Digital Twins play a crucial role in bridging the physical and virtual worlds. Given the dynamic and evolving characteristics of the physical world, a huge volume of data transmission and exchange is necessary to attain synchronized updates in the virtual world. In this article, we propose a semantic communication framework based on you only look once (YOLO) to construct a virtual apple orchard with the aim of mitigating the costs associated with data transmission. Specifically, we first employ the YOLOv7-X object detector to extract semantic information from captured images of edge devices, thereby reducing the volume of transmitted data and saving transmission costs. Afterwards, we quantify the importance of each semantic information by the confidence generated through the object detector. Based on this, we propose two resource allocation schemes, i.e., the confidence-based scheme and the acrlong AI-generated scheme, aimed at enhancing the transmission quality of important semantic information. The proposed diffusion model generates an optimal allocation scheme that outperforms both the average allocation scheme and the confidence-based allocation scheme. Moreover, to obtain semantic information more effectively, we enhance the detection capability of the YOLOv7-X object detector by introducing new efficient layer aggregation network-horNet (ELAN-H) and SimAM attention modules, while reducing the model parameters and computational complexity, making it easier to run on edge devices with limited performance. The numerical results indicate that our proposed semantic communication framework and resource allocation schemes significantly reduce transmission costs while enhancing the transmission quality of important information in communication services.

Accurately predicting phenotypes from genotypes holds great promise to improve health management in humans and animals, and breeding efficiency in animals and plants. Although many prediction methods have been developed, the optimal method differs across datasets due to multiple factors, including species, environments, populations and traits of interest. Studies have demonstrated that the number of genes underlying a trait and its heritability are the two key factors that determine which method fits the trait the best. In many cases, however, these two factors are unknown for the traits of interest. We developed a cloud computing platform for Mining the Maximum Accuracy of Predicting phenotypes from genotypes (MMAP) using unsupervised learning on publicly available real data and simulated data. MMAP provides a user interface to upload input data, manage projects and analyses and download the output results. The platform is free for the public to conduct computations for predicting phenotypes and genetic merit using the best prediction method optimized from many available ones, including Ridge Regression, gBLUP, compressed BLUP, Bayesian LASSO, Bayes A, B, Cpi and many more. Users can also use the platform to conduct data analyses with any methods of their choice. It is expected that extensive usage of MMAP would enrich the training data, which in turn results in continual improvement of the identification of the best method for use with particular traits. AVAILABILITY AND IMPLEMENTATION: The MMAP user manual, tutorials and example datasets are available at http://zzlab.net/MMAP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BACKGROUND: Linkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps geneticists identify genes associated with interested inherited traits, such as diseases. There are some tools for linkage disequilibrium analysis either in a local or online way; however, there has been no such tool supporting both graphical user interface (GUI) and parallel computing. RESULTS: We developed a GUI software called LDkit for LD analysis, which supports parallel computing. The LDkit supports both variant call format (VCF) and PLINK 'ped + map' format. At the same time, users could also just analyze a subset of individuals from the whole population. The LDkit reads the data by block and then paralleled the computation process by monitoring the usage of processes. Assessment on the Human 1000 genome data showed that when paralleled with 32 threads, the running time was reduced to less than 6 minutes from ~77 minutes using the chromosome 22 dataset with 1,103,547 SNPs and 2504 individuals. CONCLUSIONS: The software LDkit can be effectively used to calculate and plot LD decay, LD block, and linkage disequilibrium analysis between a site and a given region. Most importantly, both graphical user interface (GUI) and stand-alone packages are available for users' convenience. LDkit was written in JAVA language under cross-platform support.

MOTIVATION: Plenty of Genome-Wide-Association-Study (GWAS) methods have been developed for mapping genetic markers that associated with human diseases and agricultural economic traits. Computer simulation is a nice tool to test the performances of various GWAS methods under certain scenarios. Existing tools are either inefficient in terms of computation and memory efficiency or inconvenient to use to simulate big, realistic genotype data and phenotype data to evaluate available GWAS methods. RESULTS: Here, we present a GWAS simulation tool named G2P that can be used to simulate genotype data, phenotype data and perform power evaluation of GWAS methods. G2P is a user-friendly tool with all functions is provided in both graphical user interface and pipeline manners and it is available for Windows, Mac and Linux environments. Furthermore, G2P achieves maximum efficiency in terms of both memory usage and simulation speed; with G2P, the simulation of genotype data that includes 1 000 000 samples and 2 000 000 markers can be accomplished in 5 h. AVAILABILITY AND IMPLEMENTATION: The G2P software, user manual, and example datasets are freely available at GitHub: https://github.com/XiaoleiLiuBio/G2P. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.