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355 - Supercomputing for COVID-19
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Manage episode 275711274 series 71279
Guests: Andrew Emerson, Daniel Jacobson
Host: Markus Voelter Shownoter: Andy Joiner
In this episode we look at how supercomputers are used to help with managing the pandemic. It’s a double-header with two guests. We start with Cineca‘s Andrew Emerson. As part of the EXSCALATE 4 COV EU-funded research project, he works of virtual screening of existing drugs regarding their potential efficacy against SARS-CoV-2. In part two we talk with Dan Jacobson of the Oak Ridge National Laboratory. He and his team used a big data analysis to understand how the virus “works”, and they figured out very interesting mechanisms and pathways.
Introduction
00:03:14Andrew Emerson | Cineca Supercomputer Center | Exscalate4Cov Project | Computer Aided Drug Design | Simulation | Modelling | Synthesize | Side Effects | Active Ingredient | COVID-19 | SARS-CoV-2 | Virus | Drug Repurposing/Drug Repositioning | Toxicology | Virtual Screening | Protein | Enzyme | Cell | Replication | Inhibit | DNA | Cell Membranes | Amino Acid | RNA | Gene | Gene Expression | Genome | Lock and Key Model | Screening | Virtual Screening | Dompé | Parallel Process | Abstraction (PDB - Protein Data Bank) | Bonding | Experimental data (Proteins - accurate 3d data | Drug molecules - basic data) | X-Ray Diffraction | NMR | Cryogenic Electron Microscopy | Electromagnetic Force | Van der Waals Force | Electrostatic Interaction | LiGen | Molecular Docking | Toxicology | Few seconds per molecule for virtual screening
Molecular Dynamics Simulation
00:31:06Molecular Dynamics Simulation | Thermal effects | Stable State | Statistical techniques | Numerical Simulation | Newton's Laws of Motion | Bond vibration | Coulomb's law | Multi-Body Problem | Unfold | Molecular dynamics simulation can take about a week | Clustering | Degrees of Freedom | Energy Surface | Boltzmann Distribution | Virtual screening filtered ~400,000 possible drugs to ~7000 to go to the laboratory | Vaccine | Immune Response | ~100 of ~7000 screened molecules were interesting | In Vitro Tests | 40 effective molecules limited virus replication | Antiviral | Cortisone
Computer Software and Hardware
01:09:44GROMACS | Open Source | GPU | Homology Model | C++ | CUDA | Marconi 100 | Galileo Linux Cluster | Eni | HPC5 | Nvidia V100 | Scheduling
Results
01:20:24Raloxifene | Clinical Trials | Dimer | Protease | Physical Chemistry | Computational Chemistry | Vector (Biology) | Vector (Mathematics)
Bradykinin Storm Analysis
01:30:59Dan Jacobson | Computational Systems Biologist | Oak Ridge National Laboratory (OLCF - Oak Ridge Leadership Computing Facility) | Evolution | Pathogenicity | 3D Structure | Human pathogenesis | Demographic factors | Bradykinin Storm Paper | 17000 samples across 57 different tissues | Regulatory circuits | Bronchoalveolar Lavage fluid | Bronchoscope | Terminal Bronchioles | Luminal surface | Gas Exchange | Pathways (RAS - Renin-Angiotensin System) | Blood Pressure | Inflaitory RResponses | ACE2 | Cell Entry | ACE | Proteolytic Enzyme | Proteolytic cleavage | Peptide | Hypertensive | Upregulated (Ang-(1-9) - Angiotensin (1-9)) | AGTR2 receptor | Receptor | Bind | Kallikrein Kinin Pathway | C1-Inhibitor Protein | Biosynthesis | Vasodilation | Hyperpermeability | Plasma | Capillaries | Immune Cells | Transcription | Hyaluronic Acid | Hydrogel | Tropism | Renin | Vitamin D | Catabolise | Metabolite | Expression | Calcifediol | Icatibant | Dexamethasone | Phospholipase A2 | Arachidonic Acid | Cascade | Chemotaxis | Combinatorial Therapies
Computational Tools
01:56:58Machine Learning | Functional Inference | Explainable AI | Data Analytics | ChIPseek | Transcription Factors | Traits | Phenotypes | Combinatorial Space | P-Values | Permutation Tests | Neural Network | Black Box | Classification Problem (IRF - Iterative Random Forests) | Decision Tree | Iterative Approach | Summit Supercomputer | Flash Memory | Gordon Bell Prize 2018 | Tensor Cores | Matrix Multiplication | Exascale Barrier | Hyperparameter Sweeps | Monte Carlo Simulation | R | Python | Parsers
347 tập
Fetch error
Hmmm there seems to be a problem fetching this series right now. Last successful fetch was on August 12, 2024 16:58 ()
What now? This series will be checked again in the next day. If you believe it should be working, please verify the publisher's feed link below is valid and includes actual episode links. You can contact support to request the feed be immediately fetched.
Manage episode 275711274 series 71279
Guests: Andrew Emerson, Daniel Jacobson
Host: Markus Voelter Shownoter: Andy Joiner
In this episode we look at how supercomputers are used to help with managing the pandemic. It’s a double-header with two guests. We start with Cineca‘s Andrew Emerson. As part of the EXSCALATE 4 COV EU-funded research project, he works of virtual screening of existing drugs regarding their potential efficacy against SARS-CoV-2. In part two we talk with Dan Jacobson of the Oak Ridge National Laboratory. He and his team used a big data analysis to understand how the virus “works”, and they figured out very interesting mechanisms and pathways.
Introduction
00:03:14Andrew Emerson | Cineca Supercomputer Center | Exscalate4Cov Project | Computer Aided Drug Design | Simulation | Modelling | Synthesize | Side Effects | Active Ingredient | COVID-19 | SARS-CoV-2 | Virus | Drug Repurposing/Drug Repositioning | Toxicology | Virtual Screening | Protein | Enzyme | Cell | Replication | Inhibit | DNA | Cell Membranes | Amino Acid | RNA | Gene | Gene Expression | Genome | Lock and Key Model | Screening | Virtual Screening | Dompé | Parallel Process | Abstraction (PDB - Protein Data Bank) | Bonding | Experimental data (Proteins - accurate 3d data | Drug molecules - basic data) | X-Ray Diffraction | NMR | Cryogenic Electron Microscopy | Electromagnetic Force | Van der Waals Force | Electrostatic Interaction | LiGen | Molecular Docking | Toxicology | Few seconds per molecule for virtual screening
Molecular Dynamics Simulation
00:31:06Molecular Dynamics Simulation | Thermal effects | Stable State | Statistical techniques | Numerical Simulation | Newton's Laws of Motion | Bond vibration | Coulomb's law | Multi-Body Problem | Unfold | Molecular dynamics simulation can take about a week | Clustering | Degrees of Freedom | Energy Surface | Boltzmann Distribution | Virtual screening filtered ~400,000 possible drugs to ~7000 to go to the laboratory | Vaccine | Immune Response | ~100 of ~7000 screened molecules were interesting | In Vitro Tests | 40 effective molecules limited virus replication | Antiviral | Cortisone
Computer Software and Hardware
01:09:44GROMACS | Open Source | GPU | Homology Model | C++ | CUDA | Marconi 100 | Galileo Linux Cluster | Eni | HPC5 | Nvidia V100 | Scheduling
Results
01:20:24Raloxifene | Clinical Trials | Dimer | Protease | Physical Chemistry | Computational Chemistry | Vector (Biology) | Vector (Mathematics)
Bradykinin Storm Analysis
01:30:59Dan Jacobson | Computational Systems Biologist | Oak Ridge National Laboratory (OLCF - Oak Ridge Leadership Computing Facility) | Evolution | Pathogenicity | 3D Structure | Human pathogenesis | Demographic factors | Bradykinin Storm Paper | 17000 samples across 57 different tissues | Regulatory circuits | Bronchoalveolar Lavage fluid | Bronchoscope | Terminal Bronchioles | Luminal surface | Gas Exchange | Pathways (RAS - Renin-Angiotensin System) | Blood Pressure | Inflaitory RResponses | ACE2 | Cell Entry | ACE | Proteolytic Enzyme | Proteolytic cleavage | Peptide | Hypertensive | Upregulated (Ang-(1-9) - Angiotensin (1-9)) | AGTR2 receptor | Receptor | Bind | Kallikrein Kinin Pathway | C1-Inhibitor Protein | Biosynthesis | Vasodilation | Hyperpermeability | Plasma | Capillaries | Immune Cells | Transcription | Hyaluronic Acid | Hydrogel | Tropism | Renin | Vitamin D | Catabolise | Metabolite | Expression | Calcifediol | Icatibant | Dexamethasone | Phospholipase A2 | Arachidonic Acid | Cascade | Chemotaxis | Combinatorial Therapies
Computational Tools
01:56:58Machine Learning | Functional Inference | Explainable AI | Data Analytics | ChIPseek | Transcription Factors | Traits | Phenotypes | Combinatorial Space | P-Values | Permutation Tests | Neural Network | Black Box | Classification Problem (IRF - Iterative Random Forests) | Decision Tree | Iterative Approach | Summit Supercomputer | Flash Memory | Gordon Bell Prize 2018 | Tensor Cores | Matrix Multiplication | Exascale Barrier | Hyperparameter Sweeps | Monte Carlo Simulation | R | Python | Parsers
347 tập
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