Biomedical Engineering Reference
In-Depth Information
EC2 images are stored as AMI in S3 and can be private or public. Essentially
the AMI is a snapshot of the boot disk of the virtual computer. The user
launches an instance of an AMI, then selects the size of the instance to launch.
Before launching the instance, the user generates a key pair fi le to use in
accessing the fi le. With this fi le, the user can use SSH to log onto the instance.
23.2.2
Other Cloud Computing Resources
Although Amazon has taken a very prominent position in the cloud comput-
ing industry, there are other providers that also provide similar services.
Microsoft Azure is similar to Amazon's AWS but is organized into Web and
worker roles rather than instance types. One of the complications of cloud
computing is that applications developed for one system cannot be easily
transferred to a competing system. This has caused a fear that users would be
locked into a single vendor. Recently an open-source cloud system has been
developed. Open Stack [3] is software developed for cloud computing that is
distributed on the Apache license model. Open Stack is not a provider of
services, but the software can be used by an institution to establish its own
private cloud.
23.3
EXAMPLES OF BIOINFORMATICS CLOUD COMPUTING
RESOURCES
23.2.1
Proteomics
Proteomics is a good test case for the use of cloud computing in bioinformatics.
Most high-throughput proteomics experiments are carried out using what is
referred to as bottom-up shotgun proteomics [4]. What this means is that,
instead of measuring the abundance of proteins directly, the proteins in the
samples are fi rst converted to peptides by digestion with proteases, usually
trypsin, and then the peptide composition of the sample is analyzed and the
protein composition is inferred from the peptides present in the sample. This
is done because the peptides are smaller and less complex biochemical entities
that behave better in chromatography and mass spectrometry systems than
whole proteins. Peptides are ionized and charged peptide ions are transported
through the instrument in proportion to the ratio of the peptides' mass and
charge (
m
/
z
). Smaller or higher charged ions move faster than larger or less
charged ions. At an intermediate stage in the instrument, the ions can be frag-
mented by interaction with inert gas or other means. The pattern of fragments
roughly corresponds to the amino acids that compose the peptide. Peptides
are identifi ed by comparing these MS/MS fragmentation spectra to theoretical
spectra in which the assumption is made that fragmentation occurs at each
peptide bond in the peptide. There are a number of available algorithms that
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