I have a new PhD position available; I am looking to extend some work that I was involved with a while ago now, but into a new area of biology. The idea is that we build an ontological model of the mitochondria, and the knowledge that exists about it. We should be able to build a light-weight model that covers many areas of the biology as an entire system. This will be useful both as an integration point (a traditional use for ontologies), but also so that we can make predictions and search for inconsistencies in the model. In other words, the ontology should be an integral part of the scientific process; we represent a hypothesis ontological and then let the reasoner search for the data for contradictions.

This is quite exciting, as we did the original work quite a few years ago, and it looked very promising; despite the gap, I still think this could work really well. Since that time, system biology has gained currency; this work fits, as we aim to look at the mitochondria as a whole. Instead of an in depth mathematical model of part of the mitochondria, as is common in systems biology, we will have a light-weight logical model of both what we know about the mitochondria and how we know it.

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PhD Studentship, 2010

EPSRC PhD Studentship Building a logical model of biology: the Ontology of Mitochondria

For this project, you will use cutting edge technology designed for the Semantic Web, and apply it to the new field of systems biology. Specifically, you will develop an OWL ontology, a formal, logically specified model, to describe the mitochondria, a subsystem of the cell. You will use this to integrate large amounts of real-world data, to search for inconsistencies and produce a predictions about the underlying biology. From a computing perspective, this will result in insights both about the technology, and its scalablity; from a systems biology perspective, you gain understanding of the value of models which are wider than traditional mathematical models; from a biomedical perspective, you may gain insight in the functioning and behaviour of a medically important system of the cell.

This is a challenging multi-disciplinary project; applicants are not expected to understand all its aspects at the outset; as a result, it is of interest to those from either a computing science, computational biology or bioinformatics background. Any experience of ontologies, modelling or mitochondrial biology will be an advantage, but is not required. A willingness to learn is critical; students will spend significant time in both a computing science and biology environment, and will become familiar with both.

You should have either a First or 2.1 in Computing Science, a Biological Science or Mathematics, and a distinction level Masters degree in a related subject. Equivalent experience will also be considered.

Depending on how you meet the EPSRC’s eligibility criteria, you may be entitled to a full or a partial award. A full award covers tuition fees at the UK/EU rate and an annual stipend of £13,290 (2009/10). A partial award covers fees at the UK/EU rate only.

For further details, please contact Phillip Lord <phillip.lord@newcastle.ac.uk>.