Hi, I'm bmpvieira,

About Me

Interested in Machine Learning, Genomics, Open Science and the Web.

Scientist by education and programmer by profession. Over the years, I've coded mostly in Node.js (JavaScript), Python, R, and Shell scripting to analyse Big Genomic Data.

Founded and lead Bionode.io, an Open Source community to build scalable code and tools for bioinformatics by leveraging Node.js.

In 2016, the Mozilla Science Lab awarded me a fellowship (one of four, out of 483 submissions) to travel around the world and champion open science through workshops and hackathons.

Reproducibility and scalability are important to me, thus I've also become an expert in Docker, Singularity, Nix (package manager) and cloud computing.

Worked for research labs and startups, I enjoy being at the intersection of industry and academia.

Skills

TypeScript
JavaScript
Python
R
Bash
Rust
Bioinformatics
Machine Learning
PyTorch
Datashader
Dask
Git
Scrum
TravisCI
NixOS
Docker
VSCode

Education & Experience

For more information, have a look at my curriculum vitae .

Projects

Modular and universal bioinformatics

Demo
Node Streams

XIV Congress of the European Society for Evolutionary Biology

Demo
Express MongoDB

Open Source Projects

Github profile and CV

Github
personal

Personal website

Github
personal

Custom Nix packages not yet available on NixOS/nixpkgs

Github

GFF parser

Github

Pixels Camp v4.0 (March 2020) call for talks — submissions

Github

Streamable FASTA parser.

Demo Github

Node.js module for working with the NCBI API (aka e-utils).

Demo Github

📦 Stencila's Nix packages collection

Github

🐳 A Docker image builder for researchers

Demo Github

Back-end of the Python 101 course for biologists

Github
course fcul

For QMUL's Genome Bioinformatics MSc module BIO721P & SIB's Spring school in bioinfo & population genomics

Demo Github

QMUL's programming in R course

Demo Github

A Web App for analysing GEO (Gene Expression) data

Github

Nix Packages collection

Github

Dockerfiles

Github

The go-to place for materials, contributions and work for the 2016 Mozilla Fellows for Science.

Github

Lightning Talks from the Mozilla Festival October 28-30, 2016

Github

:bangbang: :page_facing_up: :mag: an API and web interface to check if a paper has been retracted

Demo Github

NPM module that wraps request to allow Stream of URLs as input

Github

OBF Google Summer of Code

Github

2017 MozFellows Workweek - SF

Demo Github

try bionode using docker

Github

My Dockerfiles. Trusted Builds also available in the Docker registry

Github

Transform stream for Node.js that allows you to run your transforms in parallel without changing the order

Github

Github

HTML to Reveal.js

Github

A web wrapper for GeneValidator

Github

Intuitive local web frontend for the BLAST bioinformatics tool

Demo Github

Demo Github

Spawn and expose docker containers over http and websockets

Github

A simple Heroku app template for deploying Dat

Demo Github

real-time replication and versioning for large tabular data sets. pre-alpha!

Demo Github

Bionode Demo at CW15

Github

Talk about the PSMC, given in the Evolution Group Lab Jolly at the Queen Mary, University of London.

Github

Hiring a genomicist

Github

Bionode demo for a wurmlab meeting

Demo Github

Random scripts repo (for when using gist isn't the best).

Github

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.

Github

Small talk given at the outreach event for the Population Genetics Group 2015 meeting

Demo Github

Auto correct and generate reports for exams results stored in Dat

Github

Proxy to access resources that lack the Access-Control-Allow-Origin * header

Github

Node.js module for working with Streams of objects.

Demo Github

dockerfiles for nodeschool

Github

MSc Bioinformatics - QA and Assembly

Demo Github

Talk for TGAC - AllBio 2014

Demo Github

Talk given at wurm lab meeting, before allbio14.

Demo Github

interactive nodeschool online

Github

Fetch elife XML from AWS S3 into Dat

Github

Node.js Stream interface for Amazon Web Services (AWS)

Github

Stream interface for the Node.js module pace

Github

Github

Converts XML to JSON, using Streams and sax. This can be used with above-memory-limits XML files, as long as they're mostly composed of a repetitive tag.

Github

Quickly figure out time in other timezones.

Github

Github

Github

Genome Annotation for the Masses

Github

misc code and scribbles from our hack days

Github

Python 101 course administrative stuff

Github
course fcul

AngularJS app that uses many APIs. Used in the new CoBiG² website.

Demo Github
fcul website

Python 101 course slides

Github
course fcul

Dockerfile for Trusted Build of the image with the Afra project dependencies

Github

Lightning talk (5 min) given at the Citizen Cyberscience Summit 2014

Github
qmul talk

Lightning talk (2 min) for the Collaborations Workshop 2014 at the Software Sustainability Institute

Github

Talk given in a seminar at the Queen Mary, University of London.

Github

My Archlinux PKGBUILDs files

Github

Tools for bioinformatics

Github

Some configs that I share among servers

Github

Stuff that I've made in inkscape, gimp, etc, for various purposes.

Github

Contact

You can reach me via the channels below.