Mantis team visits the Cardiff University Brain Research Imaging Centre (CUBRIC) to learn more about its role in supporting researchers’ quest for the secrets of the human brain.
•OCF / IBM server cluster [soon to be replaced and re-housed offsite]
•Mixture of high-powered workstations
•Brain scanning machines are the original ‘big data’ generators
As you may know, the team at Mantis likes to visit public sector organisations to understand their function, and how IT supports their operations. It’s part of our ongoing, internal training programme. This week with visited the Cardiff University Brain Research Imaging Centre [CUBRIC].
Set up six-years ago and funded by a research council grant, the Centre provides access to state-of-the-art brain scanning technologies, which support collaborative research from around the World. Spiro Stathakis who is IT Systems Manager at CUBRIC [and our guide for the visit] told us that: “The Centre is part of the School of Psychology but collaborates with other clinical schools at the local hospital and School of Bio Sciences at the University. The Centre is quite well known in the world of neuro-imaging and we have some great people working here.”
He adds: “Initially the Centre was available for post-doctoral research. After a few years this was expanded and we began supporting the PhD programme and more recently we are now offering support for the MSc programme in neuro-science too.”
The Centre has a range of brain scanning technologies available to researchers. These include structural and functional magnetic resonance imaging [MRI and fMRI] electro- and magneto-encephalography [EEG and MEG] and trans-cranial magnetic stimulation [TMS].
Grant-funded researchers pay to use the Centre’s technology and this helps to sustain CUBRIC. The centre also sells out of hours scan time to a local private medical facility.
We met one of the Centre’s research staff, Dr Suresh Muthukumaraswamy, who explained the different types of research undertake. This includes researching how people with conditions such as bi-polar, Alzheimer’s, and Dyslexia, for example, might have brains that react differently. Plus, his own areas of interest, pharmacology, where he says the team is making good progress in how drugs affect the brain, which can have potential to treat diseases and develop new drugs. He talked particularly about the MEG technology and why it was so important.
“There are only eight such MEG machines in the UK, Dr Muthukumaraswamy told us. “The other MEG machines are based Kings College London, Oxford, Cambridge, Nottingham, York and Glasgow. It’s a magnetic version of an EEG machine [think people with electrodes over their head]. We use this to create an online recording of the brain. This machine has 275 detectors. We get a 1000 recordings from each detector every second, this creates 1Gb data every 10-minutes. The machine picks up magnetic fields that the brain creates.”
The machine is very sensitive. He jumps up and down on the floor which makes the steel bars that reinforce the walls vibrate, the machine detects the tiny electro magnetic fields that the vibration creates. In his work he must use mathematics to isolate non-brain magnetic fields – people jumping up and down the floor, passing traffic, pace makers, etc. Dr Muthukumaraswamy can use this data with his work.
“There is friendly competition with the other MEG centres, but mostly collaboration amongst the MEG community. On our own we’re quite weak, so we help each other, we do work together a lot.”
Spiro also showed us the MRI machine [actually he showed us a replica shell used to help patients ‘get accustomed’ to the machine but it looks the same]. The building itself was constructed around the machine, because of its size. It’s very delicate scanning technology – non radioactive, non invasive and very good for studying patients. Anna took the opportunity to test out the machine by lying on the bed and getting a feel for how a patient might respond! With the replica shell it is also possible to mimic the noise of the actual machine. The real machine costs in excess of £1million.
IT / Technology
In terms of IT, the Centre has a high performance server cluster and storage facility built around six-years ago by OCF using IBM hardware. The cluster is used by researchers to processes and analyse data generated by the brain scanning technology. I think for all us it was a surprise how noisy the cluster was; it was far from deafening, but you certainly couldn’t put the cluster in an office and expect to achieve a day’s work. The heat expelled from the machines was offset with cooling fans, but nonetheless our clothes were being noticeably moved by the flow of air.
In terms of space, the cluster was smaller than expected. Including cabling, storage, servers and racking, it filled a small office. The cluster is due to be replaced and rehoused elsewhere on campus in the next few months. Spiro told us: “The current 300-core cluster fills 3-racks in a server cabinet; the new cluster will provide 1200 cores of processing power, but it will fill just 2-racks in a server cabinet!” Supercomputers are getting more powerful, but are also physically shrinking!
In most cases, Spiro can access the server cluster remotely for repairs and maintenance, although he checks the facility regularly.
He adds: “Personal workstations are available to researchers. They are upgraded ad-hoc, but a lot around the building are the original machines from 6-years ago when the centre was built. We’re slowly upgrading on an as need-be basis. The workstations in and around the MEG machine, all managed by Dr Muthukumaraswamy, were a mixture of Mitsubishi, Dell and Fujitsu hardware. He runs a Linux Operating System and uses Windows where necessary.
“Researchers can take data off-site. Data is anonymised which renders it safe to be taken away. If it was comprised or exposed an individual could not be identified. To be honest, it would be difficult to stop people taking data way because there is such as plethora storage mediums. Plus, we want people to be able to work remotely, collaborate and use data off site for many other legitimate needs.”
With few other facilities around the country boasting the range of scanning technologies or ‘modalities’ available at CUBRIC, a server cluster and expert staff, the facility really is unique. We’re looking forwarding to returning in a few month’s time when the new server cluster is installed and crunching data.