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GenSAS v5.1: A Web-Based Platform for Structural and Functional Annotation and Curation of Genomes

    The Genome Sequence Annotation Server (GenSAS) is an online platform that provides a pipeline for whole genome structural and functional annotation. Users can upload genome sequences and select from a variety of tools for repeat masking, prediction of gene models and other structural features as well as functional annotation tools. GenSAS integrates with JBrowse and Apollo to provide visualization and editing.

    Data from: Life history changes in Trogoderma variabile and T. inclusum due to mating delay with implications for mating disruption as a management tactic

      Egg and progeny counts for Trogoderma variabile and Trogoderma inclusum adults with delays in mating. These data were generated to examine the effect of mating delay on life history and reproductive capacity as a cue to the use of mating disruption tactics such as pheromone lures. Survivorship was calculated as the last day egg counts were recorded for an individual. Blocks were adults that were all mated on the same day. Reps are an individual female. Control beetles are coded with either an "f" or an "m" for female and male and were never mated. Male control data was examined for similarity to female control data but was not used in further analysis and comparison. The experiment was all done at 30C, 65% relative humidity and a 16 light/8 dark photoperiod. Adults were transferred every 2 days to new vials and eggs were then counted and save for progeny counts. Trogoderma variabile populations were laboratory colonies for over 20 years. T. inclusum populations were collected in Kansas in August of 2012. We did not transform these data.

      Integrated Farm System Model (IFSM)

        The Integrated Farm System Model (IFSM) is a process-based simulation of dairy, beef, and crop farming systems. This whole farm model provides a tool for evaluating the long term performance, economics, and environmental impacts of production systems over many years of weather.

        Dairy Gas Emissions Model (DairyGEM)

          The Dairy Gas Emissions Model (DairyGEM) uses process level simulation and process related emission factors to predict ammonia, hydrogen sulfide, VOC and greenhouse gas emissions along with the carbon, energy and water footprints of dairy production systems.

          APEX – Agricultural Policy/Environmental eXtender Model

            Agricultural Policy/Environmental eXtender (APEX) has components for routing water, sediment, nutrients, and pesticides across complex landscapes and channel systems to the watershed outlet as well as groundwater and reservoir components. A watershed can be subdivided as much as necessary to assure that each subarea is relatively homogeneous in terms of soil, land use, management, and weather. APEX was constructed to evaluate various land management strategies considering sustainability, erosion (wind, sheet, and channel), economics, water supply and quality, soil quality, plant competition, weather, and pests. The routing of water, sediment, nutrient, and pesticide capabilities are some of the most comprehensive available in current landscape-scale models and can be simulated between subareas and channel systems within the model. APEX can perform long-term continuous simulations for modeling the impacts of different nutrient management practices, tillage operations, conservation practices, alternative cropping systems, and other management practices on surface runoff and losses of sediment, nutrients, and other pollutant indicators.

            Environmental Policy Integrated Climate (EPIC) Model

              Environmental Policy Integrated Climate (EPIC) model is a cropping systems model that was developed to estimate soil productivity as affected by erosion. EPIC simulates approximately eighty crops with one crop growth model using unique parameter values for each crop. It can be configured for a wide range of crop rotations and other vegetative systems, tillage systems, and other management strategies. It predicts effects of management decisions on soil, water, nutrient and pesticide movements, and their combined impact on soil loss, water quality, and crop yields for areas with homogeneous soils and management.

              iSnobal

                iSnobal is a physically-based distributed snowmelt model. A coupled energy and mass-balance model iSnobal is used to simulate the development and melting of the seasonal snowcover.

                Water Erosion Prediction Project (WEPP)

                  The Water Erosion Prediction Project (WEPP) model is a process-based, distributed parameter, continuous simulation, erosion prediction model for use on personal computers running Windows 95/98/NT/2000/XP/Vista/Windows7. The current model version (v2012.8) available for download is applicable to hillslope erosion processes (sheet and rill erosion), as well as simulation of the hydrologic and erosion processes on small watersheds. Included in the download package is the WEPP model (version 2012.8), WEPP Windows interface (August 2012), CLIGEN climate generators (versions 4.3 and 5.3), documentation and example data.

                  Gramene

                    Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species.