains. PubMed, NCBI.

Screenshot of IT Query main window

IT CRISPR - A graphical user interface written in PyQt to assemble and track progress of CRISPR sequence experiments in BioNumerics.

Screenshot of IT CRISPR main window

There are some additional scripts for working with BioNumerics in the same repository.

2011

Citebot - An Android app to retrieve full text and PDF of research articles published in the Public Library of Science (PLoS) journals.

Screenshot of Citebot

about:authors - An application for interactive visualization of author profiles on ScienceDirect and Scopus. (participant, 2011 Apps for Science contest).

2007

biograph- a software written in PHP for simple Lineweaver-Burke plots.

Bioinformatist.org - Wiki project with step by step instructions for installing Bioinformatics software. First prize winner, the 2007 BioWiki contest.

2005

VLinux - Live Linux CD with Bioinformatics software pre-installed.

Screenshot of VLinux desktop

Built RPM packages of some Bioinformatics software. These are now integrated into the openSUSE science project.

Plotdope - PERL script to plot DOPE output from Modeller.