Setting up an ’omics platform in a small biotech - Open Source Software in Life Science Research - page 242

This not only provides a suitable backup, but also keeps track of all
changes in a set of fi les, maintaining a record of transactions.
10.7.4 'omics tools
Running an 'omics platform requires the use of a range of tools. A
good place to start exploring the range currently available are the
resources provided by the European Bioinformatics Institute (EBI). There
are online versions of most tools, but local installations provide
greater throughput for those run most frequently, also ensuring high-
priority analyses are not subject to delays sometimes experienced on
shared resources. Typically at OGT, there are local installations of
major systems such as the Ensembl [9] Homo Sapiens genome database,
providing immediate query responses as part of our processing
pipeline. Pointing the same scripts to the same databases or web
services held externally at the EBI would result in queries running much
more slowly. When there are only a few queries this does not matter so
much, but as the number of queries increases to hundreds and thousands
then the impact is greater. A local installation is also critical from a
security point of view, particularly where the data are confi dential.
Customers are always happier being told that all systems are internal,
and there have been situations where this has been stipulated as an
absolute necessity. Of course, there is the overhead of maintaining
these installations, but in the long run this is a cost worth meeting.
The following is a list of general FLOSS tools that are routinely used in
our pipelines.
￿ ￿ ￿ ￿ ￿
10.7.5 Bioinformatics tools
■ BLAST [10] - almost certainly the most used 'omics application. The
Basic Local Alignment Search Tool, or BLAST, allows comparison of
biological sequence information, such as the amino acid sequences of
different proteins or the nucleotide sequence of DNA. A BLAST search
enables a researcher to compare a query sequence with a library or
database of sequences, and identify library sequences that resemble the
query sequence;
■ MSPcrunch [11] - this is a less well known but powerful tool that
makes processing of large-scale BLAST analyses straightforward. Data
can be easily parsed on a range of parameters. Also, there is a useful