computer software | Ag Data Commons

CottonGen Sequence Retrieval

Sequence Retrieval allows users to download nucleotide and protein sequences including chromosomes, scaffolds, genes, mRNAs, transcript coding sequences, protein, reftrans contigs and unigene contigs. For the sequences aligned to larger sequences, such as genes, mRNAs and transcript coding sequences, a numeric value specifying the number of upstream bases and downstream bases can be entered.

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CottonGen Primer3

Primer3web version 4.0.0 allows users to pick PCR primers from a DNA sequence.

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CottonGen Map Viewer

MapViewer is a graphical tool for viewing and comparing *Gossypium* spp. genetic maps. It includes dynamically scrollable maps, correspondence matrices, dot plots, links to details about map features, and exporting functionality. It was developed by the MainLab at Washington State University and is available for download for use in other Tripal databases.

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CottonGen JBrowse

CottonGen has an instance of the JBrowse genome browser for viewing genome data. A list of the Whole Genomes and Chloroplast Genomes is available together with a JBrowse tutorial for more details about how to navigate and use JBrowse.

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CottonGen BLAST

CottonGen offers BLAST with genome, transcriptome, peptide and marker sequence databases from *Gossypium* species. This can be done using nucleotide sequences or peptide sequences. BLAST functionality is similar to that on NCBI.

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Java Newhall Simulation Model (jNSM)

The Java Newhall Simulation Model or jNSM is a mesoscale model that is appropriate for use in regional geospatial analyses that support the MLRA update of published digital soil geographic databases (SSURGO/STATSGO2). This software can be used with monthly, serially complete records from weather stations, Soil Climate Analysis Network (SCAN) stations, and local soil climate monitoring sensors.

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CottonGen CottonCyc Pathways Database

The CottonGen CottonCyc Pathways Database supports searching and browsing the CottonCyc databases: * Cyc pathways for JGI v2.0 *G. raimondii* D5 genome assembly * Cyc pathways for CGP-BGI v1.0 *G. hirsutum* AD1 genome assembly

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CottonGen Breeding Information Management System (BIMS)

BIMS, the Breeding Information Management System, is a secure and comprehensive online breeding management system developed for the generic Tripal Database Platform which allows breeders to store, manage, archive and analyze their private breeding program. Breeders can load data in templates provided as well as output from the Field Book App, an android app for collecting phenotype data. In addition to the private breeders BIMS, users without accounts can also view the publicly available breeding data. The fully developed version will allow users to: * Fully integrate their data with publicly available genomic, genetic and breeding data in the community database. * Utilize their integrated pedigree, phenotype and genotype data in performing genomic analysis and making breeding decisions. * Use open-source new genomics tool and breeding decision tools with seamless access to HPC.

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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.

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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.

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