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CottonGen: Cotton Database Resources

    CottonGen (https://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data to enable basic, translational and applied research in cotton. Built using the open-source Tripal database infrastructure, CottonGen supersedes CottonDB and the Cotton Marker Database, which includes sequences, genetic and physical maps, genotypic and phenotypic markers and polymorphisms, quantitative trait loci (QTLs), pathogens, germplasm collections and trait evaluations, pedigrees, and relevant bibliographic citations, with enhanced tools for easier data sharing, mining, visualization, and data retrieval of cotton research data.

    LandPKS (Land Potential Knowledge System): Mobile App for Extension, Land-Use and Project Planning, M&E and On-Farm Research

      **LandPKS** comprises a free modular mobile phone app connected to cloud-based storage, global databases, and models, downloadable from Google Play or the iTunes App Store; a system for storing and accessing user data; and a system for sharing data, information and knowledge. LandPKS is being developed to help users determine the sustainable potential of their land, including its restoration potential, based on its unique soil, topography and climate. The land potential assessments will be updated based on new evidence regarding the success or failure of new management and restoration systems on different soils.


        [AgBase](https://agbase.arizona.edu/index.html) Version 2.0 is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products including gene ontology annotations. Its long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase uses controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species.


          GOSSYM is a dynamic, process-level simulation model of cotton growth and yield. GOSSYM essentially is a materials balance model which keeps track of carbon and nitrogen in the plant and water and nitrogen in the soil root zone. GOSSYM predicts the response of the field crop to variations in the environment and to cultural inputs. Specifically, the model responds to weather inputs of daily total solar radiation, maximum and minimum air temperatures, daily total wind run, and rainfall and/or irrigation amount. The model also responds to cultural inputs such as preplant and withinseason applications of nitrogen fertilizer, row spacing and within row plant density as they affect total plant population, and cultivation practices.

          2DSOIL version 03

            2D finite element water, solute, and heat mover model for plant models.

            WinFlume 1.06.0006

              WinFlume is a Windows-based computer program used to design and calibrate long-throated flume and broad-crested weir flow measurement structures. The software was developed through the cooperative efforts of the Bureau of Reclamation, the Agricultural Research Service, and the International Institute for Land Reclamation & Improvement . Primary funding for WinFlume's development has come from the Bureau of Reclamation's Water Conservation-Field Services Program.


                The genosim package simulates genotypes, breeding values, and phenotypes; simulates DNA sequence read depth (numbers of A and B alleles); and resolves SNP conflicts between parent and offspring genotypes.