Data Provisioning for the Object Modeling System (OMS)

The Object Modelling System (OMS) platform supports initiatives to build or re - factor agro - environmental models and deploy them in different business contexts as model services on cloud computing platforms. Whether traditional desktop, client - server, or emerging cloud deployments, success especially at the enterprise level relies on stable and efficient data provisioning to the models. In this paper we describe recent experience and trends with tools and services to supply data for model inputs. Solutions range from simple pre - processing tools to data services deployed to cloud platforms. Also, systematic, sustained data stewardship and alignment with standards organizations impart stability to data provisioning efforts

An Exploratory Investigation on the Invasiveness of Environmental Modeling Frameworks

Environmental modeling frameworks provide an array of useful features that model developers can harness when implementing models. Each framework differs in how it provides features to a model developer via its Application Programming Interface (API). Environmental modelers harness framework features by calling and interfacing with the framework API. As modelers write model code, they make framework-specific function calls and use framework specific data types for achieving the functionality of the model. As a result of this development approach, model code becomes coupled with and dependent on a specific modeling framework. Coupling to a specific framework makes migration to other frameworks and reuse of the code outside the original framework more difficult. This complicates collaboration between model developers wishing to share model code that ma y have been developed in a variety of languages and frameworks. This paper provides initial results of an exploratory investigation on the invasiveness of environmental modeling frameworks. Invasiveness is defined as th e coupling between application (i.e., model) and framework code used to implement the model. By comparing the implementation of an environmental model across several modeling frameworks, we aim to better understand the consequences of framework design. How frameworks present functionality to modelers through APIs can lead to consequences with respect to model development, model maintenance, reuse of model code, and ultimately collaboration among model developers. By measuring framework invasiveness, we hope to provide environmental modeling framework developers and environmental modelers with valuable in formation to assist in future development efforts. Eight implementations (six framework-based) of Thornthwaite, a simple water balance model, were made in a variety of environmental modeling frameworks and languages. A set of software metrics were proposed and applied to measure invasiveness between model implementation code and framework code. The metrics produced a rank ordering of invasiveness for the framework-based implementations of Thornthwaite. We compared model invasiveness results with several popular software metrics including size in lines of code (LOC), cyclomatic complexity, and object oriented coupling. To investigate software quality implications of framework invasiveness we checked for relationships between the Chidamber and Kemerer (1994) object oriented software metrics and our framework invasiveness measures. For the six framework-based implementations of Thornthwaite we found a five-fold variation in code size (LOC). We observed up to a seven-fold variation in total cyclomatic complexity, and a two to three-fold variation in object oriented coupling. For the model implementations we found that total size, total complexity, and total coupling all had a significant positive correlation. The raw count version of our invasiveness measures correlated with application size (LOC), total cyclomatic complexity, total efferent coupling (fan out) and total afferent coupling (fan in). Large size, complexity, and high levels of coupling between units (classes, modules) in a software system are often cited in software engineering as causes of high maintenance costs due to poor understandability and flexibility of the code. This study provides initial results but further investigation is desired to evaluate the utility of our invasiveness measurement approach as well as the software quality implications of framework invasiveness

Environmental Modeling Framework Invasiveness: Analysis and Implications

Environmental modeling frameworks support scientific model development by providing an Application Programming Interface (API) which model developers use to implement models. This paper presents results of an investigation on the framework invasiveness of environmental modeling frameworks. Invasiveness is defined as the quantity of dependencies between model code and the modeling framework. This research investigates relationships between invasiveness and the quality of modeling code. Additionally, we investigate the relationship between invasiveness and two common framework designs (lightweight vs. heavyweight). Five metrics to measure framework invasiveness were proposed and applied to measure invasiveness between model and framework code of several implementations of Thornthwaite and the Precipitation-Runoff Modeling System (PRMS), two hydrological models. Framework invasiveness measurements were compared with existing software metrics including size (lines of code), cyclomatic complexity, and object-oriented coupling with generally positive correlations being found. We found that models with lower framework invasiveness tended to be smaller, less complex, and have lower coupling. In addition, the lightweight framework implementations of the Thornthwaite and PRMS models were less invasive than the heavyweight framework model implementations. Our initial results suggest that framework invasiveness is undesirable for model code quality and that lightweight frameworks may help reduce invasiveness

Melanesian mtDNA Complexity

Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups). Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at ∼30–50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval ∼3,500–8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal) Austronesian influence in this region remains unresolved

Genomic analyses inform on migration events during the peopling of Eurasia.

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.Support was provided by: Estonian Research Infrastructure Roadmap grant no 3.2.0304.11-0312; Australian Research Council Discovery grants (DP110102635 and DP140101405) (D.M.L., M.W. and E.W.); Danish National Research Foundation; the Lundbeck Foundation and KU2016 (E.W.); ERC Starting Investigator grant (FP7 - 261213) (T.K.); Estonian Research Council grant PUT766 (G.C. and M.K.); EU European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre (R.V.; M.Me. and A.Me.), and Centre of Excellence for Genomics and Translational Medicine Project No. 2014-2020.4.01.15-0012 to EGC of UT (A.Me.) and EBC (M.Me.); Estonian Institutional Research grant IUT24-1 (L.S., M.J., A.K., B.Y., K.T., C.B.M., Le.S., H.Sa., S.L., D.M.B., E.M., R.V., G.H., M.K., G.C., T.K. and M.Me.) and IUT20-60 (A.Me.); French Ministry of Foreign and European Affairs and French ANR grant number ANR-14-CE31-0013-01 (F.-X.R.); Gates Cambridge Trust Funding (E.J.); ICG SB RAS (No. VI.58.1.1) (D.V.L.); Leverhulme Programme grant no. RP2011-R-045 (A.B.M., P.G. and M.G.T.); Ministry of Education and Science of Russia; Project 6.656.2014/K (S.A.F.); NEFREX grant funded by the European Union (People Marie Curie Actions; International Research Staff Exchange Scheme; call FP7-PEOPLE-2012-IRSES-number 318979) (M.Me., G.H. and M.K.); NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01 (S.Tis.); Russian Foundation for Basic Research (grant N 14-06-00180a) (M.G.); Russian Foundation for Basic Research; grant 16-04-00890 (O.B. and E.B); Russian Science Foundation grant 14-14-00827 (O.B.); The Russian Foundation for Basic Research (14-04-00725-a), The Russian Humanitarian Scientific Foundation (13-11-02014) and the Program of the Basic Research of the RAS Presidium “Biological diversity” (E.K.K.); Wellcome Trust and Royal Society grant WT104125AIA & the Bristol Advanced Computing Research Centre (http://www.bris.ac.uk/acrc/) (D.J.L.); Wellcome Trust grant 098051 (Q.A.; C.T.-S. and Y.X.); Wellcome Trust Senior Research Fellowship grant 100719/Z/12/Z (M.G.T.); Young Explorers Grant from the National Geographic Society (8900-11) (C.A.E.); ERC Consolidator Grant 647787 ‘LocalAdaptatio’ (A.Ma.); Program of the RAS Presidium “Basic research for the development of the Russian Arctic” (B.M.); Russian Foundation for Basic Research grant 16-06-00303 (E.B.); a Rutherford Fellowship (RDF-10-MAU-001) from the Royal Society of New Zealand (M.P.C.)

Data associated with “Little South Poudre Watershed Climate and Hydrology 1961-1971”

This dataset contains temperature, precipitation, stream discharge, and snow course data as reported in Meiman and Leavesley (1974). Data were entered into Excel spreadsheets, formatted to reflect the tables in the report. Data were also reformatted and saved as .csv files to facilitate machine readability and long-term accessibility. The stream discharge data contains data from 1961 to 1971. The streams measured were Fish Creek and Upper and Lower Hourglass. Other gauges in the Little South Fork of the Cache la Poudre Watershed can be found through the USGS (https://waterdata.usgs.gov/nwis). The snow course data is from 1938 to 1971 depending on location. Locations included are the Hourglass Lake Snow Course (NRCS Station: 05J11), Bennett Creek Snow Course (NRCS Station: 05J33), Pingree Park Snow Course, and Sheep Saddle Snow Course. The snow courses with NRCS station numbers can be found through the NRCS site (https://www.nrcs.usda.gov/wps/portal/nrcs/detail/national/water/snowsurvey)

QUT seeks to heal wounds without scars

Treatment of wounds represents a significant challenge at all levels of our society, in terms of cost (physical, emotional and financial) to patients, the economy and to the wider Australian and global communities. Despite this, relatively little research is directed at this hidden health problem. The Tissue Repair & Regeneration team at QUT is addressing this challenge using advanced biotechnological, biomaterials and bioengineering strategies. Our interdisciplinary team is focussed on delivering practical innovations in wound healing, with an emphasis on diabetic and venous ulcers, as well as burns. This 'snapshot' of our research briefly describes some of the research projects we are pursuing at QUT: interactions of growth factors with other components of the extracellular milieu in tissues; cellular mechanisms associated with wound healing and scar remediation; diagnostic and prognostic markers of healing; novel, relevant, ex vivo 3D skin equivalent models for pre-clinical evaluation of new wound therapeutics; and the design and production of "smart" bioactive wound dressings. The overall goal of our research is to generate new technologies and wound management interventions that keep patients healthy and obviate their need to depend upon the cost-intensive hospital-based health care sector