Fellows 2016

By Terhi Nurmikko-Fuller, Institute Fellow and Postdoctoral Research Associate at the University of Oxford.

The first week in February 2016 was a busy one for me. The previous week had been centred around the inspirational Going Digital with Humanities Research at the University of Manchester. Now it was time to arrange the diary and head off to the Natural History Museum in London for the Software Sustainability Institute's Fellows inaugural meeting. Excellent, I love this venue, I almost - almost - became a paleontologist just because of the sauropod that dominates the main hall.

For the meeting we were tasked with coming along with a short presentation on what we had planned for the Fellowship. I pitched Digital Humanities Oxford Summer School, and in particular the Linked Data for Digital Humanities workshop.

The registration isn’t open yet, but those curious to have a bit of a taster might want to check out last year’s timetable. After my presentation, I received feedback from the other members of institute and the other fellows and it was invaluable. This…

Continue Reading

by Vincent Knight, Institute Fellow and Lecturer in Operational Research, School of Mathematics, Cardiff University

From the 25th till the 29th of January the University of Namibia (UNAM) hosted PyCon Namibia. This brought together more than 100 delegates from a variety of backgrounds and countries: USA, UK, Canada, Holland, Brazil, Zambia, Zimbabwe, Nigeria and of course Namibia were all represented with 63 UNAM students and 30 local DjangoGirls attendees.

 

 

The conference was a great success, whilst it was not just aimed at researchers (many of the attendees were from local industry), it involved academic research based talks on the study of queues, the simulation of quantum systems, game theory and even a lightning talk about the Sustainable Software Institute itself. One talk, given by a recent Namibian graduate described his work understanding the highly congested set of queues that appear during the student registration process. This work involved, Python, Django and the mathematical analysis of queues. For a full description of the event you can read the report at the official conference website.

The local industrial attendees included the Praekelt foundation and…

Continue Reading

A fast speed blog from the Fellows 2016 inaugural meeting produced while discussing 'Which commonly held ideas in research software are impeding progress and need to be retired?'

by Melodee Beals, (Loughborough University), Vincent Knight (Cardiff University), Neil Chue Hong (University of Edinburgh) and Jon Hill (University of York).

In this tweet the idea of sharing code as a sufficient and beneficial practice in reproducible research is exposed: 

“You can download our code from the URL supplied. Good luck downloading the only postdoc who can get it to run, though #overlyhonestmethods”

 

In the past, research methodology (or equivalently code) would be shared in a detailed fashion (by travel from one institution to the other for example or - for the last 350 years at least - in journals or letters). In the modern ‘sharing’ age brought to us by the internet, it is falsely believed that…

Continue Reading

Site Reliability Engineer, Backend Infrastructure, Cisco Meraki

Interests

Configuration management, monitoring, and resource allocation for large scale distributed systems.

Research

My research centers on the effective use of distributed systems to accomplish computational science or engineering related tasks. The majority of my publications have been in two distinct areas: resource allocation and scheduling for virtualised HPC or Cloud systems, and simulation of large scale distributed systems.

In the area of resource allocation and scheduling I have authored a number of papers on Dynamic Fractional Resource Scheduling (DFRS). A key feature of this approach is that it defines and optimizes a user-centric metric of performance and fairness. The methods employed for DFRS can be applied to both service-hosting and parallel computing environments and the problem formulation supports a mix of best-effort and QoS scenarios.

In relation to simulation of large scale and distributed systems I am the originator and a current developer of SMPI, a set of compiler front-ends and compatibility libraries for the on-line simulation of MPI applications. One of the key goals of the SMPI project is that source code should compile and run properly in simulation with no or minimal modification in order to do performance prediction for large-scale computations and explore what-if scenarios. SMPI has been validated via a large set of experiments in which SMPI is compared to popular…

Continue Reading

Lecturer in Digital Humanities, Centre for Digital Humanities Research, Australian National University

Interests

Using Linked (Open) Data and semantic web technologies to support and diversify scholarship in the Digital Humanities. Empowering researchers by demystifying technological practicalities, providing training, and disseminating information about tooling and software. Interdisciplinary research agendas. Ontologies. Background in ancient history and GLAM, lover of games, also keep stumbling into music.

Research

I'm part of the Centre for Digital Humanities Research at Australian National University. I'm the course convenor and lecturer on our Digital Humanities courses, and end up talking about a range of interdisciplinary topics from digital culture to critical evaluation and digital literacy. In my research, I look at using Linked Data and semantic web technologies as a way of answering research questions in the humanities. I enjoy knowledge representation and ontologies in particular. I work on a bunch of different projects, building on my PhD thesis (which looked at ancient Sumerian literature and my postdoc, which I did at Oxford University's e-Research Centre(and where I worked on the Transforming…

Continue Reading

Senior Lecturer in Operational Research, School of Mathematics, Cardiff University

Interests

I am interested in stochastic processes and queueing theory. Some particular interests include applications to real life situations such as healthcare but also the iterated prisoner's dilemma.

Research

I am part of a research group at Cardiff that applies particular mathematical techniques to real world problems (this is called Operational Research). Some examples of the work I have done include modelling game theoretic choice of hospitals by patients and also modelling the queue for ambulance services.

I mainly use Python for my modelling work, taking advantage of the fact that it's an object oriented language, to be able to quickly write agent based models of interaction. I then use these models to:

1. Run "what if" scenarios (for example, helping hospital managers answer questions like: "what would happen if I moved some beds from this ward to that ward?").

2. Validate analytical results for theoretical purposes and/or to run similar "what if" scenarios at a lower computational cost.

Another area of my research revolves around the Iterated Prisoner's Dilemma.

This follows a 1980s computer tournament run by Axelrod. I am one of the core developers of the Axelrod python package which aims to make research in this area easier and importantly reproducible.

Online Presence

Continue Reading

caroline-jay.jpgSenior Lecturer in Computer Science, School of Computer Science, University of Manchester

Interests

My research has two strands: developing novel human-computer interaction techniques using reproducible methods, and studying software engineering, so we can improve the way we do it.

I'm a strong advocate for Research Software Engineering, which (I would argue) will have a greater impact on the resilience, reliability and reproducibility of science than any other single factor - as well as being an important creative research process in its own right.

Research

My research involves investigating how humans perceive and use technology, and applying the results to create new forms of interaction. I am qualified in both Computer Science (MSc, PhD) and Psychology (BA, CPsychol), and work across a number of domains, including healthcare, the Web/IoT and television. A key part of my work is modelling how people interact with technology, particularly in challenging situations, such as 'in the wild' when the user's task is unknown, or more when more than one device is in use. Current projects include CityVerve, the largest IoT demonstrator in the UK, Implicit Device Interaction, looking at how we 'sense' behaviour with the BBC, and Britain Breathing, which is using mobile crowdsourcing to…

Continue Reading

Postdoctoral Research Associate, Love Lab, Department of Experimental Psychology, University College London

Interests

For my postdoctoral work I am investigating the role of labels in categorisation, e.g., does labelling animals as “dogs” help children detect their commonalities? My interests are interdisciplinary, combining psychology, computer science, and neuroscience. I create computational models as a way of evaluating, instantiating, developing, and refining cognitive theories.

Research

Cognitive modelling aims to understand the nature of and relationship between the computational (the what), the algorithmic (the how), and the implementational (the physical substrate) levels. Framing questions about cognition using models leads to theory-testing and predictions/explanations. For these reasons, computational modelling plays a vital role in cognitive science.

My focus is on modelling how infants categorise. Specifically looking at the effect labels (i.e., words to denote category membership, e.g., “dog”) have on babies’ performance. Infants and adults can categorise stimuli often effortlessly using perceptual information and linguistic labels as input. For example, an infant can learn that the label “dog” denotes animals with fur, that bark, fetch sticks, have four legs, etc., by exposure to various types of dog. Thus they generalise “dog” to every animal that is a dog, but not to cats. Babies learn that certain labels apply to certain classes of things but not others.…

Continue Reading

Data Infrastructure and Algorithms Group Leader, Research Faculty, The Genome Analysis Centre

Interests

My main interests are in enterprise-grade software development, data management and associated high-performance computing (HPC) infrastructure, sequence analysis and quality control pipelines, novel visualisation strategies for sequencing and biological data, metadata and the Semantic Web, and the open source for open science ethos. I believe all science outputs should be available for all to use, and there are many ways to make this happen through community, software, policy, and transparency throughout.

Research

The Data Infrastructure and Algorithms group focuses on research into understanding how best to manage, represent and analyse data for open science, as well as exploring new hardware, algorithms and methodologies to develop tools to push the boundaries of data-driven informatics in the life sciences. TGAC is host to one of the largest computational resources dedicated to life science in Europe, and we apply our research expertise around this capability to develop infrastructure platforms for data and software dissemination and publication, assembly algorithms for viral and microbial metagenomics, large-scale data visualisation, and best practice and training in bioinformatics. We have active grants to undertake data federation (Grassroots Genomics, Wheat Information System), data description and citation (Collaborative Open Plant Omics - COPO) and data analysis (iPlant UK, Galaxy), as…

Continue Reading

Professor, Department of Computer Science, University of Bath

Interests

James works in what is now perceived to be the frontier between Mathematics and Computer Science. Special areas include Computer Algebra and Cryptography, but also manages High-Performance Computers

Research

Computer Algebra is the science of getting computers to do mathematical problems. The first applications were in differentiation. My original work was in integration, and in proving that integrals cannot be simplified, and I still work there. I have also done algorithmic and complexity theoretic research in computational geometry. More recently, I have collaborated with Maplesoft and the University of Western Ontario, as well as the Chinese Academy of Sciences in Chongquing and Macquarie University, in computational real algebraic geometry software, some of which has made its way into the commercial Maple product (and was a REF 2014 Impact CaseStudy), other parts are available for download from Bath, and may require downloads from Western Ontario as well. Wrestling with this software complexity, and EPSRC’s requirements for publication of research data, has been an interesting exercise, and I would like to see this process streamlined, and more support given to researchers, and am trying to do that at the University of Bath.

I am also involved in the OpenMath project, producing vendor-…

Continue Reading
Subscribe to Fellows 2016