Applying Translational Principles to Data Science Curriculum Development

This paper reports on a curriculum mapping study that examined job descriptions and advertisements for three data curation focused positions: Data Librarian, Data Steward / Curator, and Data Archivist. We present a transferable methodological approach for curriculum development and the findings from our evaluation of employer requirements for these positions. This paper presents " model pathways " for these data curation roles and reflects on opportunities for iSchools to adopt translational data science principles to frame and extend their curriculum to prepare their students for data-driven career opportunities

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes

Searching for SNPs with cloud computing

Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three

Megadepth: efficient coverage quantification for BigWigs and BAMs

Motivation A common way to summarize sequencing datasets is to quantify data lying within genes or other genomic intervals. This can be slow and can require different tools for different input file types. Results Megadepth is a fast tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files, using substantially less memory than the next-fastest competitor. Megadepth can summarize coverage within all disjoint intervals of the Gencode V35 gene annotation for more than 19 000 GTExV8 BigWig files in approximately 1 h using 32 threads. Megadepth is available both as a command-line tool and as an R/Bioconductor package providing much faster quantification compared to the rtracklayer package. Availability and implementation https://github.com/ChristopherWilks/megadepth, https://bioconductor.org/packages/megadepth. Supplementary information Supplementary data are available at Bioinformatics online

An evaluation framework to determine the impact of the Lyme Bay Fisheries and Conservation Reserve and the activities of the Lyme Bay Consultative Committee on ecosystem services and human wellbeing.

This research evaluates the social and economic impact of the management measures that form the Lyme Bay Reserve and the partnership activities of the Lyme Bay Consultative Committee (LBCC) on Lyme Bay resource users. For the purpose of this evaluation it is the combination of the 2008 Statutory Instrument (SI) closure and the more recently designated Site of Community Interest (SCI) that form the boundary of the Lyme Bay Fisheries and Conservation Reserve, termed as the Lyme Bay Reserve. Data is analysed between 2005 and 2015. The results show that the habitats and species of Lyme Bay interact to support the delivery of several ecosystem processes (e.g. primary and secondary production, formation of species habitat) and the realisation of ecosystem services (e.g. fish for food). Overall it is clear that the closure of the area to mobile fishing gear has benefitted static gear fishermen by separating spatial conflict between gear types. The closure has enabled reef habitats to recover which in turn has supported increased catches of some reef associated species e.g. scallops. Further management and support measures agreed through the LBCC have clearly been successful in improving the well-being for those fishermen directly involved in the project. This research represents collaboration between Plymouth University, Exeter University, The Blue Marine Foundation and CEFAS. Input into the evaluation was provided by the Devon and Severn Inshore Fisheries and Conservation Authority (IFCA), the Southern IFCA, local fishermen and fishery representatives

Plant-Derived Polysaccharide Supplements Inhibit Dextran Sulfate Sodium-Induced Colitis in the Rat

Several plant-derived polysaccharides have been shown to have anti-inflammatory activity in animal models. Ambrotose complex and Advanced Ambrotose are dietary supplements that include aloe vera gel, arabinogalactan, fucoidan, and rice starch, all of which have shown such activity. This study was designed to evaluate these formulations against dextran sulfate sodium (DSS)-induced colitis in rats and to confirm their short-term safety after 14 days of daily dosing. Rats were dosed daily orally with vehicle, Ambrotose or Advanced Ambrotose. On day six groups of rats received tap water or 5% Dextran Sulfate sodium. Ambrotose and Advanced Ambrotose significantly lowered the disease scores and partially prevented the shortening of colon length. An increase in monocyte count was induced by dextran sulfate sodium and inhibited by Ambrotose and Advanced Ambrotose. There were no observable adverse effects after 14-day daily doses. The mechanism of action of the formulations against DSS-induced colitis may be related to its effect on monocyte count

Differential expression analysis for sequence count data

*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.

*Results:* We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. 

*Availability:* A free open-source R software package, _DESeq_, is available from the Bioconductor project and from "http://www-huber.embl.de/users/anders/DESeq":http://www-huber.embl.de/users/anders/DESeq

Evaluation of expression and function of the H+/myo-inositol transporter HMIT;

BACKGROUND: The phosphoinositide (PIns) signalling pathway regulates a series of neuronal processes, such as neurotransmitter release, that are thought to be altered in mood disorders. Furthermore, mood-stabilising drugs have been shown to inhibit key enzymes that regulate PIns production and alter neuronal growth cone morphology in an inositol-reversible manner. Here, we describe analyses of expression and function of the recently identified H+/myo-inositol transporter (HMIT) investigated as a potential regulator of PIns signalling. RESULTS: We show that HMIT is primarily a neuronal transporter widely expressed in the rat and human brain, with particularly high levels in the hippocampus and cortex, as shown by immunohistochemistry. The transporter is localised at the Golgi apparatus in primary cultured neurones. No HMIT-mediated electrophysiological responses were detected in rat brain neurones or slices; in addition, inositol transport and homeostasis were unaffected in HMIT targeted null-mutant mice. CONCLUSION: Together, these data do not support a role for HMIT as a neuronal plasma membrane inositol transporter, as previously proposed. However, we observed that HMIT can transport inositol triphosphate, indicating unanticipated intracellular functions for this transporter that may be relevant to mood control

recount3: summaries and queries for large-scale RNA-seq expression and splicing

We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recount3 and snapcount R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features. Monorail can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio