Ricardo Avila

Welcome to my bioinformatics and data science homepage.

Switching Your GTK Theme Based on Time of Day

Using systemd timers to automatically switch between light/dark GTK themes in a GNOME desktop. This may not be a data science post, but knowing systemd timers can certainly be handy for many applications where we want to run scheduled jobs on a Linux workstation.

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Interweaving R and Python with Reticulate

I love Python for general programming and data manipulation... but R has amazing statistical libraries. Do you also wish you could combine both? Here is a small demonstration of how acess Python objects from R using the Reticulate library.

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Mining Pharos with MySQL and Python

Accessing SQL databases with Python can be useful in many situations. Here, we use MySQL Connector and Python’s Pandas library to retrieve and manipulate data for Pharos targets. The goal is to obtain a dataset of targets that contain more than 15 active compounds, along with information about their different target classes.

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Mapping Pharos Targets to PDB Structures

The SIFTS (Structure Integration with Function, Taxonomy and Sequence) database provides mappings between UniProt genes and PDB structures, among other things. Using these mappings, we count the number of targets from the NIH's Pharos database which have ligands with known binding affinities, and at least one structure in the Protein Data Bank.

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