In 2007, after 25 years working in the Telecoms industry (working on the same product, System X,for almost all of that time) I took voluntary redundancy from Ericsson, and completed a 4 year MSc/PhD within MOAC before moving on to take up a post doc position in the Systems Biology Centre at Warwick
Life before MOAC provides a little of the background as to how I came to make such a radical career move.
These web pages provide information on my interests in water, my PhD, as well as information on the work I carried out during my 1 year MSc.
The enigma that is water
The Life before MOAC page describes how a long standing interest in vibrational modes led to an interest in the physics and chemistry of water. This led to the presentation of a paper at the 6th conference on the Physics, Biology and Chemistry of water where I explored how the different properties of the two spin isomers of water might help us understand some of the strange properties of water, many of which were covered in other papers presented at this conference.
My PhD: Informative sequence-based models for fragment distributions in ChIP-seq, RNA-seq and ChIP-chip data
The PhD is centred on trying to improve our ability to predict the locations where proteins, or transcription factors, bind to DNA in order to regulate gene expression. More details.
One of the outcomes of the work is a paper which will be submitted to NAR entitled "Improved modelling of RNA-seq and ChIP-seq bias using multiple alternative nucleotide distributions"
I have placed a set of programs, spreadsheets and sample data onto the web to allow the results in this paper to be reproduced
My initial work has been to look at the different ways of scoring the match between a DNA sequence and the transcription factor consensus sequence.
My PhD: Software development
As with an increasing amount of Biology and Genetics, a significant amount of these work involves mathematical modelling and the initial stages of the PhD involved reconfiguring and updating some of the software systems used within the group. Much of this involves open source software, where the documentation is minimal, and help is often found on other peoples Blogs where they have recorded there experience of using the software.
In turn, I have created a series of web pages which document what I have learnt in the process. Topics covered include:
Installing and building software on Windows PCs:
- Installing Perl on a windows PC
- Creating mixed .NET and classic C++ applications using Visual C++ (Documentation elsewhere is confused or wrong)
- Installing OpenSSL on Windows
- Executables build using Visual Studio 2005 fail to run on other PCs after KB971090 has been applied
Installing and building software on Apple MACs
- Problems building code that uses the Carbon library
- Installing gcc on Apple darwin platforms (because the bundled gcc is ancient)
notes on using PERL
- Installing the PERL EnsEMBL API for accessing gene data
- Creating a Soap client for a complex Soap interface in Perl (Because documentation elsewhere is poor)
- Calling Perl from within a C++ application (Because documentation elsewhere is incomplete)
- Performance comparisons between Perl and C++ (Conclusion: Perl is slow)
Installing and using software within Systems Biology
- Running the APPLEs software on a PC (*)
- Using cisGenome for analysing ChIP-seq data (*)
- Notes on how SVN is used to store software within the System Biology group (*)
- Installing the Bifa Server dlls (*)
- Using Warwick 'sitebuilder' to create web pages (such as this one) (*)
- Using various Warwick computing platforms (*)
- Using Boost on the System Biology Server (*)
Creating multiplatform applications
(*) indicates webpages that are restricted to Warwick University members.
My MSc: Mathematical Biology and Biophysical Chemistry
After the first six months of taught modules, including exams which I thought I had left behind me many years ago, I carried out three mini projects, which provided stepping stones to my PhD.
The first two mini-projects were linked, the first being laboratory wet-work in Biological Sciences , and the second being Biophysical Chemistry experimental work using the FtsZ protein produced as part of the first mini-project.
Mini project 2: How does YgfE bundle FtsZ? (Prof. Alison Rodger)
The third mini-project is the Mathematical/Computing based mini project, which was unrelated to the first two projects and led into my PhD.
Mini project 3: Modelling and Predicting Transcription Factor Binding Sites (Dr. Sacha Ott)
And finally.. Look at the pictures on the right in the 'also in the news' secton of the following BBC web page: