Welcome to the Computational Science Laboratory
Computational science in biomedicine and machine learning
The group research interests are rooted in application of computation to solve real world problems. Specifically, we develop new methods and algorithms and we apply them to computational chemistry, drug design, protein folding, etc.
The group and the spin-off company Acellera has collaborated with major industries worldwide like Sony, Nvidia, HTC mobile, UCB, Pfizer, etc.
Biomedicine. We use large distributed computational resources (GPUGRID.net) with thousands of GPUs for molecular dynamics simulations, binding prediction, binding kinetics, Markov state models, online sampling methods (ACEMD, HTMD). The approach is computational driven but we like to collaborate with experimental laboratories and industries where we work by rationalizing experimental results.
Machine Intelligence. In this new research line we develop machine learning approaches applied to the biological data. We are particularly interested in dimensionality reduction, artificial neural networks, unsupervised learning, reinforcement learning, sparce coding, deep and hierarchical learning.
- HTMD - HTMD is a Python platform for computational biology, including molecular simulations, docking, Markov state models, molecule manipulation, build tools for Amber and Charmm, visualization (webGL and VMD), adaptive sampling and more. Imagine setting up an entire computational experiment in a single, simple Python script.
- ACEMD - ACEMD has pioneered the use of GPUs for molecular simulations allowing for high-throughput simulations and ultimately leading to HTMD. ACEMD is still one of top molecular dynamics code, simple to use with a NAMD like syntax and compatible with input files from Charmm and Amber.
- Playmolecule - Most of our methods, predictors and machine learning approaches are publicly available via this webGL enabled site.
- Multiscale Laboratory GitHub - More tools are available in our github account. Follow us there.
- HTMD github repository - HTMD main repository publicly accessible in github. Contribute!
- The youtube channel of Acellera - Acellera posts a lot of material here
Current member of our research group
In our group we always value having the best people from different background and expertises
- Gianni De Fabritiis - Head of Computational biophysics laboratory at University Pompeu Fabra, Icrea research professor, Founder at Acellera
- Jose Jimenez - Phd student at University Pompeu Fabra
- Miha Skalic - Phd student at University Pompeu Fabra
- Alejandro Varela - Phd student at University Pompeu Fabra
- Pablo Herrera Nieto - Phd student at University Pompeu Fabra
- Stefan Doerr - Postdoc at University Pompeu Fabra and staff at Acellera
- Adria Perez - PhD student at University Pompeu Fabra
- David Tamayo - Collaborator, developper at Acellera
- Alberto Cuzzolin - Collaborator, staff scientist at Acellera
- Gerard Martinez - Collaborator, Staff at Acellera
- Joao M. Damas - Collaborator, staff scientist at Acellera
- Matt J. Harvey - Collaborator and HPC analyst at Imperial College London
Apply for a position
We are always looking for talented people who would like to join our laboratory. We praise on diversity of expertises, e.g. mathematics, chemistry, computer science, statistics, physics, biology, biotechnology, etc. If you are a passionate, hard working, self-motivated person with the ambition to do great science, send us an email at email@example.com.
These positions are closed but we might have similar ones in the future.
Gianni De Fabritiis, GRIB, Barcelona Biomedical Research Park (PRBB), C/ Dr. Aiguader 88, 08003, Barcelona, Spain.
Email: gianni.defabritiis at upf.edu