Bruno’s journey into becoming a Mozilla Science Lab fellow

How did I found out about Mozilla’s work in Science?

My interest in genetics got me into biology, but I always liked programming. So after my MSc, I started doing more web development (besides bioinformatics) and going to conferences and meetups. I ended up going to Lisbon JavaScript 2013, and I thought I was the only scientist there.

But then I saw @billdoesphysics (from TRIUMF and CERN), and Angelina Fabbro (she worked at Mozilla!) give a talk about bad code in science! They mentioned how physics had been increasingly generating more data (e.g. 200 TB/week), but the field hadn’t kept up with progress coming from the open source and industry world regarding best coding practices (modularity, code reviews, tests, etc.). Thus, many big and important science projects had accumulated bad code and technical debt. They could no longer scale to the new volumes of data.

Their talk deeply resonated with me since even though I was (and still am) early in my career, I could see the same happening in biology. More data exponentially being generated but no incentives to spend more time in improving software rather that writing novel papers. Another key point from their talk was that anyone can do science (i.e. get more developers and academics working together!).

Bill and Angelina at LXJS 2013 saying we should educate scientist on the merits of open-sourcing their code

Soon after I moved to London to start a PhD in Bioinformatics at WurmLab.github.io with Yannick Wurm, and do research on the genetic diversity of eusocial insects. The week I arrived, Mozilla Festival was happening. MozFest is a beautifully organised chaos of a conference, where you have a building with nine open floors, and it feels like several conferences (open science, arts, journalism, etc.) are literally happening on top of each other.

Firefox on stage at MozFest 2013

There I saw more how science and the web can and should work together. Since then, I haven’t missed a MozFest. Because of all this, the Mozilla Science Lab was on my radar, and when they announced this fellowship it looked exactly like what I wanted to do! Unfortunately, when the first call for application happened, I was still half-way through my PhD so it was too soon for me to apply. On the second call I was on my last year and had run out of funding (it’s normal in the UK to do 4 years PhD, while only 3 years are funded…) so this opportunity was a perfect match! I could finish writing up my PhD, while contributing to my field through Open Science and Open Source projects.

How is it to be a Mozilla Science Lab fellow?

During my PhD, I founded bionode.io, an open source community project. Bionode’s aim is to build highly reusable tools and code by leveraging the Node.JS community. This fellowship gave me more time bandwidth to dedicate to this project and help build critical mass and momentum to carry it on after the fellowship.

Mozilla Science Lab table at MozFest 2016 Science Fair
Bionode.io workshop at MozFest 2016

I’ve also never traveled as much in my life as during this fellowship. Either for workweeks with other fellows, conferences, or workshops. This has given me a better perspective on the open science community, the institutions involved (and funding), and allowed me to meet In Real Life (IRL) many of the people I’ve been following online!

Crowd at CSVconf last week in Portland (try to spot the alpaca)

This fellowship has been an amazing, maybe even life changing, experience that I’m certain will impact my career. It has given a lot of visibility to my work and projects. And they even generously let you dedicate 20% of your time to carry on your research. However, this fellowship isn’t meant to fund your graduate studies, it is meant to champion changes in the way science is done. This is by building open and inclusive communities. So while I’m very happy with what I’ve achieved with bionode.io, it obviously has also been challenging for me to do the fellowship while still writing up the papers for the thesis. I think I could have enjoyed the fellowship even more if I was “done” with my previous work. But I do not regret anything since this “research break” has also given me a good perspective on my PhD and the strength to carry it through. You should see this experience more as a break to learn, meet, teach and try new things you usually would not be able to do, and that will make your next scientific research better, more reusable and more impactful!

Overall there are so many good things I take out of it, and some I will probably only realise the full scope in a few months or years after it’s all over. But the most important one is my new #mozfellows family, with which I’m sure we will accomplish stunning Open Science!!!

Science MozFellows at MozFest 2016

I feel very grateful to have been one of the selected fellows this year and would like to thank the Mozilla Science Lab for giving me this opportunity, Helmsley for funding it, and WurmLab.github.io for hosting and helping me.

Talking about a “Truly reproducible scientific paper” at Mozilla’s Working Open Workshop in Montreal

My application

I highly recommend this fellowship to anyone who loves Open Science!!! Which should actually just be called Science. Please don’t hesitate to reach out to me for any question (Bruno Vieira on Twitter and everywhere else). I’ll leave my application here below, hoping it will be useful for some to get ideas on writing yours! :D

What research fields are you in? (25 words)

Biology, evolution, genomics, bioinformatics and web development in general. In particular, comparative genomics of insects to understand the evolution of sociality.

What is your research focus? (50 words)

I’m comparing the genomes of social species (e.g., bees) with their solitary relatives to understand how sociality affects genetic diversity. This is relevant for conservation (among others). I make analysis pipelines that fetch data from the web, process it on HPC clusters, and visualise it on the web.

Describe to us your current research team. (50 words)

My current research team is big and very diverse in terms of skillsets ( http://wurmlab.github.io/team). We have a mix of wet lab biologists, bioinformaticians, web developers, mathematicians and biohackers. We are very open and help each other a lot. We go on retreats together. We interact a lot with other groups.

Supervisor name (10 words)

Yannick Wurm

Supervisor title (10 words)

Senior Lecturer in Bioinformatics

Describe to us how open science advances your research. (100 words)

Challenges in biology shifted from data generation to analysis (40,000x cheaper to sequence than in 2007). Now TONS of data are open and available. However, the rapid pace at which the shift happened means that it remains extremely challenging to analyse these data.
 My PhD research benefited tremendously from open data and methods. We spent 0$ and 0 minutes generating DNA sequences. My raw data compressed is 7 TB. Sharing my code before publication was responsible for the spontaneous generation of a new open source community project around it (bionode.io). I think all science should be open, transparent and reproducible.

Are you leading any projects related to open science? (100 words)

I founded BioNode.io which aims at leveraging Node.js and its community to make highly reusable tools and code that run everywhere for bioinformatics. We focus on using native Node.js Streams to make it scale by processing biological data in chunks. It all started 2.5 years ago when I shared my code on GitHub. Now we have contributors and users from all around the world. We are mentoring a Google Summer of Code student from Toronto. We organised a workshop at Mozfest 2015 and shared another with dat-data.com in 2014. We recently did a hackathon at Google Campus London.

How do you see Mozilla advancing your work? (50 words)

Mozilla would allow me to dedicate full time to leading bionode.io and contribute to other scientifically relevant open source projects, some of which I have connections with, e.g., dat-data.com, biojs.net and ipfs.io. It would facilitate sharing my work, organise open research hackathons and workshops, and get more collaboration opportunities.

What do you see as the opportunities for impact around open research at your university? Could you leverage this opportunity in a potential project? (50 words)

There is opportunities to organise events (e.g., training) to improve open research practices in the community, and include in undergrad students programs.
Foster Bionode.io development to benefit many open source projects in my university (e.g., wurmlab.github.io/tools) and outside.
My supervisor is a software.ac.uk fellow, we can use his network.

What do you think needs to change most immediately in scientific research? (100 words)

Mentality — Science needs to be an Open Source project. The established way in which science is reported through journals (mostly closed, unparseable formats like PDFs, in silos) and the excessive focus and over- promotion of positive results in detriment of methods or less impactful results hurts science transparency and reproducibility.
Tools — Some technological barriers combined with the lack of incentives for good code and reproducible methods make it hard for scientists (especially early career) to justify spending any extra time to be more open. This, added to the fear of being scooped, makes that the default is to do closed science.

What project in the field do you find most inspiring to further science and the web? (50 words)

Due to the massive amount of data generated in biology, being able to version control and distribute it efficiently would have an enormous impact on research. Dat-data.com aims to solve that. It is JavaScript and can run browser-side to be available everywhere.

Why is the the open web important to you? (25 words)

Sharing knowledge is the basis for human progress. The open web is the fastest and most efficient way to do it. Closed practices hurt everyone.