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.

RiboPlot

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 and as a conda package.

Related publication: RiboGalaxy: a browser based platform for the alignment, analysis and visualization of ribosome profiling data https://www.ncbi.nlm.nih.gov/pubmed/26821742. PubMed, NCBI.

Sample plot from RiboPlot

gwips_tools is 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.


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.


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

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).


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.


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.