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.
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.
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.
- 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).
- biograph — a software written in PHP for simple Lineweaver-Burke plots.
- Bioinformatist.org (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.