Computational Science group of GRIB
The Computational science research group led by Gianni de Fabritiis is dedicated to 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, founded in 2006, has collaborated with major industries worldwide like Sony, Nvidia, HTC mobile, UCB, Pfizer, etc.
The current research lines of the group are:
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.
Web Resources
- 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
The Computational Science group of GRIB is integrated in the Research Programme on Biomedical Informatics, GRIB. The GRIB is a joint research programme of the Hospital del Mar Medical Research Institute (IMIM) and the Department of Experimental and Health Sciences of the Universitat Pompeu Fabra. The GRIB mission is to develop and apply computational methods and information technologies for a better understanding and prediction of biological phenomena, giving especial emphasis to those related to the human diseases, their prevention, diagnosis and pharmacological treatment.
Main projects
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1.
CompBioMed: A Centre of Excellence in Computational Biomedicine
CompBioMed is a user-driven Centre of Excellence in Computational Biomedicine, to nurture and promote the uptake and exploitation of high performance computing within the biomedical modelling community. European project funded by the H2020 for period 2016-2019.
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2.
Conformational kinetics, binding and modulation of disordered protein domains
2015-2017 (BIO2014-53095-P) MINECO
Institutions
Bioinformatics expertise:
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Algorithmics (26)
- AIZON (Aizon)
- Algorithms, Computational Biology, Complexity and Formal Methods (UPC)
- Amalfi Analytics (Amalfi)
- Artificial Intelligence Research Institute (CSIC)
- Biomedical Signal Processing and Interpretation (IBEC)
- Chemometrics for Environmental Omics (CSIC)
- Comparative Bioinformatics (CRG)
- Computational & Mathematical Biology (CRM)
- Computational Biology and Complex Systems Group (UPC)
- Computational continuum mechanics (UPC)
- Computational RNA Biology group of GRIB (UPF, IMIM)
- Computational Science group of GRIB (UPF, IMIM)
- Computer Vision and Robotics Group (UdG)
- Control Engineering and Intelligent Systems (UdG)
- Data and Signal Processing Research Group (UVic-UCC)
- Distributed Computation Group (UdL)
- High Performance Computing Applications for Science and Engineering - Bioinformatics (UAB)
- IN2 Ingeniería de la Información (IN2)
- Internet Computing & Systems Optimization (FUOC)
- Laboratory of Relational Algorithmics, Complexity and Learnability (UPC)
- Laboratory of Systems Pharmacology and Bioinformatics (UAB)
- Modelling, Identification and Control Engineering (UdG)
- Numerical Genomics - Statistical and population genomics (CRAG)
- Research Group on Statistics, Econometrics and Health (UdG)
- Signal and Information Processing for Sensing Systems (IBEC)
- Soft Computing (UPC)
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Chemoinformatics (12)
- Biological Chemistry and Biotechnology Group (URL)
- Cheminformatics & Nutrition (URV)
- Computational and Theoretical Chemistry (CSIC)
- Computational Science group of GRIB (UPF, IMIM)
- Computer-aided Drug Design and Knowledge Management (ESTEVE)
- Electronic and Atomic Protein Modelling (BSC)
- Modeling of Biological systems & Drug Design (UB)
- Molecular Engineering Group (URL)
- Nostrum Biodiscovery ()
- Pharmacelera ()
- PharmacoInformatics Group of GRIB (UPF, IMIM)
- The Computational Chembiological Team (UAB)
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High Performance Computing (HPC) (13)
- Artificial Intelligence Research Institute (CSIC)
- Computational Bioinformatics Node (National Institute of Bioinformatics - INB) (BSC)
- Computational continuum mechanics (UPC)
- Computational Science group of GRIB (UPF, IMIM)
- Computer Vision and Robotics Group (UdG)
- Distributed Computation Group (UdL)
- High Performance Computing (IGTP)
- High Performance Computing Applications for Science and Engineering - Bioinformatics (UAB)
- IN2 Ingeniería de la Información (IN2)
- Internet Computing & Systems Optimization (FUOC)
- Made of Genes (MoG)
- Pharmacelera ()
- Roche Diagnostics (Roche)
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Structural Bioinformatics (20)
- Bioinformatics and Medical Statistics (UVic-UCC)
- Biological Chemistry and Biotechnology Group (URL)
- Cancer genetics and epigenetics (IGTP)
- Computational and Theoretical Chemistry (CSIC)
- Computational continuum mechanics (UPC)
- Computational Science group of GRIB (UPF, IMIM)
- Electronic and Atomic Protein Modelling (BSC)
- Functional Proteomics (UAB)
- Gene Function and Evolution lab (CRG)
- GPCR Drug Discovery group of GRIB (UPF, IMIM)
- Laboratory of Computational Medicine (UAB)
- Modeling of Biological systems & Drug Design (UB)
- Molecular Biotechnology Centre (UPC)
- Nostrum Biodiscovery ()
- Protein Engineering Laboratory (UdG)
- Protein Folding and Conformational Diseases (UAB)
- Protein Interactions and Docking (BSC)
- Structural BioInformatics group of GRIB (UPF, IMIM)
- Structural Informatics & Network Biology (IRB Barcelona)
- Translational Bioinformatics group (VHIR)
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Systems Biology and Networks (27)
- Algorithms, Computational Biology, Complexity and Formal Methods (UPC)
- Bioinformatics and Medical Statistics (UVic-UCC)
- Bioinformatics Core Unit (CRAG)
- Bioinformatics Platform (IDIBAPS)
- Biological Chemistry and Biotechnology Group (URL)
- Computational Biology and Complex Systems Group (UPC)
- Computational Biology of RNA processing (CRG)
- Computational Science group of GRIB (UPF, IMIM)
- Control Engineering and Intelligent Systems (UdG)
- Data and Signal Processing Research Group (UVic-UCC)
- Evolution of Insect Metamorphosis (UPF, CSIC)
- Functional Genomics group of GRIB (UPF, IMIM)
- Genome Data Science (IRB Barcelona)
- Integrative Systems Biology, Metabolomics and Cancer (UB)
- Laboratory of Systems Pharmacology and Bioinformatics (UAB)
- Mathematical Modeling of Metabolic Processes (UdL)
- Molecular Modelling and Bioinformatics (UB, IRB Barcelona)
- Nonlinear dynamics, nonlinear optics and lasers (UPC)
- Nutrition, Eumetabolism and Health (UdG)
- Science and Engineering of Emerging Systems (URV)
- Sequentia Biotech (SeqBio)
- Statistics and Bioinformatics Unit (VHIR)
- Structural BioInformatics group of GRIB (UPF, IMIM)
- Structural Informatics & Network Biology (IRB Barcelona)
- The CRG Bioinformatics Unit (CRG)
- Theoretical Chemistry, Modelling and Molecular Engineering (UdG)
- UPC Dinamical Systems (UPC)
Bioinformatics services offered
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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.
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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.
https://www.acellera.com/products/molecular-dynamics-software-GPU-acemd/