A Prototype of a Decision Support System for River Basin Water Quality Management in Central and Eastern Europe

This Working Paper documents the implementation of a prototype of a Decision Support System (DSS) for regional water quality management applied to a case study of the Nitra River in Slovakia. With the goals of flexibility and simplicity in mind, two different approaches and tools have been implemented and tested. First, the object-oriented development tool ORVAN was used for fast prototyping of the mathematical programming model and for scenario analysis. Second, a problem-specific generator was implemented to generate various single criterion and multiple criteria optimization problems useful in examining the water quality problem. The resulting mixed-integer optimization problems were solved by the MOMIP package. Provided in the paper are the following: a complete formulation of the mathematical model, a detailed discussion of the data used, documentation of the developed software, an overview of interesting results, and recommendations for future work. Since only preliminary data were available at the time of performing the reported research, results are given merely as illustration of the methodology and software and should not he considered policy recommendations. For the latter task a verified data set and water quality model will be required

SMORE: Synteny Modulator of Repetitive Elements

Several families of multicopy genes, such as transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs), are subject to concerted evolution, an effect that keeps sequences of paralogous genes effectively identical. Under these circumstances, it is impossible to distinguish orthologs from paralogs on the basis of sequence similarity alone. Synteny, the preservation of relative genomic locations, however, also remains informative for the disambiguation of evolutionary relationships in this situation. In this contribution, we describe an automatic pipeline for the evolutionary analysis of such cases that use genome-wide alignments as a starting point to assign orthology relationships determined by synteny. The evolution of tRNAs in primates as well as the history of the Y RNA family in vertebrates and nematodes are used to showcase the method. The pipeline is freely available