Fellow profiles

Richard Abel

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Lecturer, Department of Surgery and Cancer, Imperial College London

Interests

Richie is primarily interested in developing 3D imaging techniques, such as CT and MRI for diagnosing metabolic bones disease, as well as monitoring treatment outcomes. 

Research

Many scientists are concerned with characterising both the size and geometry of objects and organisms, particularly the internal structure or composition. For example the internal architecture of bones, thickness and shape of cartilage in human joints, fluid low around blood circulatory systems or porosity of oil-bearing rocks. All of these studies require that object or organism under investigation not be damaged.

Richie is an expert in Micro-Computed Tomographic (CT) scanning. Micro-CT is a non-destructive radiographic imaging technique that produces 3D models of an object or tissue on a computer based on density distribution, as measured by X-ray transmission. The resulting 3D volumes can be used to create ‘virtual’ computerised models of specimens that can be manipulated, sectioned, prepared, dissected and measured as though in the hand, but – unlike handheld specimens - with internal as well as external morphology. This allows access to the morphological information contained inside fragile, rare, valuable or small specimens.

Richie largely applies micro-CT to understand the structure and function of bone, particularly in humans. The research is question driven but entirely dependent on computer software for reconstructing, processing and rendering CT models in three-dimensions. In order to carry out these tasks Richie uses many free software packages written by scientists, such as BoneJ, Quant3D and SPIERS. As well as in software developed in house, such as PhaseQunat and Acrobot Planner. As such Richie is very concerned with the sustainability of the software packages and, more importantly, future software developments for better processing and measuring 3D CT computer models.

Caitlin Bentley

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PhD Candidate, ICT4D Research Centre, Royal Holloway University of London

Interests

International development and development aid and assistance, civil society, organizational learning and knowledge sharing, and open development.

Research

In the past 30 years, Civil Society Organisations (CSOs) have emerged as actors working towards developmental goals, and they tend to be valued as positive contributors. Many donors shifted considerable resources from governments to CSOs during the 1980s, creating new funding opportunities for CSOs. The relationship between donors and CSOs is complex. In particular, donors seek assurance that their contributions are being well invested, and CSOs are under greater pressure to provide evidence for donors. This has given rise to a powerful efficiency movement that has shaped relationships between them. CSOs and donors are significantly affected by the Monitoring and Evaluation (M&E) systems that they have put in place; high levels of written communication are required, and employees engaged in M&E are often separated from field programmes. Such conditions magnify the burden of reporting while minimising opportunities for CSOs and donors to enhance experiential learning.

My research focuses on the ways through which relationships between bilateral donors and CSOs, working in the field of development, are mediated by the technological communicative means at their disposal, and how knowledge is shared across cultural and spatial divides that separate them. The purpose of my research is to examine how Information and Communication Technologies (ICTs) can simplify and extend accountability processes, whilst simultaneously adding knowledge sharing and learning benefits between donors and CSOs. My ultimate aim is to explore how ICT-supported knowledge sharing and learning affects development impact and can potentially support regional and sectoral development learning and decision-making for donors and CSOs. 

Alex Chartier

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PhD Candidate, Invert centre for imaging science, University of Bath

My Interests

My interests are the physics of the Earth's upper atmosphere, especially the ionosphere, data assimilation and forecasting. The fields of tomography, modelling and sustainable software development are key to delivering my research objectives.

My research

My research goal is to produce ionospheric forecasts to mitigate effects on human activities, such as satellite positioning, transpolar aviation and power systems. I am a student at the University of Bath, sponsored by the Met Office and registered with the Systems Centre. My work is funded by the EPSRC.

In my research to date, I have adapted the University of Bath's ionospheric imaging software to accept a new observation type. This greatly improves the vertical resolution of the ionospheric images produced, allowing scientists to study the physical processes in the equatorial ionosphere. I have also adapted the imaging software to include a model state estimate when solving for the 'best guess' of current conditions. This is a necessary step in the production of forecasts.

I have recently begun a collaboration with scientists from the USA, from the Space Weather Prediction Centre (SWPC) and the National Center for Atmospheric Research (NCAR). These organisations share the objectives of the Met Office: to produce forecasts of the upper atmosphere. My collaborators have a generic data assimilation scheme, which produces 'best guesses' of model states with any atmospheric model and observations. Their work in the upper atmosphere is at an early stage, but they have high performance computing facilities and code that will allow me to take my work to the next level. To date, we have incorporated observations from the University of Bath's imaging software into the US assimilation scheme and run experiments with simulated observations at the location of the real observations. Future work will run the scheme with real observations. A simulation study will determine which model fields are most important to the progression of the ionosphere into the future.

Mike Croucher

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Head of Applications Support for the faculty of Engineering and Physical Sciences, University of Manchester

Interests

Science, engineering and mathematical software, high performance computing, programming in many languages. Helping researchers do more with less.

Research

I am part of a team at The University of Manchester that supports the computational research of several thousand academic staff and postgraduate students across the full range of Science, Technology, Engineering and Mathematics subjects. I specialise in optimising code written in languages such as MATLAB, Python and Mathematica, but have also undertaken projects in many other systems and languages such as R, Scilab,C, Fortran and even Visual Basic. Improvements in execution time of up to three orders of magnitude have been achieved although the typical speed-up of a MATLAB project is in the range of 2-5x.

I also provide advice and support for software licensing, application deployment and choice of development environments for both teaching and research.

Additionally, I support many science and engineering applications, along with programming on high performance and high throughput computational systems (i.e. the open source Condor system). I teach introductory MATLAB training courses to University staff and postgraduates, arrange seminars on multiple topics and offer one-to-one programming advice for academic colleagues, including the advantages of open source alternatives to commercial packages when available.

I am also the author of www.walkingrandomly.com, a blog focused on mathematics, mathematical software and programming.

Adam Crymble

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PhD Candidate, Department of History, King's College London

Interests

I am interested in how access to large bodies of historical sources in an electronic format can change the way historians are able to analyse and understand the past. A billion words tell a different story than a thousand. But just how do we distill a billion words into something meaningful?

Research

Digitization initiatives in the humanities have increased the number of textual sources humanists have readily available to unmanageable levels. This new abundance of material means humanists are now faced with the problem of identifying the most relevant materials for their research amidst an ever-growing digital archive; this is a tricky challenge for many scholars. My own research looks at a small corner of this larger problem through a case study: which set of texts in a large collection are about an Irish person? And how can we determine this without reading the whole collection?

Many of us have been trained by search engines to believe that keywords are the best way to find relevant material. In practice, the limits of what historical sources typically contain makes this a real issue. Often a source will contain little more than a person’s name and a few scant details. What seemed like a simple information retrieval challenge, turns out to be much more complex.

My research has been able to solve this challenge by deriving an algorithm that can tell by a person’s name the likelihood of an Irish connection. Coupled with keyword searching and a process known as nominal record linkage, this three-pronged approach has allowed me to efficiently and effectively classify tens of thousands of historical records into piles of relevant or not relevant. For me, this is exciting, as it opens up a future in which academics working with historical sources can ask for relevant records, rather than forcing historians to keyword search an (often arbitrary) set of terms that may or may not have been used by the original authors. I believe this shift can put the historical community more firmly on the path towards reproducible research, and more comprehensive sets of relevant sources with which to work.

James Hetherington

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Research Software Development Team Leader, Research Computing and Facilitating Services, Information Services Division, University College London

Interests

Scientific software development. Software as scientific communication. Computable publication. Test driven design. Correctness and quality in scientific computing. Reproducibility, provenance and audit for research software. Domain specific languages. Programmability. Supercomputing. Refactoring. Science as a service. Deployment, stability and systems programming. Configuration management. Continuous integration. Multiscale modelling. Code sharing and reuse.

Research

I am a research software developer, combining the skills and experience of a computational scientist with those of a professional software engineer. As leader of UCL’s new Research Software Development team, I work with researchers to produce maintainable, usable, well-tested scientific software that will have a lasting impact.

As a scientific software developer at UCL’s Centre for Computational Science, I worked to bring software engineering best practice into biomedical computational research projects, focusing on high-performance interactive, steerable models and simulations with clinical relevance.

As senior scientific innovator at AMEE UK Limited, I developedsystems to make it easier for organisations to understand their environmental impacts, producing web-based models of carbon footprinting. I conceived, prototyped, and led development and release of AMEE Explorer, winner of a Best of What’s New award in Popular Science Magazine in 2010.

As a senior developer in the Model Management group at the MathWorks I worked on model metadata, on searching for, linking and combining models, on managing the differences between similar models and on workflows for modelling in industrial organisations.

At the DTI Beacon project at the UCL Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX) I helped to develop a framework for combining models using different biological assumptions, mathematical formalisms, and computational platforms. We used this to build a multi-scale model of glucose homeostasis.

My doctoral work at Cambridge involved the construction of models of the Large Hadron Collider, determining for various proposed fundamental theories whether they can be tested experimentally. I developed a computational platform automating the solution of a broad class of such problems.

Cefn Hoile

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PhD Candidate, Highwire Doctoral Training Centre, Lancaster University

Interests

Cefn's work focuses on enabling non-programmers to imagine and create behaviours for digital objects. He facilitates physical computing workshops, emphasising open source hardware and software, and engages in bespoke prototyping consultancy for a wide variety of clients. He is currently completing a PhD at the University of Lancaster.

Research

Cefn's PhD has the working title "The Participatory Design of Firmware". It is hosted at the radically post-disciplinary Highwire Doctoral Training Centre in Lancaster University. He proposes a three-year research programme workshopping with domain experts to specify the behaviour of prototype devices which have been created specifically for these experiments. Case study workshops will include inviting paraglider pilots to craft behaviours for a prototype GPS alti-vario flight instrument, and asking piano teachers, players and refuseniks to invent interactive games and exercises to drive a full-color piano key-lighting display.

As part of his exploratory work so far, Cefn has pioneered the adoption of a ultra-low-cost Arduino-compatible clone, freely-documented at http://shrimping.it, recently featured on Hackaday  and the basis for a programme of educational workshops within schools, after school code clubs and hack spaces in the North of England and increasingly all over the world.

To join Highwire, Cefn left his role as Principal Researcher after ten years prototyping technologies for BT's R&D labs, working between the Ipswich research campus and the MIT Media Lab in Boston. As a founder member of Ipswich's lively Curiosity Collective digital arts group, he is fascinated by the potential of a fluid boundary between science, art, technology and design. He now lives and works in the West End of Morecambe, running free technology access workshops and creating unusual interactive artworks and electronics kits in his spare time.

Kayla Iacovino

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PhD Candidate, Department of Geography, University of Cambridge

Interests

Volcanology and experimental petrology, experimentally recreating volcanic systems to understand deep magmatic processes and volcanic plumbing systems, active volcano monitoring

Research

I study volcanoes from the inside out. Using high-pressure and high-temperature instrumentation in the laboratory, my research focuses on understanding the deep volcanic processes that are the origins of the volcanic activity we see on the earth's surface. A better understanding of these dynamic geochemical processes helps us to understand how volcanoes work -- the chemistry of their lavas, the composition of the gasses they release into the atmosphere, the impacts of eruptions on local and global populations, and what makes them erupt in the first place.

By combining lab-constrained geochemical data with in situ measurements of real, active volcanoes, we can better understand the impacts of volcanoes on our world in the past, present, and future. Making the link between surface and subsurface means we can better interpret data from active volcano monitoring in order to understand what our observations tell us about concurrent volcanic activity.

My research takes me to interesting places. So far, for my PhD, I have travelled to Antarctica, Ethiopia, Chile, Costa Rica, France, and Italy in search of volcanoes and academic collaborations. Every step of the way, I require sustainable software to collect, parse, and analyse my data. Especially in the field, where software requirements can be specific, I require that my software is easy to use, compatible across platforms, and lightweight so as not to bog down a small field laptop. Moreover, it needs to be adaptable and versatile. Without the good practices in software development and sustainability advocated by the SSI, working with my data would be a struggle, and many opportunities to adapt and grow our software for new uses would be lost. It is my hope that leading by example and vocalising far and wide the need for sustainable software practices will help them to become mainstream practice in research.

Stephan Lautenschlager

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PhD Candidate, Department of Earth Sciences, University of Bristol

Interests

Functional morphology and biomechanical modelling in extinct and extant vertebrates, visualisation and reconstruction of hard- and soft tissue anatomy in fossil animals

Research

My research focuses on what is now rapidly becoming an individual sub-discipline in earth sciences and palaeontology, known as “virtual palaeontology”. It combines classic palaeontology and latest computational methods and techniques to investigate fossil life.

Using modern computer technology, such as computed tomographic (CT) or synchrotron scanning, 3D visualisation and modelling, as well as finite element analysis (FEA), I investigate the biomechanical function and properties of dinosaurs (and other fossil animals). I am interested in how morphology relates to function and how both factors evolve and change throughout time. My current research centres on the biomechanics and functional morphology of therizinosaurs, an enigmatic clade of theropod dinosaurs, found in Cretaceous deposits in Asia and North America.

My further research interests aim at the reconstruction of hard- and soft tissue structures in fossils, including the visualisation of cranial musculature or the endocranial anatomy (brain and inner ear). Drawing upon my background as a professional software engineer, I explore the application of different software tools, but also comparative anatomy and “traditional” palaeontology to elucidate fossil morphology. As a result, the reconstructed anatomy can reveal a vast amount of information on the biology (sensory and cognitive function, bite forces), behaviour and ecology (dietary strategies, feeding behaviour, predator-prey interaction) of extinct animals.

Nick Pearce

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Teaching Fellow, The Foundation Centre, Durham University

Interests

Social Media, Digital Scholarship, e-learning, Sociology, Critical Theory, Anthropology.

Research

My background is in critically examining the potential for new technologies to transform academic practice. So far this has encompassed the use of such technologies as social media, video conferencing and high performance computing in research, teaching, public engagement and marketing. Over the course of this fellowship I hope to start a dialogue between sociologists and anthropologists and coders/ programmers and promote a deep engagement between the two disparate communities.

There are a number of potential ways of doing this. I will develop a workshop to get social scientists to consider their present use of software, and how learning to code can help enhance their practice through the development of new tools, or the customisation of existing tools. I will also promote the work of the software sustainability institute to new communities of users across the social sciences.

Allen Pope

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PhD Candidate, Scott Polar Research Institute, University of Cambridge

Interests

Glaciology, remote sensing (satellite imagery and altimetry), recent glacier & ice cap change, data integration, polar research, career development, education & outreach, and tweeting @PopePolar

Research Profile

I am interested in understanding changes to glacier surfaces and what that means for their future change and behaviour.

My PhD research takes advantage of the increased spatial and spectral resolution of the Airborne Thematic Mapper (ATM) relative to Landsat ETM+ imagery in order to develop a more effective method for classifying glacier zones. Field research collecting in situ reflectance of various glacial surfaces with a field spectroradiometer in Ny-Ålesund, Svalbard and Langjökull, Iceland is a crucial component. These data serve as a starting point for understanding the best way to work with the remote sensing data. This method can be used to understand changing glacier melt, hydrology, biodiversity, and more.

Ongoing research begun during my MPhil is centred on using photoclinometry to interpolate an incomplete LiDAR survey of Langjökull Icecap, Iceland and using the resulting data set to investigate how the icecap has evolved over the last decade. Findings included a revised mass balance of the icecap, visualization of a recent surge of outlet Hagafellsjökull Eystri, and potential clues as to the future behaviour of the icecap.
In my research, I use a wide range of software tools – both proprietary and open source – to process, analyse, and present data. 

Anna Powell-Smith

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Freelance Software Developer

Interests

I’m interested in using data to tell new kinds of stories. My areas of interest include open data, civic hacking and transparency, online mapping, JavaScript frameworks, NoSQL, data journalism and data visualisation.

You can see examples of my work at http://anna.ps.

Research

I’m a freelance developer, working mostly in JavaScript and Python. In my professional life I work with startups, corporates and non-profits on front- and back-end web development and data visualisation.

I became interested in software for research after creating Open Domesday http://domesdaymap.co.uk, the first free online copy of Domesday Book. I built Open Domesday in my spare time, using data created by the University of Hull - my goal was to create an accessible, attractive, and free version of Domesday Book.

Working with Professor John Palmer, who created the original data, the project has been able to release the dataset and high-quality images of Domesday under a Creative Commons licence, and create an API that is used by the British Museum and others.

I’ve created several other applications using datasets, such as England & Wales Baby Names http://names.darkgreener.com. This is a popular interactive visualisation and search tool for baby names, based on Office of National Statistics data, that was widely covered in the media.

My goal as an SSI Fellow is to help researchers publish and communicate their data to the widest possible audience, create sustainable code, and find the right software tools to support their research.

I have an MA in English from Cambridge and an MPhil in Computer Speech, Text & Internet Technology, also from Cambridge.

Barry Rowlingson

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Research Fellow, Faculty of Health and Medicine, Lancaster University.

Interests

Developing statistical models for spatial epidemiology, with applications in disease modelling in the UK and developing nations. Working with health agencies to add value to data and provide practical solutions.

Research

The occurrence of diseases in a population forms a complex pattern in space and time. Our knowledge of that pattern comes to us in incomplete form, via surveys or reports from health agencies. Statistics is essential to understanding and predicting the patterns of disease incidence.

At Lancaster I work with a small group developing and using statistical methods in spatial, and increasingly spatio-temporal, epidemiology. Current projects include predicting meningitis outbreaks in sub-Saharan Africa, looking at socio-economic factors affecting the 2009 H1N1 (Swine flu) outbreak in the UK, and working on a real-time anomaly detection system based on NHS Direct/111 telephone reporting data.

My role is primarily to implement new methods in software, although I also do full analyses and help design the statistical methods. We use open-source software throughout, mostly coding in R with occasional chunks of C for speed. I've also developed web reporting systems which I code up in Python with Javascript on the client.

Since most of our work is spatial, I do a lot of mapping and GIS work. Producing informative map graphics can be a challenge - I work with open-source mapping systems such as Quantum GIS, and develop plugins
for it. For my web systems I use OpenLayers to deliver easy-to-use maps of things such as predictions and incidence to partner organisations. This way we can produce spatial dashboards of statistical analytics enabling rapid management decisions.

I'm an active member of the UK section of the Open Source Geospatial Foundation, currently planning the FOSS4G 2013 conference in Nottingham.

Melody Sandells

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Research Fellow, Environmental Systems Science Centre, University of Reading 

Interests

Earth observation of snow and soil moisture, snow physics, snow crystal growth, melt and freeze processes, effect of vegetation on snow, soil water flow, microwave remote sensing, microwave emission models, data assimilation, land surface heterogeneity and hydrology.

Research

Snow is an important part of the water cycle, with over 1 billion people dependent on melt for their water supply. However, we know very little about the global distribution of snow, nor whether it has changed over time. Current methods of estimating snow mass from satellite observations use techniques from the late 1980s, have some poor assumptions behind them, and consequently large errors associated with the measurements. My research aims are to develop algorithms to improve global snow mass and soil moisture estimates from satellite data at microwave wavelengths. This should lead to better water management and risk assessment for flooding and drought conditions.

Scattering of electromagnetic radiation is hugely sensitive to the size of the snow crystals, so we need to know this well in order to retrieve snow mass from the satellite data. Near-infrared reflectance, and physically-based models of the snow will give us an idea of how large the snow crystals are, to help with snow mass retrievals. Remote sensing of the soil moisture detects water content of the top few centimetres of soil, so we need to use computer simulations of water movement to relate the surface soil moisture to the water contained deeper in the soil.

We will use data assimilation techniques to blend physically-based models with passive microwave and other satellite data. Once this system has been developed, we can use it to monitor components of the water cycle, as well as apply it to a 30+ year dataset of observations to examine whether the snow mass has changed with the climate.

Robin Wilson

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PhD Candidate, Geography and Environment & Institute for Complex Systems Simulation, University of Southampton

Interests

Extracting quantitative data from satellite images, atmospheric correction of satellite data, open-source software in GIS and Remote Sensing, reproducible research

Research

My research focuses on quantitative remote sensing: that is, extracting quantitative measurements in real-world units from satellite images. I am interested in the whole process, from original data collection, through pre-processing, processing and creation of output maps and visualisations.

I am currently studying for a PhD at the University of Southampton, jointly working within Geography and Environment and the Institute for Complex Systems Simulation, focusing on novel methods for obtaining atmospheric data from satellite images. The aim is to produce data on atmospheric aerosol contents at a far higher spatial resolution than before (around 20-30m rather than 5-10km), which can then be used for a wide range of applications including analysis of urban air pollution and removing the effects of the atmosphere in satellite images.

Much of my previous work has also focused on atmospheric effects in satellite data, including work on Radiative Transfer Modelling of a cloudy atmosphere and on automating the Empirical Line Method of atmospheric correction. As part of my PhD work I have produced a Python interface to the 6S atmospheric Radiative Transfer Model which has been released as open-source software and is seeing wide use within the community.

My work is almost entirely computer-based, and I have written many pieces of code to help me in my research - some of which has been released as open-source code (see www.github.com/robintw).