Computational Biomedicine – SuperMUC Allocation
UCL and LRZ of ComPat have been awarded a two year project at Leibniz Supercomputing Centre with an allocation on SuperMUC of 28 million core hours over two years, effective immediately. The project is led by Prof Dr Dieter Kranzmüller, Director of LRZ and Professor of Computer Science at Ludwig Maximillians Universitet, Munich. Partners include Prof Peter Coveney of the Centre for Computational Science at UCL, together with Dr Herman van Vlijmen of Janssen.
Much of this award is concentrated on executing advanced workflows centred on molecular dynamics simulation of ligand-protein interactions, exploiting the development of important software services and tools by the UCL and LRZ teams. The central quantities of interest when assessing a potential drug are the thermodynamics (binding affinity or binding free energy) and kinetic (on- and off-rates) properties of its binding to the target protein. Historically, the pharmaceutical industry has avoided engagement with molecular dynamic and high performance computing due to the lack of accuracy and reproducibility, and long turnaround times. The purpose of current award is to develop high fidelity, computationally based, predictive mechanistic models of biomedical systems which can be applied in support of drug discovery and personalised medicine utilizing today’s top-level computational infrastructure. SuperMUC is a Tier-0 resource, meaning it is one of the international class of supercomputers, to designate that it supports projects which are internationally leading and command an equivalent scale of supercomputing.
One particular strength of the planned work is the collaboration between UCL, LRZ and Janssen R&D to study large, legacy internal datasets from Janssen. Our work in this area, in developing and applying the Binding Affinity Calculator (BAC) is helping to transform the field, making free energy calculations rapid, accurate, precise and reproducible. It requires access to powerful computational resources, of the kind available on SuperMUC.
The award coincides with the publication of a special report (available here) celebrating ten years of the Gauss Centre for Supercomputing, which features an article on Benefitting Public Health, based on UCL-CCS’s Giant Worflow performed across the combination of the entirety of Phases 1 and 2 of SuperMUC in June 2016. This was deemed to be one of the major accomplishments of the Gauss Center for Supercomputing in the ten year period of its existence. You can read the article on pages 6 & 7 in the following link.
ComPat Paper – Multiscale Computing in the Exascale Era
Alowayyed, Groen, Coveney, and Hoekstra have published a ComPat paper on “Multiscale Computing in the Exascale Era” in the Journal of Computational Science, the paper is available online now
Peter Coveney at ISC 2017
Peter Coveney gave a talk on “Rapid, Accurate & Reliable Binding Affinity Calculations for Drug Discovery” at the “High Performance Computing in Life Sciences” session at ISC 2017 on June 20th.
Peter Coveney at IWSG 2017
Peter Coveney gave a keynote talk at IWSG 2017 on “Exploiting International e-Infrastructures for Large Scale Computational Science” on June 19th 2017.
InSiDE, Spring 2017 Edition Out Now
Twice per year, the Gauss Centre for Supercomputing publishes the journal InSiDE. It reports on applications, systems and performance, news and courses of the three member centres (HLRS, LRZ, JSC). The Spring 2017 Edition is out now:
Articles of particular interest include:
1) GCS: Delivering 10 Years of Integrated HPC Excellence for Germany
Featuring our giant workflow project on SuperMUC, led by Peter Coveney. The project ran simulations on the system for 37 hours straight, using nearly all of SuperMUC’s 250,000 compute cores.
2) “Rapid and Accurate Calculation of Ligand-Protein Binding Free Energies” by Peter Coveney and Shunzou Wan
This article concerns the work of Peter Coveney’s group in the development of an automatic workflow that ensures drug binding affinity results are both accurate and reproducible, and can be delivered rapidly.
3) New Chairman of the Board of Directors at LRZ
Dieter Kranzlmüller has begun his new role as Chairman of the Board of Directors at ComPat Partner Leibniz Supercomputing Centre (LRZ).
You can read the full issue here.
Proceedings of ICCS 2017
The Proceedings of the International Conference on Computational Science, ICCS 2017, have been published in Procedia Computer Science. The proceedings were edited by Petros Koumoutsakos, Michael Lees, Valeria Krzhizhanovskaya, and can be found here.
ComPat Paper on Cover of JCTC Issue
The Journal of Chemical Theory and Computation have awarded the cover for their April issue to the ComPat paper from Agastya Bhati, Shunzou Wan, David Wright, and Peter Coveney, “Rapid, accurate, precise and reliable relative free energy prediction using ensemble based thermodynamic integration”. You can view the issue here, the cover image is shown below:
ComPat Paper Published
Pavel Zun, Tatiana Anikina, Andrew Svitenkov and Alfons Hoekstra have published “A Comparison of Fully-Coupled 3D In-Stent Restenosis Simulations to In-vivo Data” in Frontiers in Physiology. The paper is available here.
Robbie Sinclair wins Symposium Student Presentation Contest
Robbie Sinclair has won first prize in the Computer-Based Modeling and Experiment for the Design of Soft Materials Symposium Student Presentation Contest held at the 2017 MRS Spring Meeting.
His paper “New Insights into Graphene Exfoliation with Molecular Dynamics” represents the first public exposure of a scientific development in the understanding of graphene properties which is of central importance to understanding its formation, synthesis and role in nanocomposites.
ComPat Wired Article
Roger Highfield has published a WIRED article on “How weather forecasts could help develop ‘designer’ drugs personalised to your illness”, featuring Peter Coveney and the ComPat’s recent JCTC paper. You can find the article here.
Materials Research Society Spring 2017 Meeting
ComPat capabilities for materials science and engineering were promoted at the Materials Research Society Spring 2017 Meeting in Phoenix, Arizona, USA, between 18-21 April.
Peter Coveney was the founding organiser of the Symposium entitled “Computer-Based Modelling and Experiment for the Design of Soft Materials”.
A photograph of the members of the organising committee. They are from left to right: Olga Kuksenokova, Clemson University; Veena Tikare, Sandra; Valeriy Ginsburg (Dow Chemical)
Coveney also gave the following talks at the meeting:
1. Gels, Biopolymers and Active Matter.
2. Polymer-Based Composites and Nanocomposites.
3. Propoerties and Processing of Clay-Polymer Nanocomposites Modelled Using a Multiscale Approach.
4. New Insights into Graphene Exfoliation with Molecular Dynamics.
Peter Coveney at the 253rd ACS National Meeting
Peter Coveney is to give three talks at the 253rd ACS National Meeting in San Francisco, California, April 2-6, 2017. The first talk will be audio-recorded and be made available shortly after the event.
1) Computer-based design of advanced materials: Chemically specific multiscale modelling of polymer-clay nanocomposites
DIVISION: Division of Chemical Information
SESSION: Materials Informatics & Computational Modeling
SESSION TIME: 8:30 AM – 12:00 PM
DAY & TIME OF PRESENTATION: Sunday, April, 02, 2017 from 11:35 AM – 12:00 PM
ROOM & LOCATION: Metropolitan I – Park Central San Francisco
2) High performance and/or cloud computing for free energy prediction using molecular dynamics simulations?
DIVISION: Division of Computers in Chemistry
SESSION: Should I Move My Computational Chemistry or Informatics Tools to the Cloud?
DAY & TIME OF PRESENTATION: Sunday, April, 02, 2017 from 2:05 PM – 2:35 PM
ROOM & LOCATION: Nob Hill – InterContinental San Francisco
3) Rapid, accurate, precise and reliable relative free energy prediction using ensemble based thermodynamic integration
DIVISION: Division of Chemical Information
SESSION: Advances in High-Throughput Screening
DAY & TIME OF PRESENTATION: Monday, April, 03, 2017 from 1:45 PM – 2:10 PM
ROOM & LOCATION: Metropolitan I – Park Central San Francisco
Call for Participation: PRACEdays17
The call Contributions and Posters for PRACEdays17 in Barcelona on 16 – 18 May 2017 is now open. PRACEdays17, the central event of the European HPC Summit Week, will bring together experts from academia and industry who will present their advancements in HPC-supported science and engineering. You can respond to the call here. The call is open until 3 January 2017.
Call for Abstracts: Multiscale Modelling and Simulation Workshop, 14th Edition
The 14th International Workshop on Multiscale Modelling and Simulation will be running as part of ICCS 2017, which will take place in Switzerland.
Please find the call for papers here, along with further details about the workshop. The deadline for short abstracts is December 15, 2016.
The accepted papers will be included in the open-access Procedia Computer Science series and indexed by Scopus, ScienceDirect, and Thomson Reuters Conference Proceedings Citation (former ISI Proceedings) – an integrated index within Web of Science. The papers will contain linked references, XML versions and citable DOI numbers.
After the conference, selected papers will be invited for a special issue of the Journal of Computational Science (Impact Factor: 1.231, 5-Year Impact Factor: 1.760).
Cover Article in Physical Chemistry Chemical Physics
Peter Coveney and Shunzhou Wan have published a paper “On the calculation of equilibrium thermodynamic properties from molecular dynamics” in the leading journal Physical Chemistry Chemical Physics. The paper appears on the cover of the issue along with the cover image and can be viewed here. The paper establishes the fundamental necessity for performing ensemble averages to compute macroscopic properties, in particular the free energy of binding of ligands to proteins. Such calculations can be done fast and accurately on petascale supercomputers, using the replica computing pattern of the ComPat project.
“Big data need big theory too” Making Waves
The first month of usage data for the Philosophical Transactions A theme issue on “Multiscale modelling at the physics–chemistry–biology interface” is now available. There were a total of 7921 article views in October, over 5000 of which were for Peter Coveney, Edward Dougherty, and Roger Highfield’s paper “Big data need big theory too”. It’s currently the most read article published by Phil Trans A. You can access the paper here.
ComPat Experimental Execution Environment
Information relevant to users and developers of the Experimental Execution Environment of the ComPat project can now be found on the ComPat EEE wiki here.
Theme Issue in Philosophical Transactions of the Royal Society A
Peter Coveney is the co-editor of a Philosophical Transactions of the Royal Society A Theme Issue ‘Multiscale modelling at the physics–chemistry–biology interface’. Read more at the link.
Included in the issue are two pieces from Coveney: “Bridging the gaps at the physics–chemistry–biology interface” and “Big data need big theory too”, both available at the link.
Roger Highfield has published an article with “WIRED” on Why we can’t trust ‘blind big data’ to cure the world’s diseases.
Chemistry World Article
Roger Highfield and Peter Coveney have published an article on the Chemistry World website, titled Big data needs big theory”. You can view the article here.
Blog: Big Data needs Big Theory too
Peter Coveney has written a critique of the blind use of big data in biology on the Science Museum website, titled “Big Data needs Big Theory too”.
The VPH2016 conference is taking place on September 26-28, 2016
in Amsterdam. For more information, please visit the website.
2017 MRS Spring Meeting Call for Papers
Giant Workflow on SuperMUC
Distinguished science writer and journalist Dr Roger Highfield has written a blog post about the experience of running a Giant Workflow on Phases 1 and 2 of SuperMUC. You can read about the activity here.
Solvay Symposium Gallery
A webpage has been created for the Solvay Symposium on “Bridging the Gaps at the PCB Interface” that took place on 19-21 April 2016. It includes a gallery of pictures that can be viewed here.
Peter Coveney Vice Chair of EXDCI Working Group
Peter Coveney has been made the vice chair of a working group on Life Sciences and Health for EXDCI (“European eXtreme Data & Computing Initiative”). The objectives of EXDCI are to coordinate the development and implementation of a common strategy for a European HPC Ecosystem. More about the initiative can be found on their website.
COST Action on Open Multiscale Systems Medicine
COST Action CA15120 on Open Multiscale Systems Medicine (OpenMultiMed) started on April 5th 2016, with COMPAT’s Peter Coveney and Alfons Hoekstra as participants. The overarching aim OpenMultiMed is to gather a critical mass of international researchers and coordinate them as a team that develops and evaluates a transdisciplinary framework for multiscale systems medicine, consisting of novel concepts, methodologies and technologies. For more information, please follow the link.
UvA are hiring for COMPAT
UvA are currently hiring for a Postdoctoral researcher in Lattice Boltzmann cell based blood flow modelling. For more information, follow this link.
Supercomputing 2016 (SC16) takes place in Utah on November 13th-18th 2016, workshops related to COMPAT will be announced shortly. For more information, visit the SC16 website here.
The European HPC Summit Week and PRACEdays16
The European HPC Summit is being held from 9 to 12 May in Prague, Czech Republic. The full week will include the organization of several HPC workshops including:
· EXDCI Workshop from Monday noon to Tuesday noon
· PRACEdays16 from Tuesday noon to Thursday afternoon
· ETP4HPC Extreme-Scale Demonstrators Workshop on Thursday
COMPAT will be present at PRACEdays16, which is a workshop aimed at HPC for Innovation: when Science meets Industry. You can read more about PRACEdays16 here, and about The European HPC Summit Week here.
2017 MRS Spring Meeting & Exhibit
The 2017 Materials Research Society (MRS) Spring Meeting & Exhibit will take place on April 17-21 2017 in Phoenix, Arizona. The call for proposals page notes:
As part of the early stages of planning the program for the 2017 MRS Spring Meeting (April 17-21, 2017 Phoenix, Arizona), we are interested in your input on future symposium topics. Our goal is to plan a meeting that includes both new, rapidly developing areas in Materials Science as well as topics within the traditional core scope of the Spring Meeting.
You can find out more about the conference and submitting proposals here.
2016 MRS Spring Meeting & Exhibit
The 2016 Materials Research Society (MRS) Spring Meeting & Exhibit takes place on March 28-April 1 2016 in Phoenix, Arizona. You can find out more about the conference here.
IPP is looking for people to work on ComPat!
The Max Planck Institute for Plasma Physics in Garching, Germany, is looking for, in line with its development program for young scientists, a Postdoctoral researcher (m/f) for the multiscale coupling of Fusion codes in the division of Numerical Methods in Plasma Physics (NMPP).
The official advertisement can be found here.
Call for Papers: EASC2016
The Exascale Applications and Software Conference 2016 will take place in Stockholm, Sweden. The aim of the conference is to bring together developers from different application fields to present the problems they face on the road to exascale, their approach to solve these challenges and to share their experience gained during the petascale period. For more information visit the website: www.easc2016.com. The event takes place on April 26-29, 2016, the paper submission deadline is March 21 2016.
Multiscale Modelling and Simulation Workshop at ICCS 2016
COMPAT is involved in the organisation of the 13th International Workshop on “Multiscale Modelling and Simulation” at the International Conference on Computational Science (ICCS) 2016 on June 6 – 8, San Diego, USA. The workshop provides a forum for multiscale application modellers, framework developers and experts from the distributed infrastructure communities to identify and discuss challenges in, and possible solutions for, modelling and simulating multiscale systems, as well as their execution on advanced computational resources and their validation against experimental data. You can submit a paper and read more about it here.
The deadline has now been extended to Jan 31!
COMPAT Vacancy at LRZ
There is an Open Position in Distributed High Performance Computing at Leibniz Supercomputing Centre (LRZ) in Munich, Germany, for more information see here.
Peter Coveney at MRS 2015
Peter Coveney has given a talk at the MRS Fall Meeting & Exhibit 2015 in Boston, United States, on December 3rd 2015. The talk was titled “Towards the Virtual Laboratory: Modelling Clay-Polymer Nanocomposites Using a Multiscale Approach”. Peter spoke about advanced multiscale simulation systems used to predict the properties of polymer-clay nanocomposites based on their molecular structures and composition, (J.L. Suter, D Groen, P.V. Coveney, Adv. Mater. 2015, 27, 966-984)
HPC Paper from COMPAT
COMPAT Nano Letters Paper
James Suter, Derek Groen, and Peter Coveney have published a paper titled “Mechanism of exfoliation and prediction of materials properties of clay-polymer nanocomposites from multiscale modeling” in ACS Nano Letters. The paper represents a major breakthrough in the development and application of multiscale modelling and simulation for accelerating materials design and discovery based on the concept of a “virtual laboratory”. They show how commercial companies, manufacturers worldwide, and government laboratories and university researchers can can use advanced modelling methods to enhance their productivity. The paper is available online here.
The Solvay Symposium
The Solvay Symposium on “Bridging the Gaps at the PCB Interface” will take place on 19-21 April 2016 at the International Solvay Institutes Brussels. The Symposium will be centered about the rising multi-modelling paradigm, with special focus on emergent phenomena flourishing at the PCB interface. You can read more about it here.
COMPAT consortium member Peter Coveney is on the organising and scientific committee for the event, and Alfons Hoekstra is a confirmed speaker.
Introducing the COMPAT project
The 3-year Horizon 2020 funded COMPAT project launched on October 1st 2015. The main motivation of COMPAT is the urgent need to push the science forward, and stay world leading in simulation driven science and engineering. Our ambition is to establish new standards for multiscale computing at exascale, and provision a robust and reliable software technology stack that empowers multiscale modellers to transform computer simulations into predictive science.
The kick-off meeting for COMPAT took place in Amsterdam on October 5th and 6th 2015. You can find out more about us on the website and our twitter account (@compatproject).