A big cloud for big science

Last week, a major European collaboration called Helix Nebula – the Science Cloud was announced. Its goal is to provide a Pan-European cloud computing platform for scientific research. Commercial partners are bringing the latest computing advancements to enable cheaper science and better collaboration in biomedical, particle physics, and natural disasters research.

Helix Nebula supports Europe’s Digital Agenda as outlined by European Commission Vice-President Neelie Kroes.“It is a true win-win: the cloud market will grow, bringing opportunities for existing suppliers and new entrants. And Cloud buyers, including the public sector, will buy more with less and become more efficient,” she said during her speech at the World Economic Forum in Davos, Switzerland, in January 2012.

To start, Helix Nebula three flagship projects will partake in a two-year pilot phase that represents a proof of concept between big science and industry. These are the ATLAS experiment at CERN in Switzerland, the European Molecular Biology Laboratory (EMBL) in Germany, and the European Space Agency (ESA).

Each partner has specific needs and issues they aim to address.

Larger-scale genome analysis

A gray short-tailed opossum. The European Molecular Biology Laboratory is setting up a new service to simplify analysis of large genomes, such as those from mammals. Assembling genomes can provide a reference for studying an animal at the genomic level, where an understanding can be built of what genes it has and how they work. Researchers can also gain a much deeper insight into the evolutionary relationships between organisms by comparing their genomes, and to understand which parts of the genome have specific functional importance. Image courtesy LA Dawson, Wikimedia Commons.

“Over the last three years, our users have had to deal with more and more data. Our ability to produce scientific data is currently outpacing our computing infrastructure’s ability to deal with it,” said Jonathon Blake, a bioinformatician at EMBL.

“My role is focused on the management of large amounts of sequencing data and finding ways to get the most out of it for our users. In genomic assembly, we require machines with large amounts of RAM computer storage - up to one terabyte. A cloud workspace will remove the issues of our researchers establishing an infrastructure themselves. By expanding our data processing into the cloud, we hope to establish a very flexible and extensible infrastructure to make it easier for users to access resources on demand, providing swift and secure data transfer and management,” he said.

This requires biological researchers to become familiar with new computational methods. 

“Some wet lab (those working at the laboratory bench) biologists have had a steep learning curve coming to terms with next-generation sequencing data analysis. Researchers will have to get used to data processing in clouds and the data management issues involved. Hopefully, the public will benefit from a scientific research infrastructure producing results quickly at efficient cost,” he said.

The two other research organizations in Helix Nebula collaboration are already testing the feasibility of using commercial clouds in the scientific process, albeit on a small scale.

Faster analysis of natural disasters

“For us, the problem is not technical. The problem is to make a sustainable business model and system,” said Wolfgang Lengert, mission manager for the European Space Agency’s European Remote Sensing satellites that observed the Earth’s atmosphere, land, cryosphere (ice sheets), and oceans from 1999 until 2011.

The 8.9 magnitude Japan Tōhoku earthquake in March 2011. Yellow contours are areas where the earthquake struck. The colored loops represent previous quakes. To provide data faster for scientists analyzing the Sendai area, ad-hoc cloud computing assets were created by a team made from a Taiwanese station (CSRSR), Remote Sensing 2 (ERS-2) satellite data, CSTARS  in Miami, and CNR//IREA in Italy. Image courtesy ESA / CSRSR / CSTARS / IREA.

“We’ve been using cloud assets since 2008," he said. For example, to support a Japan earthquake monitoring station in Taiwan, they set-up a system for scientists to quickly analyze seismic data. With clouds, they didn't need to go through a system procurement process which would've taken a month, they were running within a day.

"We have a strong heritage from our computer grid system, Grid Processing on Demand (G-POD); but, with the cloud, we have a much more open system. Scientists will have a one-stop-shop to get all their space data, tools (both commercial and open source), and research support on demand. We are aiming to establish an Earth observation system called the SuperSite Exploitation Platform (SSEP) to enable the scientific community to better understand geophysical phenomena such as earthquakes or volcanoes," said Lengert.

With Helix Nebula collaboration researchers will be able to combine data and tools outside of the European Space Agency.

"If the SuperSite Exploitation Platform works out, it could easily extend out to include atmosphere, costal, forest, and ocean research. I’m sure we are participating in a historical set up. Policy makers and national agencies will benefit from the new scientific knowledge for the assessment and mitigation of geological risks,” said Lengert. 

Currently, the analysis software tools that researchers use are very costly.

“If we have everything on Helix Nebula, users only pay for the usage of these tools and not the full license, which would save us a lot. Users could also bring in new custumers to commercial tool providers, thus increasing their revenue,” said Lengert.

Expanding particle physics simulations

The ATLAS experiment at CERN is also testing particle simulations with cloud company CloudSigma.

“The workloads are simulations which are normally run on the grid. The results so far are encouraging, but we have not yet tested using cloud storage, and that will be an important test. The use of cloud resources will, and should, be hidden from the physicist by the experiments' software frameworks and analysis environments,” said Ian Bird, WLCG Project Leader.

Even though the Helix Nebula collaboration has just started, Bird is confident that it will grow.

“This is not a large collaboration; especially, when compared to the WLCG and Large Hadron Collider experiments. We have only done limited tests so far, and we don't have much experience working with these partners yet, but we are very used to working in huge global collaborations,” he said.

Now, Helix Nebula is looking to expand the number of applications and cloud suppliers following the deployment of its flagship projects.