So far in this chapter, you have learned how to write MPI parallel routines, access these directly from your R scripts, and turn these routines into reusable R packages. In the remainder of this chapter, we will show you how this capability has been used to exploit supercomputers in the quest to identify signs of bacterial infection and sepsis in blood samples of newborn babies.
Genomics helps us find those genes in a baby that have increased or decreased levels of activity in response to a bacterial infection. By knowing which genes are involved in the immune system's response to bacterial infection (or indeed, how the immune system is subverted by bacteria), we can (a) look at how the activity of these genes differ from baby to baby, and (b) use them to diagnose a bacterial infection from the gene expression measurements in a blood sample.
The remainder of this chapter, therefore, comprises a brief introduction to Genomics followed by a description of how an...