Biology Reference
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the organizing structure for both the data and the software. Fourth,
they may contain bioinformatician-users moving around in the space
and manipulating data, software, or the directory structure. The way
in which these four elements interact with one another is both intricate
and tightly constrained. For instance, beyond the necessity of logging
into any machine, certain kinds of data may be manipulated only by
certain individuals (often, those who created them). Further, users may
not store data just anywhere or execute software on any computer: data
must be placed in particular directories or directory structures, and pro-
grams must be run on dedicated machines.
The “farm” system in place at the EBI illustrates the care that is
taken to control and monitor movement through the virtual space. The
“farm” or “compute farm” is a set of computers (549 in November
2008) used by the EBI for running programs requiring intensive cal-
culation or data manipulation. For most users, it is not possible to log
into the farm directly. Instead, bioinformaticians log into a computer
called “farm-login,” which is connected to the farm. In order to run a
computationally expensive program, users must submit a “job” using a
system called LSF. This program allocates the job to one or more of the
machines in the farm. According to the internal wiki:
All users of the farm initially have equal priority. The queueing
system uses a policy called “Fair-share” to ensure equal distri-
bution of work. LSF will dynamically change your priority de-
pending on how much time you have recently consumed on the
farm. If you have been running lots of jobs, LSF will lower your
priority to allow other users' jobs to be dispatched in preference
to yours. Conversely, if you have not used much farm time, LSF
will increase your priority with respect to other users. 36
The farm is designed to “farm out” the computational work in an ef-
fi cient and equitable manner. The metaphor of working the land is ap-
propriate—if the total network of computers is imagined as a space, it
is also imagined as one in which certain resources (disk space, compu-
tational power, memory) are valuable commodities that must be tightly
regulated. Regulating space allows its productivity to be maximized.
What are bioinformaticians doing in virtual space? At the most lit-
eral level, they are usually interacting with screens of text—typing com-
mands, writing programs, and moving or copying fi les. Almost always,
they will be in more than one place at once—there is no limit to the
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