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Primeur weekly 2017-01-30

Exascale supercomputing

Co-design centres to help make next-generation exascale computing a reality ...

Quantum computing

Supercool electrons ...

D-Wave announces D-Wave 2000Q quantum computer and first system order ...

Temporal Defense Systems purchases the first D-Wave 2000Q quantum computer ...

Fast track control accelerates switching of quantum bits ...

Focus on Europe

Bright Computing teams up with SGI to co-sponsor UK HPC & Big Data event ...

When life sciences become data sciences ...

PRACE Spring School 2017 - HPC for Life Sciences, registration is open ...

ITER and BSC tighten their collaboration to simulate the process of fusion power generation ...

Netherlands eScience Center to issue annual report ...

Middleware

BSC releases PyCOMPSs version 2.0 as a PIP installable package ...

Hardware

RSC gets the highest Elite status in the Intel Solutions for Lustre Reseller Programme ...

Finding a needle in the ocean ...

GIGABYTE selects Cavium QLogic 10/25GbE FastLinQ technology to power its next generation servers ...

Setting up light paths using the SURFnet Network Dashboard ...

Minerva will calculate gravitational waves faster than the Albert Einstein Institute's previous supercomputer ...

Applications

Big Brother will have some difficulty 'watching you' in future ...

Engineers eat away at Ms. Pac-Man score with artificial player ...

Mummy visualization impresses in computer journal ...

Berkeley launches RISELab, enabling computers to make intelligent real-time decisions ...

Model sheds light on inhibitory neurons' computational role ...

Using Big Data to understand immune system responses ...

Artificial intelligence uncovers new insight into biophysics of cancer ...

PPPL scientist uncovers physics behind plasma-etching process ...

Computer-aided drug design ...

IBM expands choices for PowerAI developers with TensorFlow ...

Hussein Aluie awarded hours on supercomputer at Argonne ...

CWI develops algorithms that shorten response time of ambulance ...

A rising peptide: Supercomputing helps scientists come closer to tailoring drug molecules ...

The Cloud

Oracle expands Startup Accelerator Programme to further promote global Cloud innovation ...

Technical computing hub UberCloud receives funding from Earlybird ...

Computer-aided drug design


Demonstration of small molecules - candidate drugs binding to a protein implicated in cancer. A simulation approach is employed with which candidate drugs are optimised and the best is selected for experiments. REF: Structural characterization and computer-aided optimization of a small-molecule inhibitor of the Arp2/3 complex, a key regulator of the actin cytoskeleton. Baggett AW, Cournia Z, Han MS, Patargias G, Glass AC, Liu SY, Nolen BJ. ChemMedChem. 2012, 7(7):1286-94.
26 Jan 2017 Brussels - In May 2016, Dr. Zoe Cournia - a computational chemist at the Biomedical Research Foundation, Academy of Athens (BRFAA) - was presented with the inaugural PRACE Ada Lovelace Award for HPC. The award - named after the British mathematician widely thought to have written the first algorithm for a machine - was created to recognise women who have made outstanding contributions to the field of high performance computing in Europe.

Dr. Cournia's work involves using simulations to investigate how mutations in proteins can lead to cancer. Using data acquired from these simulations allows researchers to investigate potential mechanisms by which small molecules can bind to mutated proteins and inactivate them. "We look at small cavities on proteins where small molecules can potentially bind", explained Dr. Cournia. "We then design candidate drugs specifically for those cavities, which are then tested in the lab by our collaborators."

"We have come up with a number of drug candidates, which have so far been shown to be effective in biological assays and mouse models."

"I believe that our work is a good example of how computers help develop products that have the potential to save millions of lives worldwide. I am honoured to receive this prestigious award and hope that this serves as inspiration to other female researchers in the field."

Dr. Cournia and her team are now advancing their projects, and are looking to move their research beyond the state-of-the-art. This will be achieved by mapping the entire landscape of motion of a mutant protein, simulating a system of 400.000 atoms. "We also want to try and recreate the proteins in virtual reality for educational purposes", stated Dr. Cournia. "This will be useful in helping us to grasp the movement of proteins and how drugs interact with them, and we also hope that students in schools can try it out to see for themselves what we are doing. Hopefully this might push some of them on to following a career in science."

News of Dr. Cournia's success has been well received in her home country, Greece, and she has subsequently been the subject of numerous articles and interviews. Her success has been featured on national TV (NET, STAR channel, SKAI, Alpha), Lifo, politicsonline.gr and news247.gr, and she believes that this kind of publicity is much needed by the HPC community. "The award has helped to increase the visibility of HPC to the public and helped them realise how important a role it plays in our everyday lives", she stated. "Every product we use, from cell phones to cars to aeroplanes to clothes, at some point goes through a stage of testing which uses HPC."

Popular promotion of science is sometimes to the public is sometimes successful; television programmes on astronomy and the natural world are some of the most popular in existence. However, there still remains a huge disconnect between the research community and the general public. "Many people think that research is impossible to understand", stated Dr. Cournia. "That is why it's important to set an example showing that research and science are not difficult and are accessible to everyone. Awards like this help to demonstrate this, and I hope that I can be a role model to young people, showing them that they can make a difference by improving people's quality of life through a career in science."

"I also want the public to see that taxes invested in research do not go to waste", she continued. "I think the perception is often that this money goes into esoteric research which does not really benefit society, but the reality is that it often feeds into products which people use every day and even help to save lives."

A recent survey in the UK revealed how one third of teenage girls do not think they are clever enough to consider science-based careers. Women remain underrepresented in the STEM fields, which was one of the main reasons behind the launch of PRACE's Ada Lovelace Award for HPC. "It's certainly a good idea to have female role models in this field", stated Dr. Cournia. "I think perceptions are starting to change now, and setting good examples can convince women and girls that it's not a matter of gender, but a matter of preference of what you want to do in life."

Dr. Cournia is now working on a Horizon 2020 project called VI-SEEM that is aiming to encourage scientists in life sciences to get involved with their local e-infrastructures. "When I first arrived back from studying in the US to start my lab, I had no computational resources at all", stated Dr. Cournia. "I applied for a few PRACE projects, but was unsuccessful at the time. Although eventually I was successful, in the meantime I applied for access to an eastern Mediterranean e-infrastructure (LinkSCEEM), where I was able to produce preliminary results for my work that helped show PRACE that my project was worth investing in. This was hugely important for me and I now want to help encourage more scientists to use local HPC resources."

VI-SEEM is aiming to facilitate interdisciplinary collaboration in the life sciences, digital cultural heritage, and climate research by spreading the word about e-infrastructures in southeast Europe and the eastern Mediterranean. "Apart from providing the e-infrastructure services and facilities, we are also coordinating workshops on performing HPC calculations, carrying out training sessions and workshops, and generally encouraging scientists in local communities to get involved with the regional and local e-infrastructures to advance their own projects", stated Dr. Cournia. "Hopefully our activities can help introduce them to the benefits of working with computer resources and lead them on to even greater scientific discoveries in the future."

Source: PRACE

Back to Table of contents

Primeur weekly 2017-01-30

Exascale supercomputing

Co-design centres to help make next-generation exascale computing a reality ...

Quantum computing

Supercool electrons ...

D-Wave announces D-Wave 2000Q quantum computer and first system order ...

Temporal Defense Systems purchases the first D-Wave 2000Q quantum computer ...

Fast track control accelerates switching of quantum bits ...

Focus on Europe

Bright Computing teams up with SGI to co-sponsor UK HPC & Big Data event ...

When life sciences become data sciences ...

PRACE Spring School 2017 - HPC for Life Sciences, registration is open ...

ITER and BSC tighten their collaboration to simulate the process of fusion power generation ...

Netherlands eScience Center to issue annual report ...

Middleware

BSC releases PyCOMPSs version 2.0 as a PIP installable package ...

Hardware

RSC gets the highest Elite status in the Intel Solutions for Lustre Reseller Programme ...

Finding a needle in the ocean ...

GIGABYTE selects Cavium QLogic 10/25GbE FastLinQ technology to power its next generation servers ...

Setting up light paths using the SURFnet Network Dashboard ...

Minerva will calculate gravitational waves faster than the Albert Einstein Institute's previous supercomputer ...

Applications

Big Brother will have some difficulty 'watching you' in future ...

Engineers eat away at Ms. Pac-Man score with artificial player ...

Mummy visualization impresses in computer journal ...

Berkeley launches RISELab, enabling computers to make intelligent real-time decisions ...

Model sheds light on inhibitory neurons' computational role ...

Using Big Data to understand immune system responses ...

Artificial intelligence uncovers new insight into biophysics of cancer ...

PPPL scientist uncovers physics behind plasma-etching process ...

Computer-aided drug design ...

IBM expands choices for PowerAI developers with TensorFlow ...

Hussein Aluie awarded hours on supercomputer at Argonne ...

CWI develops algorithms that shorten response time of ambulance ...

A rising peptide: Supercomputing helps scientists come closer to tailoring drug molecules ...

The Cloud

Oracle expands Startup Accelerator Programme to further promote global Cloud innovation ...

Technical computing hub UberCloud receives funding from Earlybird ...