Source code is available on Github and Gitlab.

Contributions to software developed in a research group


RiboPlot is a Python program to plot and output Ribo-Seq read counts (and optionally with RNA coverage) from BAM format alignment files. I developed the program in Python, created a wrapper for Galaxy and also made it available in the PyPI and Anaconda repositories.

A sample plot from RiboPlot

Graphical interfaces in Python for BioNumerics

IT Query is a program for visualizing and managing data from a LIMS system from within a BioNumerics database.

The main window of the IT Query program

IT CRISPR is a program to assemble and track progress of CRISPR sequence experiments in a BioNumerics database.

Read more about IT Query and IT CRISPR ...

Other contributions and experiments

  • BioVM — a ready-to-use virtual machine with Bioinformatics software.
  • VIGA is a program for de novo annotation of viral genomes. I created a Docker image for VIGA and also assisted in the testing and integration of VIGA into the Galaxy platform.
  • Docker images for bioinformatics software — qiime, VIGA, pyFBA, DADA 2 and more. Available from the Docker Hub.
  • gwips_tools — Python scripts for automated download of genome annotations and reference sequences from UCSC.
  • ep_insert_text — Etherpad plugin to search and insert text from an external JSON source. (JavaScript, HTML, CSS). Demo (gif).
  • Go! — An Android app to display motivational quotes from Reddit. (Flutter, Dart)
  • Citebot — An Android app to retrieve full text and PDF of research articles published in the Public Library of Science (PLoS) journals. (Sencha Touch, PhoneGap).
  • about:authors — An application for interactive visualization of author profiles on ScienceDirect and Scopus. (participant, 2011 Apps for Science contest). (HTML, CSS, JavaScript).
  • biograph — a software written in PHP for simple Lineweaver-Burke plots.
  • (not available anymore) — A wiki project with step by step instructions for installing Bioinformatics software. First prize winner, 2007 BioWiki contest.
  • VLinux — Live Linux CD with Bioinformatics software pre-installed.
  • Plotdope — PERL script to plot DOPE output from Modeller.