Software

This is 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.

VirAnnot

Role: Contributor, Author: Enrique Gonzalez-Tortuero

VirAnnot is a program for de novo annotation of viral genomes. I had created the docker image for VirAnnot and also helped with the testing and integration of VirAnnot into the Galaxy platform.

RiboPlot

Role: Developer (under the guidance of Audrey Michel and Pasha Baranov at the LAPTI).

RiboPlot is 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

gwips_tools is a collection of Python scripts for automated download of genome annotations and reference sequences from UCSC.

Galaxy BugFix: Missing files with history export

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

IT Query

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

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

ScienceFormat

An online manuscript preparation system for Researchers (discontinued).

Others

ep_insert_text

Etherpad plugin to search and insert text from an external JSON source. Autocomplete functionality using selectize.js.

Teamwork - import tasks from Excel

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

Citebot

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

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

biograph

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

Bioinformatist.org

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

VLinux

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

Screenshot of VLinux desktop

RPM packages

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

Plotdope

Plotdope - PERL script to plot DOPE output from Modeller.