Biomedical Engineering Reference
In-Depth Information
Indeed, the consequences of the improvements in microarray technology
have been the increased demands placed on the IT infrastructure
that supports it. For example, in 2003 the densest microarray that
OGT produced contained 22 500 oligonucleotide probes. Following
hybridisation and processing, this generated a data fi le of about
12 MB. Since then, DNA spotting has improved such that more
features can be printed, and the resolution of scanners has similarly
increased so these features can be smaller. This frees up real estate on the
slide allowing for increases in feature number. At the time of writing,
the latest arrays from our microarray provider, Agilent, have 1 000 000
features and generate a data fi le around 1.4 GB. This dramatic
increase impacts across the IT system; fi les take longer to move around
the network, backups take longer to run and fi les are now too big to
deliver by email or via traditional methods such as FTP. Furthermore, we
have recently expanded our offerings to include next-generation
sequencing (NGS). This has necessitated a large investment in hardware
to provide the processing power to deal with the terabytes of data
generated. The chapters by Thornber (Chapter 22) and MacLean and
Burrell (Chapter 11) provide good background on NGS data for those
unfamiliar with this topic.
10.3 The hardware solution
Within the company there is a requirement for our hardware system to
integrate the needs of the computational biology team, who use both
Windows and Linux, with those outside the group, who work
purely within a Windows environment. For example, the PCs in the labs
used to process the microarrays must be able to write to a location
that can be accessed by the Linux-based applications used to process the
data. The approach taken at the start of OGT, and still in place
today, was to keep all data on disk arrays controlled by a Linux server.
These directly attached storage (DAS) arrays mounted on the
Linux platform are then made available to all users over the company
network. This is accomplished using the Linux utility Samba [2]. Samba
comes with a great deal of supporting information to allow users to
understand this powerful system. Essentially, there are folders defi ned
within Samba to which Windows users can map a drive. The appearance
of these drives is of a normal Windows folder, but under the bonnet the
information is being made available across the network from a Linux
server. This integration of Windows and Linux is reinforced by the fact
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