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PECMAN Software

    Peanut Curing Manager (PECMAN) is a decision support system that assists drying facility managers with inventory control. It schedules sampling and removal times, estimates time remaining on dryer and current moisture content. Cooperators have reported reduced drying costs and improved peanut quality.

    CALMIM

      The California Landfill Methane Inventory Model is a 1-dimensional soil gas transport and oxidation model that calculates annual landfill methane emissions based on the cover soil characteristics and annual climatic data for a given global location.

      Geomorphic Road Analysis and Inventory Package (GRAIP)

        Geomorphic Road Analysis and Inventory Package (GRAIP) is designed to help land managers learn about the impacts of road systems on erosion and sediment delivery to streams. GRAIP couples analytical tools with an inventory process to build an approach to roads analysis that can be locally calibrated in a repeatable fashion and with minimal effort. The full scope of GRAIP includes methods to inventory roads and analyze the inventory for surface erosion, gully risk, landslide risk and stream crossing failure risks. Methods to measure road surface erosion from sample sites are also included.

        De novo transcriptome assembly and annotations for wheat curl mite (Aceria tosichella)

          To study the impact of wheat streak mosaic virus on global gene expression in wheat curl mite, we generated a de novo transcriptome assembly using 50 x 50 paired end reads from the Illumina HiSeq 2500. Reads were assembled using Trinity (version 2.0.6) and contigs greater than 200 nt were retained. All assembled transcripts were annotated using the Trinotate pipeline using blastp searches against the Swiss-prot/Uni-Prot database, blastx searches against the Swiss-prot/Uni-Prot databases, HMM searches against the Pfam-A database, blastp searches against the non-redundant protein database, and signalP and tmHMM predictions. To reduce noise from low abundance transcripts not well supported by the data, we filtered the assembly to retain only those transcripts with TPM values >=0.5.

          Annotations of Unigenes Assembled from Schizaphis graminum and Sipha flava

            Transcriptomes were assembled de novo from pools of adult aphids that were feeding on sorghum and switchgrass. Reads from all replicates were pooled, normalized in silico to 25X coverage, and assembled using Trinity. Only the most abundant isoform for each unigene was retained for annotation and unigenes with transcripts per million mapped reads (TPM) less than 0.5 were removed from the dataset. The remaining unigenes were annotated using Trinotate with BLASTP comparisons against the Swiss-Prot/UniProt database. In addition, Pfam-A assignments were computed using hmmer, signal peptide predictions were performed using SignalP, and transmembrane domain predictions were performed using tmHMM. Gene ontology (GO assignments) were retrieved from Trinotate using the highest scoring BLASTp matches as queries.