Computational Modelling Group

AWK

AWK is a s a small, C-style programming language designed for text processing and typically used as a data extraction and reporting tool. It is a standard feature of most Unix-like operating systems. Many UNIX utilities generates rows and columns of information, AWK is an excellent tool for processing these rows and columns, and is easier to use AWK than most conventional programming languages.

For queries about this topic, contact Roshan Sood.

Projects

E ffects of Sample Contamination on Alternate Allele Frequency

Jane Gibson (Investigator), Roshan Sood

Accurate calling of genetic variants is reliant on the purity of samples, contamination will reduce the accuracy of results. Currently there are few programs able to identify contamination in samples, potentially misinforming a researcher or clinician. To better understand the changes caused by sample contamination in
silico simulations were performed where a known percentage of DNA sequence reads from a contaminating
fi le were added. Understanding the changes will assist the development of a new method and program to
detect sample contamination.

Porcupine Basin Project

Louise Watremez

The Porcupine Basin is a narrow failed rift, offshore SW Ireland, featuring extreme crustal thinning. The M61/2 survey (May 2004, T. Reston and B. O'Reilly) allowed for the acquisition of seismic refraction data across and along the basin, along 5 transects. The processing of the data along these transects will give us information about the crustal structure across the basin, faulting due to the crustal extension, nature of the upper-mantle, etc. This project is funded by Petroleum Infrastructure Programme (PIP).

People

Jane Gibson
Lecturer, Biological Sciences (FNES)
Louise Watremez
Research Fellow, Ocean & Earth Science (FNES)
Roshan Sood
None, None