Most popular ▴ See a list of all my posts! Why are there no great Windows 10 apps? How moving the Capital helps Hartlepool. Gender bias calculator The Centre of the UK Defending Uber BusTracker Imagination not needed. Part 1. Imagination not needed. Part 2. Imagination not needed. Part 3. Why Birmingham fails Who is London? Innovation on buses. Heathrow

PDFs and Data ▾ Improving PDFs for Science. Improving PDFs for Planners. PDFAttacher. A Clearer Plan Hybrid PDFs PDF test-off. PDF Profiler Making PDFs play nicely with data

Housing ▾ Counting households. 1. Counting households. 2. The housing market works (where we let it) Hexmaps Adonis is wrong on housing Car free Birmingham

Regional Growth ▾ Measuring tech in the UK and France in 10 steps. Defending the Zombie graph. Channel 4 must move to Mancheseter Measuring innovation 1: meetups Measuring innovation 2: scientific papers. The UK city-size abnormality. Cities not cheese: why France is productive. How moving the Capital helps Hartlepool. Industrial Strategy. Leeds Growth Strategy 5: Limits. Leeds Growth Strategy 4: Focus. Leeds Growth Strategy 3: Inclusive growth. Leeds Growth Strategy 2: Where to grow? Leeds Growth Strategy 1: Why grow? Imagination not needed. Part 1. Imagination not needed. Part 2. Imagination not needed. Part 3. Inclusive growth. The BBC in Manchester 1 The BBC in Manchester 2 What works (growth) North-South divide: we never tried Imitating Manchester Why Birmingham fails Who is London? Researching research Replacing UK steel The Economist & The North The State of the North, 2015 Move the Lords! Calderdale Digital Strategy Maths of inequality Income by MSOA Heathrow and localism The NorthernPowerhouse Centralism and Santa Claus Yorkshire backwards London makes us poor

Transport ▾ Fixing it ourselves: bus data in the North. Open fare data will be hard. Transport is too complex! Investment is political London loses when it blocks Leeds' growth The Centre of the UK Defending Uber BusTracker Train time map What works (growth) The Value of Time Innovation on buses. Heathrow 1975 WYMetro Plan

Politics & Economics ▾ GDP measures are like toilets. The UK's private postcodes restrict innovation. Yorkshire could learn from Ireland's success. Alternatives to GDP are a waste of time. Fiscal balance in the UK "Not like London" Innovation takes time to measure Fifa and the right In defence of the € GDP mystery Liberal protectionists 5 types of EU voter Asylum responsibilities STEM vs STEAM The Economist & Scotland BBC Bias? Northern rail consultation What holds us back? Saving the Union Summing it up

Positive ▾ Bike Lights Playful Everywhere Greggs vs. Pret Guardian comment generator Consult less, do more! More things for Leeds! Cartoons PubQuest: Birmingham

Tech ▾ What's holding back opendata in the UK? Anti-trust law saved computing 1 Anti-trust law saved computing 2 Open Data Camp Cardiff Why are there no great Windows 10 apps? Tap to pay. Open Data in Birmingham Defending Uber BusTracker Train time map Building a TechNation How the UK holds back TechNorth GDS is Windows 8 OpenData at the BBC SimFlood SimSponge See me speak Digital Health Leeds Empties Leeds Site Allocations Building a Chrome extension I hate webkit Visualising mental health Microsoft's 5 easy wins Epson px700w reset Stay inside the Bubble

Old/incomplete ▾ Orange price rises The future of University Cherish our Capital Dealing with NIMBYs Sponsoring the tube Gender bias calculator MetNetMaker Malaria PhD Symbian Loops Zwack Kegg Project The EU Eduroam & Windows 8 Where is science vital? The Vomcano 10 things London can shove Holbeck Waterwheel

Last modified: 02 August 2013

  My PhD Work 

I started a four year PhD at the White Rose Doctoral Training Centre (Universities of Leeds and Sheffield) in 2007. My work involves modelling the metabolism of the malaria-causing parasite Plasmodium falciparum and growing the parasite on human blood in the laboratory to test the predictions of my model.

If you just want to read my thesis? Download it here

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So far my biggest achievement in my PhD has been writing a piece of software called MetNetMaker to help non-specialists reconstruct metabolic networks. The software has been published in Bioinformatics Journal and is available free of charge. If you go over to www.metnetmaker.com you can download and try the software or just look at some of the tutorial videos that show it in action.

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The computational part of my research relies on a technique called Flux-Balance Analysis (FBA) and when I started my PhD I found it hard to find a good explanations of the technique. In particular I was disappointed by the quality of the wikipedia page on the subject. Over the last three years I have helped, and been enormously helped by, numerous undergraduates and Masters degree students at the University of Leeds  with my project but realised that they were having the same problems understanding Flux-Balance Analysis as I had when I started. In order to try and speed up people's learning I rewrote and greatly expanded the FBA page on Wikipedia. It is my intention to use large parts of the Wikipedia page in the introduction to my thesis. I quietly hope that my thesis examiner will pull me up for not referencing it properly and accuse me of plagiarism.

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Teaching was always something I felt could be improved when I was at University and it has been a really enjoyable and rewarding part of my PhD. I've tried a lot of new things. I think that setting extremely difficult questions to classes but then providing extremely thorough and clear answers is a great way to move beyond rote learning in classes and have received very positive feedback using this technique. I have used the internet in new ways to deliver answers to problems so that discussion can take up much more of the limited contact time teachers have with students in our Higher Education system.

I passionately believe that teaching in Higher Education in the UK is poor in all but a few cases but I'm also sure that we have all the tools we need to change this. I would love the chance to run a small part of the course, and most importantly manage the assessment, so I could try out some of the ideas I have for improving learning in Higher Education

Uuniversity of Leeds logo

I won 2nd prize in the first Annual Postgraduate Researcher Conference at the University of Leeds. You can watch my presentation here.

I passionately believe that teaching in Higher Education in the UK is poor in all but a few cases but I'm also sure that we have all the tools we need to change this. I would love the chance to run a small part of the course, and most importantly manage the assessment, so I could try out some of the ideas I have for improving learning in Higher Education