Optic fibre, Photo: Gary Sholl
The idea to connect the TU with genomic centres via dedicated glass fibres won first prize at last year’s Surfnet ‘Enlighten Your Research 3’ competition.
“Now we’ve got a ten gigabit per second connection for each university, which serves the transport of scientific data but also students reading news sites. Consequently, you’re never sure what capacity is available,” Jan Bot (MSc – EEMCS) explains, regarding the need for dedicated glass fibre connections, called lightpaths, for the exchange of genomic data.
His proposal, titled ‘Next generation networking for next generation sequencing’, was awarded first prize at the ‘Enlighten Your Research 3’ (EYR3) competition, organized by Surfnet, the academic internet provider, on 7 December 2011. Bot’s proposal entails a network of lightpaths between the TU and several other institutes: AMC, University of Groningen, Hubrecht laboratory, LUMC, VU Amsterdam, Wageningen University, Beijing Genomic s Institute in Hong Kong and Complete Genomics in California. The last two connections are specialized sequencing companies. “Blood in, bits out,” Bot says.
Bioinformatics means data, lots of data, although less then particle physics. A human genome with 23,000 genes in the current industry standard measures about 300 gigabyte. It takes a single sequencing machine a few days to sequence all the DNA fragments, after which a computer needs about a week to stitch the entire genome together. In practice, these tasks are sped up by parallel processing or by using supercomputers. Up until now, however, research samples are flown to sequencing plants, and then couriers like FedEx or UPS bring the hard disks back. Sending the data by internet or via a cloud is not powerful enough, nor is it secure.
Bot expects the genomic optical network to be operational within a year, after which the exchange of bioinformatics data will be both easier and more secure, since a light path is essentially one continuous fibre without side-branches.
EYR3’s second prize was also awarded to a TU Delft project led by Dr Henri Vrooman (Erasmus MC). He proposed connecting Leiden and Groningen medical centres to the SARA supercomputer and the TU visualization group as an infrastructure for comparing MRI images from population studies.
