Summary
Within TI Food and Nutrition research programme 3 focusses on optimising
fermentation performance, predicting product formation, optimising survival
under various conditions and determining interactions of bacteria in complex
fermentations. In many of these projects, sequencing a bacterium and predicting
its metabolic and regulatory potential from the genome sequence is crucial. The
C1007 project aimed to provide generic tools to support different projects in
their bioinformatics analyses of genomics datasets. The objectives of this
project were: (i) to create a generic genome-annotation database, (ii) to
implement genomics data in this database and (iii) to create a TI Food and
Nutrition bioinformatics wiki.
The MicroGear genome-annotation database is the central database and toolbox,
used within TI Food and Nutrition, for annotating bacterial genomes. The
database structure is adapted from CHADO, an excellent database structure for
holding genomics information. This structure, using components in the public
domain with large user and development bases, makes MicroGear extensible and
relatively easy to maintain. MicroGear is implemented on a dedicated TI Food
and Nutrition database server and has been in operation since Q1 2011. Public
genomes are available in MicroGear and a number of genomes from industrial
partners have been be added to the database to demonstrate its usability.
Furthermore, a bioinformatics wiki website has been created specifically for
this research field. The purpose of this wiki is to provide wet-lab researchers
with a central portal to bioinformatics methods and tools developed and/or
applied in TI Food and Nutrition, and to experts working at the different
knowledge institutes. As with other wikis, it requires continuous maintenance
by bioinformaticians and wet-lab biologists in order to make it a valuable and
respected bioinformatics reference for scientists at research institutes and in
industry. It has been open to the public since it became operational in the
first quarter of 2011.
Time frame: 2008 – 2011