TOLKIN – Tree of Life Knowledge and Information Network: Filling a Gap for Collaborative Research in Biological Systematics

The development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. Although significant progress has been made in recent years on developing new algorithms and tools for analyzing and visualizing large phylogenetic data and trees, implementation of these resources is often carried out by bioinformatics experts, using one-off scripts. Therefore, a gap exists in providing data management support for a large set of non-technical users. The TOLKIN project (Tree of Life Knowledge and Information Network) addresses this need by supporting capabilities to manage, integrate, and provide public access to molecular, morphological, and biocollections data and research outcomes through a collaborative, web application. This data management framework allows aggregation and import of sequences, underlying documentation about their source, including vouchers, tissues, and DNA extraction. It combines features of LIMS and workflow environments by supporting management at the level of individual observations, sequences, and specimens, as well as assembly and versioning of data sets used in phylogenetic inference. As a web application, the system provides multi-user support that obviates current practices of sharing data sets as files or spreadsheets via email

Dynamic model of basic oxygen steelmaking process based on multi-zone reaction kinetics : model derivation and validation

A multi-zone kinetic model coupled with a dynamic slag generation model was developed for the simulation of hot metal and slag composition during the BOF operation. The three reaction zones, (i) jet impact zone (ii) slag-bulk metal zone (iii) slag-metal-gas emulsion zone were considered for the calculation of overall refining kinetics. In the rate equations, the transient rate parameters were mathematically described as a function of process variables. A micro and macroscopic rate calculation methodology (micro-kinetics and macro-kinetics) were developed to estimate the total refining contributed by the recirculating metal droplets through the slag-metal emulsion zone. The micro-kinetics involves developing the rate equation for individual droplets in the emulsion. The mathematical models for the size distribution of initial droplets, kinetics of simultaneous refining of elements, the residence time in the emulsion, dynamic interfacial area change were established in the micro-kinetic model. In the macro-kinetics calculation, a droplet generation model was employed and the total amount of refining by emulsion was calculated by summing the refining from the entire population of returning droplets. A dynamic FetO generation model based on oxygen mass balance was developed and coupled with the multi-zone kinetic model. The effect of post combustion on the evolution of slag and metal composition was investigated. The model was applied to a 200-ton top blowing converter and the simulated value of metal and slag was found to be in good agreement with the measured data. The post-combustion ratio was found to be an important factor in controlling FetO content in the slag and the kinetics of Mn and P in a BOF process

Distribution of soil water and nitrate in furrow irrigation under different plastic mulch placement conditions for a maize crop: Field and modelling study

The use of plastic mulch in furrow irrigation increases irrigation efficiency and improves crop yield. In this study, the effect of the placement of plastic mulch on the furrows and/or on the ridges on reducing water loss and nitrate leaching for furrow-fertigated maize was investigated. Field experiments were carried out including four different treatments which differed according to the placement of plastic mulch on a clay loam soil: plastic mulch on the ridge, plastic mulch on the furrow bed, plastic mulch on the ridge and the furrow bed and control treatment without the mulch. The HYDRUS-2D model was used to simulate water movement and nitrate transfer within the soil. The HYDRUS-2D model was well calibrated and validated using field data. Three irrigation scenarios were also compared including 125, 100 and 75% of the crop water requirement. In the case of using mulch and full irrigation (i.e. 100% crop water requirement), nitrate losses compared to the control treatment with 25% over-irrigation decreased by 52, 44, and 30%, in the the treatments of mulch on the furrow bed, mulch on the ridge and mulch on the ridge and the furrow bed, respectively. Deep percolation of irrigation water also decreased by 53, 48, and 41%, respectively. The use of plastic mulch on the furrow bed with less irrigation depth could be used to prevent water and nitrate losses in furrow irrigation