Hello, I am Saul

Plant biologist
Aspiring bioinformatician
Lazy blogger
FOSS enthusiast

Saul Sotomayor Leyton

I am a Plant Biologist with experience in tissue culture, cloning, and protein expression, as well as RNAseq analysis. Currently, I am expanding my expertise in bioinformatics. I am also a strong supporter of FOSS, particularly in the use of Linux and Emacs.

Team Work

Independent Work

Hard Working

Education

		University of Tokyo 04/2018-04/2022 PhD in Applied Biological Chemistry
		University of Florida 08/2013-12/2015 MSc in Plant Molecular and Cellular Biology
		Mayor de San Andres University 01/2001-09/2009 BSc in Biology

Skills

Bash

Capable of writing pipelines for the processing of high-throughput sequencing data as well as general terminal use, including writing scripts for automation of simple tasks (e.g. file processing, backup).

Emacs

Used as the main application for academic work. Writing code (R, Bash, Python), Version control, Text processing (LaTeX), among others.

R

Good understanding of the packages available for mapping, annotation and quantification of high-throughput sequencing data, as well as, those for data visualization. Basic knowledge of parallel processing.

Python

Good understanding of Python, with experience in data visualization using Plotly Dash, as well as working with libraries such as NumPy and pandas.

Web devel

Good understanding of HTML and CSS, along with a basic knowledge of JavaScript. These aimed at the customization of visualization dashboards and HTML-based presentations (i.e. Reveal.js)

Projects

Degradome analysis pipeline

Main contributor April 2022 - Present

Pipeline for the analysis of degradome sequencing data using the third party PyDegradome script followed by a custom classification.

academic RNAseq pipeline

R post-PyDegradome

Main contributor Oct 2022 - Present

R package with custom functions to process PyDegradome output.

academic RNAseq R

Demo Plotly Dash

Owner Aug 2023 - Present

Demo of a Plotly dash app for the analysis of RNA degradome data.

academic Python Plotly

Emacs configuration

Owner Jan 2023 - Present

Personal configuration file using straight.el. Two versions are provided, with and without Helm.

hobby emacs

Reveal.js presentation demo

Owner Sep 2024

A sample reveal.js presentation customized using Tailwind. The presentation was created from an Emacs org-mode file using org-reveal.

hobby reveal.js emacs-org

Recent Posts

An example of literate programming written in org-mode

Introduction In this post, a more comprehensive example of using Emacs org-mode to write documents with embedded programming code is presented. The example uses different header arguments for processing the code, showcases various ways to reference code in the text, and describes customizations for better HTML/PDF export display. The next section displays the output in both HTML and PDF formats. The files used to generate the output are available on Github, as well as the files used to configure Emacs (see the Repositories section)

Monday, September 1, 2025 | 21 minutes Read

Write code with Emacs org-mode

Introduction In this post, I aim to demonstrate the use of Emacs org-mode for taking notes that incorporate programming code. The goal was to not only display code with proper formatting and syntax highlighting but also to execute it and show the results of specific code blocks, allowing readers to reproduce the entire analysis if desired. The challenge was to sift through available examples and documentation to put together a summary that brings something new to what’s already been written about this topic. Initially, I intended to focus solely on customizing the PDF output, but as I explored the documentation, I discovered other aspects that I believe are worth sharing, most notably, customization of HTML output. As a result, however, the post ended up being quite long thus, here is a brief overview of each main section:

Sunday, July 27, 2025 | 35 minutes Read

Animating content in Reveal.js using Emacs Org-mode

Introduction This post demonstrates how to use animations in a Reveal.js presentation written in Emacs org-mode (and exported with org-reveal). The animations covered include fragmented content, lightbox effects, and custom CSS classes. While fragmented content is described in the org-reveal documentation , I encountered some difficulties when applying it to elements other than list items. For lightbox effects, I present a couple of examples here, though the official documentation provides more comprehensive details and use cases. Finally, I include a couple of examples of custom CSS classes. All of these animations are meant to improve the delivery of information.

Monday, June 23, 2025 | 10 minutes Read

Awards

MEXT Scholarship to conduct PhD studies

MEXT Program - Bolivia March 2018 - March 2021

Scholarship awarded by the The Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan through its Embassy in Bolivia.

Fulbright Scholarship to conduct MSc studies

Fulbright Commission - Bolivia August 2013 - August 2015

Scholarship awarded by the Department of State of the United States of America through its Embassy in Bolivia.

Accomplishments

Academic and pedagogical organization of the classroom

CEPIES March 2024 - July 2024

This course provides the foundational theories of teaching and learning as applied to higher education. Building on this knowledge, it enables the development of academic plans for courses specific to the participant’s area of expertise.