about

I’m a Bioinformatics Developer, currently working towards a PhD in Bioinformatics. I’m experienced with software development in Python and R, particularly in what pertains to scientific software and data analysis. My main focus these days has been data pipeline development, primarily with Nextflow.

I also develop courses in subjects that interest me - I’ve taught short courses in Docker, Git (including one at Anaconda Learning!) and Nextflow (I’m also a Nextflow Ambassador!).

My interests include, but are not limited to: Metagenomics, Open Data, FOSS, Neuroscience, scientific software and reproducible science.

Check me out on these other websites:

And this is my CV.

contact

For academic inquiries, reach me through joao.cavalcante.073 at ufrn.edu.br.

If you’re looking to contact me about professional work, it’s best to reach me through LinkedIn. But feel free to hit me up in any of these websites:

projects

Attentively looking at some error logs at the CZI Open Science LatAm meeting (2023)

EURYALE

A pipeline for taxonomic classification and functional annotation of metagenomic reads.

MicroView

A reporting tool for aggregating results from taxonomic classification analyses

reconciler

A Python interface to W3C reconciliation services.

go2cell

R package to link Gene Ontology IDs to cell types via Wikidata.

Furthermore, I frequently contribute to Open Source software projects, among them:

work

Presenting my work at the Francis Crick Institute (2024)

2024

Future Innovators Programme - Sanger Institute

I collaborated with the Sanger Institute's Tree of Life Infrastructure team on new features for the nf-core toolkit, in order to enhance code reusability and collaboration, as well as facilitate the creation of new data pipelines.

Anaconda Learning Instructor

Worked with the Anaconda Learning platform to create a new Git course, focused on advanced git users looking to learn more obscure features and workflows.

2023 - 2024

Nextflow Developer - Dalhousie University

Worked for Dr. Robert Beiko's lab in the Faculty of Computer Sciences on the development of custom pipelines using Nextflow, primarily beiko-lab/ARETE, implementing them on SLURM HPC environments and guarateeing their function through automated unit tests, using nf‑test and GitHub Actions.

2022 - 2023

Bioinformatics Consultant

Worked as a freelance consultant, primarily in projects developing new bioinformatics workflows, in Nextflow, WDL, and the LatchBio platform.

2021

Google Summer of Code Student Developer

Took part in the Google Summer of Code program, developing software for the R Project for Statistical Computing. In the program, I developed dashboards and data analytics platforms to analyse social media data, primarily Twitter and MeetUp, to assist in decision-making.