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Primeur weekly 2018-02-26

Focus

The European Processor Initiative (EPI) to develop the processor that will be at the heart of the European exascale supercomputer effort ...

Quantum computing

Unconventional superconductor may be used to create quantum computers of the future ...

Developing reliable quantum computers: International research team makes important step on the path to solving certification problems ...

Programming on a silicon quantum chip ...

D-Wave locks in $20 million funding and completes prototype of next-gen quantum processor ...

Focus on Europe

Luxembourg joins the European supercomputer network PRACE ...

ICEI Public Information Event on the realisation of a federated HPC and data analytics infrastructure ...

Dutch eScience and Lorentz Centers launch Call to host workshop on digitally enhanced research ...

Middleware

Adaptive Computing announces release of Moab HPC Suite 9.1.2 ...

NCSA Assistant Director Dan Katz named BSSw Fellow ...

University of Nevada, Las Vegas' supercomputing boosted through new collaboration with Altair ...

Hardware

C-DAC focusing on cancer treatment using supercomputers as a tool ...

South-Korean Ministry of Science and Technology to announce Second National High-Performance Computing Fundamental Plan ...

IBM reveals novel energy-saving optical receiver with a new record of rapid power-on/off time ...

Computers learn to learn: Intel and researchers from Heidelberg and Dresden present three new neuromorphic chips ...

HPE helps U.S. Department of Defense to advance national defense capabilities ...

OCF deploys petascale Lenovo supercomputer at University of Southampton ...

HPE reports fiscal 2018 first quarter results ...

Ranovus announces general availability of its on-board optics and CFP2 direct detect transceiver products for 5G mobility and data centre interconnect applications ...

Mellanox appoints Steve Sanghi and Umesh Padval to Board of Directors ...

Applications

Supercomputers aid discovery of new, inexpensive material to make LEDs with high colour quality ...

AI companies to reuse crypto mining farms for deep learning in health care ...

Computer scientists and materials researchers collaborate to optimize steel classification ...

Boris Kaus receives ERC Consolidator Grant for his research in magmatic processes ...

Metabolic modelling becomes three-dimensional ...

Powerful supercomputer unlocks possibilities for tinier devices and affordable DNA sequencing ...

New Berkeley Lab algorithms create "Minimalist Machine Learning" that analyzes images from very little information ...

The Cloud

Adaptive Computing makes HPC Cloud strategies more accessible with the Moab/NODUS Cloud Bursting 1.1.0 release ...

USFlash

Gen-Z Consortium announces the public release of its Core Specification 1.0 ...

Metabolic modelling becomes three-dimensional


An international research consortium developed, with significant involvement of Luxembourg Centre for Systems Biomedicine (LCSB) scientists, the first computer model to include 3D in the representation of human metabolic processes. Credit: University of Luxembourg.
22 Feb 2018 Luxembourg - An international research consortium developed, with significant involvement of Luxembourg Centre for Systems Biomedicine (LCSB) scientists, the first computer model to include 3D in the representation of human metabolic processes.

To this end, the researchers integrated the three-dimensional structures of over 4,000 metabolic products, or metabolites as they are known, and nearly 13,000 proteins into an existing computer model. They also added an enormous volume of genetic and chemical information to the model on which the simulation runs. The name of this new computer-based tool, which has been made available to the biomedical research community recently, is Recon3D. The researchers' results on Recon3D appear in the journal Nature Biotechnology .

The importance of scientific computer models continues to increase. They make the existing knowledge tangible and thereby help scientists to accurately formulate and work on targeted problems in research. To create such models, researchers analyse all the publications and databases they can find on a topic and feed this information into their model.

Human metabolism research is one example, as Prof. Ines Thiele, head of the Molecular Systems Physiology group at the LCSB of the University of Luxembourg and an ATTRACT fellow of the Luxembourg National Research Fund (FNR), stated: "For the predecessor of Recon3D, Recon 2, a large team of research groups in different fields aggregated an enormous volume of data on the genome, chemical metabolic activities and physiological properties of the human organism." This data basis has now been considerably expanded yet again for Recon3D, Ines Thiele reported.

What is unique about the new computer model, however, is the integrated three-dimensional structural data of proteins and metabolites. Dr. Ronan Fleming, head of the LCSB Systems Biochemistry group which was responsible for integrating the structural data of the metabolites into Recon3D, stated: "So far, we have been able to say of a given metabolic reaction that substance A and B turn into substances C and D. Now, we know precisely which atoms each substance consists of, how the atoms are arranged in the starting materials and where those very same atoms can be found again in the products of the chemical reaction."

To make this possible, the researchers first had to find out which computational programme - or algorithm as scientists call it - imports the three-dimensional structures of the molecules most accurately from the literature into Recon3D. To find this out, Ronan Fleming's team researched the molecular structure of the starting materials of a series of chemical reactions and determined the whereabouts of every single atom after the metabolic reaction was completed. They then tested various algorithms on the same reactions to identify those with the best predictive power. Ronan Fleming reported: "With these results, we were then able to import very accurate structures of more than 4,000 metabolites into the computer model." Ronan Fleming's colleagues from the University of California in the United States expanded Recon3D with data on almost 13,000 protein structures, thereby bridging the research fields of structural biology and systems biology.

"Recon3D now allows us to study metabolic processes that run differently, for example, in Parkinson's patients than in healthy people, much better and with more accuracy", Ines Thiele summed up the possibilities that the new computer model offers. Dr. Andreas Dräger from the Center for Bioinformatics at the University of Tübingen (ZBIT) has put it into a standardised format so that other researchers can use the model for their scientific questions. "Recon3D lays the foundations for creating cell-type-specific models that could be used to simulate the function of tissues through to entire organs in the computer", explained Andreas Dräger and continued: "It could help to better understand the interplay between pathogens, such as bacteria or viruses, and the human host." Ronan Fleming also added that, thanks to the three-dimensional structures of the metabolites and proteins in Recon3D, it is now possible to follow, at atomic resolution, how a genetic mutation could affect the development of certain diseases. "This can open up entirely new avenues for research on therapeutic approaches", Ronan Fleming concluded.

Source: Université de Luxembourg

Back to Table of contents

Primeur weekly 2018-02-26

Focus

The European Processor Initiative (EPI) to develop the processor that will be at the heart of the European exascale supercomputer effort ...

Quantum computing

Unconventional superconductor may be used to create quantum computers of the future ...

Developing reliable quantum computers: International research team makes important step on the path to solving certification problems ...

Programming on a silicon quantum chip ...

D-Wave locks in $20 million funding and completes prototype of next-gen quantum processor ...

Focus on Europe

Luxembourg joins the European supercomputer network PRACE ...

ICEI Public Information Event on the realisation of a federated HPC and data analytics infrastructure ...

Dutch eScience and Lorentz Centers launch Call to host workshop on digitally enhanced research ...

Middleware

Adaptive Computing announces release of Moab HPC Suite 9.1.2 ...

NCSA Assistant Director Dan Katz named BSSw Fellow ...

University of Nevada, Las Vegas' supercomputing boosted through new collaboration with Altair ...

Hardware

C-DAC focusing on cancer treatment using supercomputers as a tool ...

South-Korean Ministry of Science and Technology to announce Second National High-Performance Computing Fundamental Plan ...

IBM reveals novel energy-saving optical receiver with a new record of rapid power-on/off time ...

Computers learn to learn: Intel and researchers from Heidelberg and Dresden present three new neuromorphic chips ...

HPE helps U.S. Department of Defense to advance national defense capabilities ...

OCF deploys petascale Lenovo supercomputer at University of Southampton ...

HPE reports fiscal 2018 first quarter results ...

Ranovus announces general availability of its on-board optics and CFP2 direct detect transceiver products for 5G mobility and data centre interconnect applications ...

Mellanox appoints Steve Sanghi and Umesh Padval to Board of Directors ...

Applications

Supercomputers aid discovery of new, inexpensive material to make LEDs with high colour quality ...

AI companies to reuse crypto mining farms for deep learning in health care ...

Computer scientists and materials researchers collaborate to optimize steel classification ...

Boris Kaus receives ERC Consolidator Grant for his research in magmatic processes ...

Metabolic modelling becomes three-dimensional ...

Powerful supercomputer unlocks possibilities for tinier devices and affordable DNA sequencing ...

New Berkeley Lab algorithms create "Minimalist Machine Learning" that analyzes images from very little information ...

The Cloud

Adaptive Computing makes HPC Cloud strategies more accessible with the Moab/NODUS Cloud Bursting 1.1.0 release ...

USFlash

Gen-Z Consortium announces the public release of its Core Specification 1.0 ...