9 research outputs found
Food-Level Analysis to Identify Dietary Choices With the Highest Nutritional Quality and Lowest Greenhouse Gas Emissions and Price
FUNDING This research was funded by the Scottish Governmentâs Rural and Environment Science and Analytical Services Division (RESAS) and responsive opportunity funding from the Scottish Environment, Food and Agriculture Research Institutes (SEFARI).Peer reviewedPublisher PD
Nutritional Quality, Environmental Impact and Cost of Ultra-Processed Foods : A UK Food-Based Analysis
This research was funded by the Scottish Governmentâs Rural and Environment Science and Analytical Services Division (RESAS) and responsive opportunity funding from the Scottish Environment, Food and Agriculture Research Institutes (SEFARI).Peer reviewedPublisher PD
TetraploidSNPMap: Software for Linkage Analysis and QTL Mapping in Autotetraploid Populations Using SNP Dosage Data
An earlier software application of ours, TetraploidMap for Windows, enabled linkage analysis and quantitative trait locus interval mapping to be carried out in an experimental cross of an autotetraploid species, using both dominant markers such as amplified fragment length polymorphisms and codominant markers such as simple sequence repeats. The size was limited to 800 markers, and quantitative trait locus mapping was conducted for each parent separately due to the difficulties in obtaining a reliable consensus map for the 2 parents. Modern genotyping technologies now give rise to datasets of thousands of single nucleotide polymorphisms, and these can be scored in autotetraploid species as single nucleotide polymorphism dosages, distinguishing among the heterozygotes AAAB, AABB, and ABBB, rather than simply using the presence or absence of an allele. The dosage data is more informative about recombination and leads to higher density linkage maps. The current program, TetraploidSNPMap, makes full use of the dosage data, and has new facilities for displaying the clustering of single nucleotide polymorphisms, rapid ordering of large numbers of single nucleotide polymorphisms using a multidimensional scaling analysis, and phase calling. It also has new routines for quantitative trait locus mapping based on a hidden Markov model, which use the dosage data to model the effects of alleles from both parents simultaneously. A Windows-based interface facilitates data entry and exploration. It is distributed with a detailed user guide. TetraploidSNPMap is freely available from our GitHub repository
FAIR Data Pipeline: provenance-driven data management for traceable scientific workflows
Modern epidemiological analyses to understand and combat the spread of
disease depend critically on access to, and use of, data. Rapidly evolving
data, such as data streams changing during a disease outbreak, are particularly
challenging. Data management is further complicated by data being imprecisely
identified when used. Public trust in policy decisions resulting from such
analyses is easily damaged and is often low, with cynicism arising where claims
of "following the science" are made without accompanying evidence. Tracing the
provenance of such decisions back through open software to primary data would
clarify this evidence, enhancing the transparency of the decision-making
process. Here, we demonstrate a Findable, Accessible, Interoperable and
Reusable (FAIR) data pipeline developed during the COVID-19 pandemic that
allows easy annotation of data as they are consumed by analyses, while tracing
the provenance of scientific outputs back through the analytical source code to
data sources. Such a tool provides a mechanism for the public, and fellow
scientists, to better assess the trust that should be placed in scientific
evidence, while allowing scientists to support policy-makers in openly
justifying their decisions. We believe that tools such as this should be
promoted for use across all areas of policy-facing research
Consumption of foods with the highest nutritional quality, and the lowest GHGE and price, differs between socioeconomic groups in the UK population
Financial support This research was funded by the Scottish Governmentâs Rural and Environment Science and Analytical Services Division (RESAS) and responsive opportunity funding from the Scottish Environment, Food and Agriculture Research Institutes (SEFARI).Peer reviewedPublisher PD