Compositional Data in Biomedical Research

Modern methods of compositional data analysis are not well known in biomedical research. Moreover, there appear to be few mathematical and statistical researchers working on compositional biomedical problems. Like the earth and environmental sciences, biomedicine has many problems in which the relevant scienti c information is encoded in the relative abundance of key species or categories. I introduce three problems in cancer research in which analysis of compositions plays an important role. The problems involve 1) the classi cation of serum proteomic pro les for early detection of lung cancer, 2) inference of the relative amounts of di erent tissue types in a diagnostic tumor biopsy, and 3) the subcellular localization of the BRCA1 protein, and it's role in breast cancer patient prognosis. For each of these problems I outline a partial solution. However, none of these problems is \solved". I attempt to identify areas in which additional statistical development is needed with the hope of encouraging more compositional data analysts to become involved in biomedical research

e-Research Methods Theme 6 Collecting Data

In this theme you will work through a series of texts and activities designed to help you think carefully about your approach to collecting the data for your research project.

e-Research Methods Theme 7 Data Analysis

In this theme you will work through a series of texts and activities and reflect on your view of research and the process of analysis of data and information. Most activities are supported by textual or audio material and are there to stimulate your thinking in a given area. The purpose of this theme is to help you gain a general overview of the main approaches to research design. Although the theme comprises two main sections, one on quantitative research and the other on qualitative research, this is purely to guide your study. The two approaches may be viewed as being part of a continuum with many research studies now incorporating elements of both styles. Eventually you will need to choose a research approach or methodology that will be practical, relevant, appropriate, ethical, of good quality and effective for the research idea or question that you have in mind.

e-Research Methods Theme 6 Collecting Data ZIP

Source files for theme 6

e-Research Methods Theme 7 Data Analysis ZIP

Source files for theme 7

WAIS Seminar: Research Discussion: Open Data at the Hampshire Hub

This is a research discussion about the Hampshire Hub - see http://protohub.net/. The aim is to find out more about the project, and discuss future collaboration and sharing of ideas. Mark Braggins (Hampshire Hub Partnership) will introduce the Hampshire Hub programme, setting out its main objectives, work done to-date, next steps including the Hampshire data store (which will use the PublishMyData linked data platform), and opportunities for University of Southampton to engage with the programme , including the forthcoming Hampshire Hackathons Bill Roberts (Swirrl) will give an overview of the PublishMyData platform, and how it will help deliver the objectives of the Hampshire Hub. He will detail some of the new functionality being added to the platform Steve Peters (DCLG Open Data Communities) will focus on developing a web of data that blends and combines local and national data sources around localities, and common topics/themes. This will include observations on the potential employing emerging new, big data sources to help deliver more effective, better targeted public services. Steve will illustrate this with practical examples of DCLG’s work to publish its own data in a SPARQL end-point, so that it can be used over the web alongside related 3rd party sources. He will share examples of some of the practical challenges, particularly around querying and re-using geographic LinkedData in a federated world of SPARQL end-point.

Programmable data acquisition system for research measurements from meteorological radiosondes

A programmable data acquisition system to allow novel use of meteorological radiosondes for atmospheric science measurements is described. In its basic form it supports four analogue inputs at 16 bit resolution, and up to two further inputs at lower resolution configurable instead for digital instruments. It also provides multiple instrument power supplies (+8V, +16V, +5V and -8V) from the 9V radiosonde battery. During a balloon flight encountering air temperatures from +17°C to -66°C, the worst case voltage drift in the 5V unipolar digitisation circuitry was 20mV. The system liberates a new range of low cost atmospheric research measurements, by utilising radiosondes routinely launched internationally for weather forecasting purposes. No additional receiving equipment is required. Comparisons between the specially instrumented and standard meteorological radiosondes show negligible effect of the additional instrumentation on the standard meteorological data.

Opening up climate research: A linked data approach to publishing data provenance

Traditionally, the formal scientific output in most fields of natural science has been limited to peer- reviewed academic journal publications, with less attention paid to the chain of intermediate data results and their associated metadata, including provenance. In effect, this has constrained the representation and verification of the data provenance to the confines of the related publications. Detailed knowledge of a dataset’s provenance is essential to establish the pedigree of the data for its effective re-use, and to avoid redundant re-enactment of the experiment or computation involved. It is increasingly important for open-access data to determine their authenticity and quality, especially considering the growing volumes of datasets appearing in the public domain. To address these issues, we present an approach that combines the Digital Object Identifier (DOI) – a widely adopted citation technique – with existing, widely adopted climate science data standards to formally publish detailed provenance of a climate research dataset as an associated scientific workflow. This is integrated with linked-data compliant data re-use standards (e.g. OAI-ORE) to enable a seamless link between a publication and the complete trail of lineage of the corresponding dataset, including the dataset itself.

Market research and the ethics of big data

The term 'big data' has recently emerged to describe a range of technological and commercial trends enabling the storage and analysis of huge amounts of customer data, such as that generated by social networks and mobile devices. Much of the commercial promise of big data is in the ability to generate valuable insights from collecting new types and volumes of data in ways that were not previously economically viable. At the same time a number of questions have been raised about the implications for individual privacy. This paper explores key perspectives underlying the emergence of big data, and considers both the opportunities and ethical challenges raised for market research.

Preliminary ethnoarchaeological research on modern animal husbandry in Bestansur, Iraqi Kurdistan: integrating animal, plant and environmental data

This paper presents preliminary results from an ethnoarchaeological study of animal husbandry in the modern village of Bestansur, situated in the lower Zagros Mountains of Iraqi Kurdistan. This research explores how modern families use and manage their livestock within the local landscape and identifies traces of this use. The aim is to provide the groundwork for future archaeological investigations focusing on the nearby Neolithic site of Bestansur. This is based on the premise that modern behaviours can suggest testable patterns for past practices within the same functional and ecological domains. Semi-structured interviews conducted with villagers from several households provided large amounts of information on modern behaviours that helped direct data collection, and which also illustrate notable shifts in practices and use of the local landscape over time. Strontium isotope analysis of modern plant material demonstrates that a measurable variation exists between the alluvial floodplain and the lower foothills, while analysis of modern dung samples shows clear variation between sheep/goat and cow dung, in terms of numbers of faecal spherulites. These results are specific to the local environment of Bestansur and can be used for evaluating and contextualising archaeological evidence as well as providing modern reference material for comparative purposes.