Bonsai and beyond: building tools that build minds

When Gonçalo Lopes first walked into the Instituto Gulbenkian de Ciência in 2010 – when it was still hosting Champalimaud Foundation (CF) staff before their new building opened – he felt as though he’d crossed into another world. “There was this sense of adventure”, he recalls. “Everyone was completely absorbed in their experiments, standing on the edge of what was known. They weren’t just studying the brain – they were building the tools to study it”.

From start-up to synapses

Before turning to neuroscience, Gonçalo had spent several years in Portugal’s early start-up scene. After studying at the Centre for Artificial Intelligence (CENTRIA) at NOVA University, he joined a spin-off called YDreams, founded by professors recently returned from the Massachusetts Institute of Technology (MIT). “The idea was visionary,” he says. “We were going to live in a world immersed in sensors – a world where computers weren’t just desktops, but everywhere around us”.

By 2009, he was leading a team developing interactive systems for this emerging era of ubiquitous computing. But something was missing. “I was designing smart machines without really understanding what intelligence was”, he says. “I wanted to know how living systems, like us, interact intelligently with the world”.

That’s when his mother showed him a small ad in the newspaper Expresso for CF’s neuroscience PhD programme. “It was perfect timing. I thought I’d have to leave Portugal to study neuroscience, but here was this chance to do it at home. I decided I was going to get in – by any means necessary”.

“When I interviewed with Zach Mainen, one of the programme’s directors, I told him, ‘If you don’t take me as a PhD student, I’ll work as a technician’”, Gonçalo recalls. In the end, there was no need – he was selected. “I started reading The Cell, this massive textbook on how living cells work, and learning how these tiny systems organise themselves and self-assemble into entire organisms. It completely changed my view. I stopped thinking of the brain as an abstract information-processing machine – like the deep neural networks we hear so much about today – and began to see it as part of the body, something deeply embedded in biology”.

When Gonçalo joined the first cohort of International Neuroscience Doctoral Programme (INDP) students to move into the Champalimaud Centre for the Unknown in 2011, the building was still half-empty. “There was no security, no card swipes – you could just walk straight in”.

Their first experiment in the new space? Dissecting the giant axons of cuttlefish, together with principal investigators Adam Kampff and Joe Paton, who would later become his supervisors. “We were a mixed bunch – computer scientists, psychologists, molecular biologists, mathematicians, medical doctors, engineers. Every week we were taught by some of the world’s leading neuroscientists, brought in by the faculty’s network. It was an incredible privilege”.

“One week, a Buddhist meditation group came to teach us in the prayer room at CF”, he says. “Another week, we explored interpersonal communication with Rita Venturini, a postdoc in the Mainen Lab. At the time, it all seemed a bit unconventional, but those tools for reflection and organising our thoughts would prove invaluable”. More on that later.

Giving back to the community

During his PhD, Gonçalo soon realised that to run his experiments, he’d have to build his own tools. “To understand natural intelligence, I needed a way to synchronise data from multiple instruments – measuring brain activity, behaviour, and environment all at once”, he says. “It turned out that wasn’t an easy problem”.

So he wrote a new visual programming language to solve it. That language became Bonsai, an open-source platform for experimental neuroscience that lets researchers connect hardware and data streams in real time – “a way of making instruments talk to each other”. 

“At first, I was just sharing Bonsai with people I knew”, Gonçalo says. “But it started to take on a life of its own. By the time I finished my PhD, it had grown beyond CF – students, technicians, PIs – everyone was using it”.

Today, Bonsai is used by thousands of scientists across the US, Europe, and Japan, and has become a standard in systems neuroscience. “There are many specialised tools for recording neural activity, behaviour, and stimuli”, he explains, “but what was missing was something that could bring all those signals together”.

After his PhD, Gonçalo founded NeuroGEARS – a company bridging neuroscience, games, and robotics to make scientific tools for studying behaviour more accessible and adaptable. The company supports labs adopting Bonsai and continually improves it based on feedback from researchers building new experiments. “It’s not about creating a tool and then asking people what they think”, he says. “You build it with them, from day one”.

When ideas connect

As Bonsai’s reach grew, it led to an identity crisis. “Was I a neuroscientist or an engineer? I’d made this tool, but my PhD was supposed to be about neuroscience, not programming”. The resolution came during his final year, when he moved to London to join his supervisor Adam at the Sainsbury Wellcome Centre. “I stopped going into the lab every day. I started running in Hampstead Heath in the mornings, thinking, connecting everything I’d done into something coherent”.

That process, he adds, was deeply influenced by those early PhD classes. “They’d taught us how to meditate, how to think about thinking. It helped me close the circle – to write my thesis on the role of the motor cortex, define my own questions and answers, and join the dots”.

For Gonçalo, finding connections between ideas and disciplines is central to both science and education. “I think we’re losing sight of what a university really is. It’s become too narrowly focused on training and performance – on career tracks, employability, and ticking boxes. Education should begin with dialogue and co-creation, a shared space that cultivates curiosity and values knowledge for its own sake. If I could design the perfect tool, it would be one that helps bring that kind of university back to life”.

That idea inspired one of his favourite projects: Neuronautas, a hands-on neuroscience summer camp for high-school students supported by both the Gulbenkian Foundation and CF. “It’s something I helped create with Catarina Ramos, Danbee Kim, João Frazão, Nuno Loureiro, Gil Costa, and many others at CF, and it embodies the same spirit of openness and co-creation that shaped us from the start, when everything felt fluid and in motion. It’s had a lasting impact on a generation of young Portuguese scientists and stands as testament to how education and research can evolve together”.

That same collaboration and educational mindset carries into his current work. “At NeuroGEARS, we’ve been working with a group at the Gatsby Computational Neuroscience Unit to build a system that turns doctors into scientists”, Gonçalo says. “The idea is to give each clinician the tools to ask their own questions about their patients’ progress, instead of relying on standard diagnostics alone – to empower them to measure, explore, and make informed decisions based on the data they collect. It’s like personalised medicine, but for doctors. We’re already developing a prototype for the NHS to track movement disorders such as Parkinson’s”.

As for the future, he hopes CF can keep that collaborative ethos alive even as it grows and becomes ever more established. “There’s always a danger that structure and hierarchy replace the freedom to explore”, he says. “But education is the glue that holds co-creation together. CF has travelled far in 20 years, and I hope it brings back from that journey the seeds of a new kind of open science education – one rooted in cooperation and freedom, to shape not just the future of science, but the future of how we learn”.
 

Gonçalo Lopes, Former PhD Student in Neurosciences at the Champalimaud Foundation, Current Director of NeuroGEARS

Text by Hedi Young, Science Writer and Content Developer of the Champalimaud Foundation's Communication, Events & Outreach Team
 

Full 20 Years, 20 Stories Collection here.