AlphaFold v2.0 and RoseTTAFold workshop

Registrations are now open for the AlphaFold v2.0 and RoseTTAFold workshop, hosted by NORA in collaboration with the University of Oslo, dScience, Elixir Norway, Oslo Cancer Cluster and Centre for Digital Life Norway. The workshop is open for all NORA researchers, students of NORA’s research school and friends of NORA. 

When: August 31 and September 1, 2021 

Registration for the workshop 

To watch recordings of the workshop, please follow this link.

On November 30, 2020 the results from the CASP14 assessment were released. The outstanding performance of DeepMind’s AlphaFold2 attracted great attention and the scientific community raised the question whether the code would be publicly available and whether such a result could be achieved in academia. After all, DeepMind’s resources are far beyond the reach of any single academic institution.  

These questions were answered July 15 2021. On this date, DeepMind published a paper about AlphaFold v2.0 in Nature with accompanying open code on GitHub. Notably, RoseTTAFold, another deep learning-based algorithm for protein folding was published the same day in Science. The latter is developed collaboratively between several universities with lead researchers from the University of Washington. RoseTTAFold performs nearly as well as AlphaFold v2.0 and is much more efficient in terms of computing power needed. 

In this workshop, distinguished researchers behind the AlphaFold v2.0 and RoseTTAFold algorithms will present their tools and methods. The workshop is hosted for participants who would like to get hands on experience with the tools and methods. Both algorithms will be pre-installed on Norwegian supercomputers, and workshop participants will be tutored on how to run AlphaFold v2.0 and RoseTTAFold. 

The goal of the workshop is not only to boost Norwegian and international research within protein folding and function by advanced AI methods, but also to inspire development of AI-powered biotech in Norway. 

NORA (Norwegian Artificial Intelligence Research Consortium) wants to show gratitude to DeepMind and the Rosettafold team for opening and publishing their tools. These examples of open science will surely boost research and development in the field, ultimately to the benefit for patients and humanity. 


Programme

Day 1 

09:00-12:00 Session 1: AlphaFold and RoseTTAFold – a paradigm shift for molecular biology and biotechnology? (chaired by Klas Pettersen) 

  • 09:00-09:15 Klas Pettersen, NORA: Welcome & overview of the workshop.  

  • 09:15-10:00 Jon Lærdahl, Oslo University Hospital & University of Oslo: Proteins and techniques for predicting protein structure: an introduction (download presentation here)

  • 10:00-10:10 Break  

  • 10:10-11:00: Inge Jonassen, University of Bergen: Computational structure prediction, CASP and AlphaFold (v1 and v2) 

  • 11:00-11:10 Break 

  • 11:10 – 12:00 Sameer Velankar, EMBL-EBI: AlphaFold Protein Structure Database 

  • 12:00-13:00 Lunch 

13:00-16:00 Session 2: Technical tutorial and hands on coding 

  • 13:00-13:30 Randy John Read, Cambridge University: Quality of Protein Structures from experiments and simulations 

  • 13:30-13:45 Break 

  • 13:45-16:00 Jonas Verhellen, University of Oslo (technical lead): Technical tutorial on how to use our implementations of  AlphaFold v2.0 and RoseTTAFold 

  1. How to use the algorithms? 

  2. Showcase of protein examples  

  3. Try your own candidates: Work hands on with coding. Work could be in groups or individually with tutoring. 

Day 2 

09:00-13:00 Session 3: AlphaFold and RoseTTAFold – applications and limitations 

  • 09:00-10:00 Dr. Minkyung Baek, University of  Washington:  RoseTTAFold 

  • 10:00-10:30 Philippe Paul Auguste Robert, University of Oslo: From structural biology to practice: AI applied to ultra-large datasets for therapeutics discovery

  • 10:30-11:00 Morten Dæhlen / Sabry Razick, University of Oslo: The Fox cluster at University of Oslo and requirements for running AlphaFold v2 and RoseTTAFold  

  • 11:00-11:30 Inger Berg Ørstavik, Department of Private Law, University of Oslo: Licensing and legal restrictions for use of AlphaFold, RoseTTAFold and AlphaFold Protein Structure Database

  • 11:30-11:40 Break  

  • 11:40-13:00: Jon Lærdahl, Oslo University Hospital & University of Oslo. Some case studies and results including discussions (Depending on the discussions this part may be shortened)

  • 13:00-14:00 Lunch 

14:00-16:00 Session 4: Future perspectives  

  • 14:00-14:30 Victor Greiff, University of Oslo: Future perspectives: from structure to function

  • 14:30-15:00 Jim Brase, Co-lead of The ATOM consortium and Deputy Associate Director for Computing, Lawrence Livermore National Laboratory: The ATOM consortium: from protein structure to drug discovery

  • 15:00-15:50: Panel Debate. (Panelists: Randy Read, Jim Brase, Jon Lærdahl, Inge Jonassen, Victor Greiff. Moderator: Klas Pettersen)  

  • 15:50-16:00: Klas Pettersen, NORA. Closing 


Hosted in collaboration with: 


About the Speakers

Jon Lærdahl

Research Scientist - Department of Microbiology, Oslo University Hospital & ELIXIR Norway, Department of Informatics, University of Oslo

Lærdahl has been working with structural and applied bioinformatics for more than 15 years, mainly in collaborate projects with groups at Oslo University Hospital and the University of Oslo. His background is in organic chemistry, theoretical chemistry and molecular physics.

More details can be found here: https://folk.universitetetioslo.no/jonkl

 

Inge Jonassen

Head of Department of Informatics at the University of Bergen

Inge Jonassen is the Head of Department of Informatics at the University of Bergen from 2021. He has been a full professor in computer science at the same university from 2002 and from 2003 to 2021 he led the center Computational Biology Unit. Jonassen’s research is into computational methods for the discovery and use of patterns in molecular biology data – including towards structural biology and protein structure prediction. Jonassen is also the head of the Norwegian Node of ELIXIR, the pan-European research infrastructure for biological data.

 

Sameer Velanker

Team Leader, Protein Data Bank in Europe

Sameer led the development of AlphaFold protein structure database. As a founding member of the Worldwide Protein Data Bank (wwPDB), the Protein Data Bank in Europe (PDBe) manages the worldwide biomacromolecular structure archive, the Protein Data Bank (PDB). The wwPDB partners accept and annotate worldwide depositions of biomacromolecular structures determined using X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, 3D Electron Microscopy (EM) and other structure-determination methods. PDBe is a founding member of EMDataBank, which manages the deposition and annotation of EM data in EMDB.PDBe aims to ensure that this important resource truly serves the needs of the biomedical community.

More details can be found here: https://www.ebi.ac.uk/about/people/sameer-velankar

 

Randy Read

Randy Read is a structural biologist who focuses on likelihood-based methods to solve protein structures either by X-ray crystallography or (more recently) cryo-electron microscopy. He studied biochemistry at the University of Alberta in Canada, where he obtained his B.Sc. followed by a PhD under the supervision of Michael James. After a 3-year post-doc at the University of Groningen in The Netherlands, he returned to Alberta to take up a faculty position in the Department of Medical Microbiology and Immunology. Since 1998, he has been Professor of Protein Crystallography at the University of Cambridge.

 

Jonas Verhellen

Doctoral Research Fellow - University of Oslo

Jonas Verhellen is a computational neuroscientist, who focuses on novel methods to study and cure psychiatric disease through the application of a wide array of computational techniques at the University of Oslo. As part the 4MENT Life Science convergence environment, he studies protein structures and levels derived from RNA signatures in brain organoids. Before taking up this position, he worked in the pharmaceutical industry and as a research assistant in theoretical physics where he developed computational methods to study highly-entangled systems. 

 

Dr. Minkyung Baek

Over the last decade, first as a Ph.D. student in Chemistry at Seoul National University and then as a postdoctoral scholar at the University of Washington, Dr. Minkyung Baek developed computational methods to predict protein structures and their interactions. Currently, she is focusing on developing AI-based methods for protein structure prediction and de novo protein design. 

 

Philippe Paul Auguste Robert

Postdoctoral Fellow - Department of Immunology, University of Oslo

Philippe studied theoretical computer science and experimental immunology in École Normale Supérieure de Lyon, France. He completed a PhD in computational immunology at the Helmholtz Center for Infection Research, Braunschweig, Germany, where he built predictive mathematical models for the adaptive immune response to complex inflammatory environments, in particular the differentiation of T helper cells and the optimization of vaccine design to mutated viral variants. He joined the lab of computational systems immunology at university of Oslo and is now developing AI methods for antibody discovery, to assist experimental dataset design and to maximize AI predictive capacity and reliability.

 

Morten Dæhlen

Professor and Centre Leader - dScience - Centre for Computational and Data Science

Dæhlen is centre leader for dScience – Centre for Computational and Data Science. He is also professor in computational mathematics/informatics. His main research has been within computational methods - machine learning, visualization and geometric modelling. He has worked on basic scientific problems as well as applied challenges in collaboration with companies and units in public sector. 

 

Dr Sabry Razick

Chief engineer for the  Department for Research Infrastructure Services at the University of Oslo

Sabry is currently working as a Chief engineer for the  Department for Research Infrastructure Services at the University of Oslo, Norway. He is responsible for Machine learning infrastructure team at the department and also provides advanced user support for the Metacenter, which is the national coordination for high performance computer (HPC) systems located in main Universities of Norway. He is also an expert in it service management (ITSM) and acts as the project leader for ITSM implementation group for the Metacenter. In addition he works as a group member of the CodeRefinery (https://coderefinery.org) project, which focuses mainly on training related to software development.   

Sabry holds a Masters in Engineering from Chalmers University of Technology Sweden, a PhD from University of Oslo where he focused on building iRefIndex, which a consolidated protein interaction database. 

 

Inger Berg Ørstavik

Professor - Department of Private Law

Ørstavik has since 2014 been associate professor with the Department of Private Law. She obtained her Ph.D. in 2010 with the thesis "The innovation spiral - questions in patent law, contract law and competition law relating to improvements of patented inventions". The thesis was awarded H.M. the King's gold medal. She has experience from the Attorney General for Civil Affairs and from the law firm Schjødt.

Ørstavik has worked with intellectual property law, competition law, contract law and dispute resolution. She has broad experience from teaching, and has taught international human rights at Fudan University in Shanghai, China. She published the book "Innovasjonsspiralen" in 2010, and has published several articles in intellectual property law and competition law.

Inger Berg Ørstavik is a director on the board of Nordic Semiconductor ASA, and she is the chairperson of the Food and Drink Industry Professional Practices Committee (MFU) Food and Drink Industry Professional Practices Committee (MFU). She also has experience as arbitrator.

 

Victor Greiff

Associate Professor for Computational and Systems Immunology at University of Oslo

Victor Greiff is an Associate Professor for Computational and Systems Immunology at the University of Oslo (Norway). His work focuses on the development of machine learning, computational and experimental tools for the analysis, prediction and engineering of adaptive immune receptor repertoires on the sequence and structural level.

 

Jim Brase

Co-lead of The ATOM consortium and Deputy Associate Director for Computing, Lawrence Livermore National Laboratory

Jim Brase is the Deputy Associate Director for Computing at Lawrence Livermore National Laboratory (LLNL). He leads LLNL research in the application of high- performance computing, large-scale data science, and simulation to a broad range of national security and science missions. Jim is co-lead of the ATOM Consortium for computational acceleration of drug discovery, and on the leadership team of the COVID-19 HPC Consortium. Jim’s research interests focus on the intersection of machine learning, simulation, and high-performance computing. He is currently leading efforts on large-scale computing for life science, biosecurity, and nuclear security applications. In his previous position as LLNL’s Deputy Program Director for Intelligence, Jim led efforts in intelligence and cybersecurity R&D.

 

Klas H. Pettersen

CEO, NORA

Since April 2019 Klas have worked as the CEO of NORA – Norwegian Artificial Intelligence Research Consortium, a collaboration between seven Norwegian universities and two research institutes within artificial intelligence, machine learning and robotics. 

He has a degree in civil engineer in physics from the Norwegian University of Science and Technology (NTNU), where he studied quantum mechanics and the theory of relativity. He further turned to to neuroscience and received a PhD in computational neuroscience in 2007 from the Norwegian University of Life Sciences (NMBU).  

After receiving his PhD he have worked as a postdoctoral researcher and research scientist. In his scientific work he have applied physics, mathematics, informatics and techniques from artificial intelligence to understand the brain. From 2014-2019 he was a research scientist at the Faculty of Medicine at the University of Oslo. From 2008 to 2013 he worked as a postdoctoral researcher and a research scientist at NMBU, in the Group for Computational Biology and later also at the Center for Integrative Genetics.  

He has also worked as a Visiting Scholar at the University of California San Diego (2015), and as a consultant for Accenture.

Published Aug. 5, 2021 2:14 PM - Last modified Aug. 31, 2021 10:56 PM