Bioscanners and Bioparsers

Abstract:

An often occuring task in nowadys biological/physiological work is
analysing, also called “parsing”, of large amounts of biological data.
Although tools has been written many times in many programming languages
for such tasks most applications do not satisfy the need of end users -
researchers with limited programming skills. Installation, speed and
output are not suited for easy usage of tools and concentrating on the
scientifc task. Instead of handwriting applications we use scanner
generators like Flex and Jflex to create fast scanners for biological
data which are easy to code, easy to maintain, easy to install and as
standalone applications without any external dependencies easy to use.
The data output of those tools is standard SQL-code not tied to a
certain RDBMS which can be used to fill the database. This allows
researches to use their database of choice and SQL statements to assembl
data from different resources and applications. Some practical examples
are provided to document the advantages of using scanners which can fill
databases to combine results from different scanning procedures.