Biomedical Engineering Reference
In-Depth Information
student, rather than very formal tutoring - but mostly through
structuring the data and tool organisation so that the biologist does not
need to think too much about the computer administration side of the
deal and can think about the data and the biological question alone.
There are a great deal of free and open source tools that can be applied
to this end.
11.3 Manage the data: relieving the
burden of data-handling
Much of our data is generated internally on our high-throughput
sequencer and image analysis machines, which send the raw data
straight to the large central storage device. Actually getting at and
using large data sets on a local machine so that they can be analysed
in any sort of software is often much more of a trial than we would
want it to be. Typically, something like FTP is used to copy the fi les
over a network from some central fi lestore to the machine with the
analysis software. FTP clients and command-line transfer can be powerful
but cumbersome, result in unnecessary copies of the fi le and, often,
the biologists are unaware of the concepts required to understand the
transfer (it can often be surprising to an informatician how little a typical
biologist knows of the nuts and bolts of dealing with computer systems).
It is much more practical to integrate the data and transfer as far as
possible with the client machine's operating system, and although
Windows and Mac OS do provide some functionality for this, they
are not much better than FTP programs. Instead we have made use
of user space fi le system drivers, which allow a user to connect to an
external fi lesystem without additional privileges to their machine or the
remote machine/fi lesystem. In this way we have been able to make our
central fi le store accessible to the desktop environment as if it were
any other mounted device, like an external DVD drive or a USB
stick (Figure 11.2).
11.4 Organising the data
Once the data can be seen by the computers they are working on,
biologists still need to be able to fi nd the fi les and folders that they need.
We have used a simple but effective trick to create a directory structure
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