Bioinformatics and data management support for environmental genomics

Abstract

The UK Natural Environment Research Council has funded the creation of a dedicated bioinformatics centre as part of a £26m Environmental Genomics initiative.

Figure 1. The Bio-Linux Computing Platform

(A) Bio-Linux is a Linux distribution customized to be user-friendly that contains approximately 60 popular bioinformatics packages. The Bio-Linux system is freely available, though researchers not supported by the EGTDC must provide their own hardware. Software developed at the EGTDC is included on the Bio-Linux system, making it easy for researchers not well versed in computing to try out these packages. The graphical menus and wide range of bioinformatics software installed on Bio-Linux makes it an ideal system for all levels of users, including beginners, power users, and developers. (B) MaxdLoad2, one of the tools installed on Bio-Linux, provides an intuitive interface to annotate experiments to MIAME standards. When completed, the experiment annotation can be exported in MAGE-ML for submission to ArrayExpress. MaxdLoad2 has been recently engineered to capture data from the “ENV” extension to MIAME.

Figure 2. The EGTDC Data Catalogue

The EGTDC data catalogue currently contains descriptions of 28 environmental genomic grants, each of which can be viewed by its accession number (http://envgen.nox.ac.uk/). Projects include the following studies. (A) How viral infections affect natural phenomena like marine algal blooms (egcat:000010). A virus-infected bloom of the microalga Emiliania huxleyi in the English Channel. Up to 50 million viruses per millilitre were observed in this bloom. (B) The use of earthworms as sentinels of heavy metal pollution in soils (egcat:000024). (C) The genes responsible for circadian and tidal rhythmicity in marine worms (egcat:000029). The “Worm Team” from left: Cas Kramer, Thierry Bailhache, Peter Olive, and Kim Last, ready for the collection of king ragworms in the Blyth Estuary. ([A] Image: Remote Sensing Data Analysis Service/Plymouth Marine Laboratory; [B] Image: Dr. A. John Morgan; [C] Image: Kim Last)