Summary

I am a PhD student in Bioinformatics and Population Genomics at the Queen Mary University of London (WurmLab) and also a Node.js Web Developer.

I founded and lead the open source community project BioNode (modular and universal bioinformatics) and I am a member of the Dat team (git for data).

I am involved in open source and open research and participate/organise workshops and hackathons.

Previously, I worked for:

  • Geekli.st on the integration with the LinkedIn API
  • ESEB2013.com as the sole web developer and built it using Node.js, Express.js, MongoDB, Redis, Jade, Stylus, Bootstrap, etc, to manage the data of 1500 participants.
  • CoBiG² at the Faculty of Sciences of the University of Lisbon as a Bioinformatician, where I analysed Next-Generation Sequencing data, using mostly Python and R. I also had SysAdmin tasks.

I have a masters in human biology and environment and an undergrad degree in cell biology and biotechnology.

Experience

Full Stack Web Developer

2012-2013 | XIV Congress of the European Society for Evolutionary Biology (ESEB 2013)

I was the sole web developer and built everything from the ground up. I am still the current maintainer.

keywords: Node.js, Express.js, Bootstrap, MongoDB, Redis, CoffeeScript, Jade, Stylus

2013 | Geeklist

I was a team member, responsible for LinkedIn integration and backend tasks.

keywords: Node.js

2013 | CoBiG²

I built the new website in Angular.js using many APIs (mostly as an experiment and for learning) but I am not the current maintainer. I open sourced the code.

keywords: Node.js, Angular.js, Bootstrap, LinkedIn API, Mendeley API, Dropbox API, Facebook API, Github API

Bioinformatician

2013-Present | Queen Mary, University of London

I am a PhD Student under the supervision of Yannick Wurm and doing research in population genomics. Specifically, looking at genetic diversity of insects.

I am also contributing for a Crowdsourcing Web App for Gene Annotation, built with Ruby, PostgreSQL and Angular.js

2009-2013 | Computational Biology & Population Genomics Group (CoBiG²)

I've analysed Next-generation sequencing data and also performed sysadmin tasks.

keywords: Python

Papers

Published
In conference proceedings

Talks

Posters

Projects

Teaching

  • 2013-Present - Demonstrator for master of bioinformatics and R practicals at Queen Mary University of London
  • 2010 (Nov 25) - Class lecture about Next-generation sequencing for the MSc in Bioinformatics and Computational Biology

Webmaster

2010-2011 | Faculty of Sciences of the University of Lisbon

Deployed and maintained

Helped deploying

Skills

  • Programming languages: JavaScript, Node.js, CoffeeScript, Python (numpy, matplotlib, etc), Java, R and Bash scripting

  • Web languages: HTML5, CSS3 and Stylus

  • Templating engines: Jade and Dust.js

  • Databases: MongoDB (used in production) Neo4J (in testing) HDF5 (in testing) SQL (learned in college)

  • Integrated Development Environments: Sublime-text 2 (used in production) Vim (in production) Cloud9 (in testing) Eclipse (in college)

  • Distributed Revision Control: Git

  • Document Markup languages: LaTeX and Markdown

  • Systems Administration: Docker Vagrant GNU/Linux (Ubuntu and Arch, server and desktop) Windows (desktop) ZFS

  • Content Management Systems: Joomla, Wordpress and Drupal

  • Editing skills: Vectorial images (Inkscape) Pixmaps images (Gimp) Audio and Video

  • Bioinformatics: Next-generation sequencing (NGS) data processing and analysis Phylogeography and phylogenetics software

  • Biology: DNA Sequencing and Bacterial Culture

Education and Teaching

Degrees

2007-2009 | Master's thesis in Human Biology and Environment

Vieira, BM (2009). Comprehending the Cost of Antibiotics Resistance in Bacteria. Faculty of Sciences of the University of Lisbon (FCUL) Grade: 17/20

2004-2007 | Degree in Cell Biology and Biotechnology

Faculty of Sciences of the University of Lisbon (FCUL) Grade: 13/20

Extra Classes

2010 | Faculty of Sciences of the University of Lisbon

  • Fundamentals of Programming from the MSc in Bioinformatics and Computational Biology Grade: 16/20

  • Introduction to Databases from the MSc in Bioinformatics and Computational Biology Grade: 17/20

Workshops organised

Workshops attended

Courses organised

Courses attended

  • 2010 - Practical Course on Phylogenetics, Centre for Environmental Biology (CBA), Lisbon, Portugal
  • 2010 - Practical Course on Phylogeography, Centre for Environmental Biology (CBA), Lisbon, Portugal

Online courses attended

Conferences attended

Hackathons organised

Hackathons attended

  • 2015 (Sep 13-19) - BioHackathon 2015, Nagasaki University, Japan
  • 2015 (Jul 8) - OpenBio Codefest 2015. The Open Bioinformatics Foundation (O|B|F), University of Dublin, Ireland
  • 2014 (Apr 5) - Prototyping a Data Discovery tool. DNAdigest Hack Day, London, England

Open Source Contributions

Node.js Modules

  • 2014-Present - bionode A Node.js JavaScript library for client and server side bioinformatics.

  • 2013 - xml2json-stream 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.

Software

  • 2013-2014 - Afra - A web application for crowdsourcing genome annotation.

  • 2013 - CoBiG² - An Angular.js web app that uses many APIs (LinkedIn, Mendeley, Facebook and GitHub) and will become CoBiG²'s new website.

  • 2009 - Colony Counter - An ImageJ plugin for automatically enumerating Escherichia coli colonies. Published in Comprehending the Cost of Antibiotics Resistance in Bacteria. Masters thesis in Human Biology and Environment. Faculty of Sciences of the University of Lisbon

Arch Linux AUR Packages Maintainer

  • casperjs-git, a browser navigation scripting & testing utility written in Javascript on top of PhantomJS
  • phantomjs-git, headless WebKit with JavaScript API
  • genepop, a population genetics software.
  • ima2, a program for fitting the isolation with migration model for multiple populations.
  • populations, population genetic software (individuals or populations distances, phylogenetic trees)
  • structure, program for using multi-locus genotype data to investigate population structure.

Documentation

Other activities

Design

Posters

Logos

Music

Sports

  • Kung Fu (Choy Lee Fut) from 2007 to 2008 (6 months) and Karate during childhood