The availability of low-cost small-factor sequencers, such as the Illumina MiSeq, MiniSeq, or iSeq, have paved the way for democratizing genomics sequencing, providing researchers in minority universities with access to the technology that was previously only affordable by institutions with large core facilities. However, these instruments are not bundled with software for performing bioinformatics data analysis, and the data analysis can be the main bottleneck for independent laboratories or even small clinical facilities that consider adopting genomic sequencing for medical applications. To address this issue, we have developed miCloud, a bioinformatics platform that enables genomic data analysis through a fully featured data analysis cloud, which seamlessly integrates with genome sequencers over the local network. The miCloud can be easily deployed without any prior bioinformatics expertise on any computing environment, from a laboratory computer workstation to a university computer cluster. Our platform not only provides access to a set of preconfigured RNA-Seq and CHIP-Seq bioinformatics pipelines, but also enables users to develop or install new preconfigured tools from the large selection available on open-source online Docker container repositories. The miCloud built-in analysis pipelines are also integrated with the Visual Omics Explorer framework (Kim et al., 2016), which provides rich interactive visualizations and publication-ready graphics from the next-generation sequencing data. Ultimately, the miCloud demonstrates a bioinformatics approach that can be adopted in the field for standardizing genomic data analysis, similarly to the way molecular biology sample preparation kits have standardized laboratory operations.
The composition of local mammalian carnivore communities has far-reaching effects on terrestrial ecosystems worldwide. To better understand how carnivore communities are structured, we analysed camera trap data for 108087 trap days across 12 countries spanning five continents. We estimate local probabilities of co-occurrence among 768 species pairs from the order Carnivora and evaluate how shared ecological traits correlate with probabilities of co-occurrence. Within individual study areas, species pairs co-occurred more frequently than expected at random. Co-occurrence probabilities were greatest for species pairs that shared ecological traits including similar body size, temporal activity pattern and diet. However, co-occurrence decreased as compared to other species pairs when the pair included a large-bodied carnivore. Our results suggest that a combination of shared traits and top-down regulation by large carnivores shape local carnivore communities globally. ; Ministry of Environment, Water, Forest and Tourism and Wildlife Conservation Society in Madagascar; Department of National Parks and United States Agency for International Development/Wula Nafaa Project in SenegalUnited States Agency for International Development (USAID); Cederberg Conservancy and Cape-Nature in South Africa; US Forest ServiceUnited States Department of Agriculture (USDA)United States Forest Service; Belize Forest Department; Belize Audubon Society; Programme for Belize; Las Cuevas Research Station; Bull Run Farm; Gallon Jug Estate; Yalbac Ranch and Cattle Company; NSF LTREB Grant [1556248]; Ministry of Ecology and Natural Resources of Misiones; National Park Administration of Argentina; Ledesma S.A.; Arauco SA; Department of National conduct surveys in Chitwan National Park; WWF Networks; US Fish & Wildlife ServiceUS Fish & Wildlife Service; Hurvis Family; WWF Team; Directorate for Nature Management; Norwegian Research CouncilResearch Council of Norway; Department of National conduct surveys in Indonesia ; We thank the Ministry of the Environment, Wildlife and Tourism, the Department of Wildlife and National Parks, and the Botswana Predator Conservation Trust for permission to conduct the study in Botswana; the Ministry of Environment, Water, Forest and Tourism and Wildlife Conservation Society in Madagascar; the Department of National Parks and United States Agency for International Development/Wula Nafaa Project in Senegal; and The Cederberg Conservancy and Cape-Nature in South Africa for permission and/or supporting the research in Africa. We thank Parks Canada staff and volunteers for collecting data in Canada, the US Forest Service for financing and collecting data in the USA along with volunteers from the Student Conservation Association, and the Belize Forest Department, Belize Audubon Society, Programme for Belize, Las Cuevas Research Station, Bull Run Farm, Gallon Jug Estate, and Yalbac Ranch and Cattle Company for permission and support in conducting research in Belize. Funding for camera trap surveys in Canada was provided in part by NSF LTREB Grant 1556248. We thank the Ministry of Ecology and Natural Resources of Misiones, the National Park Administration of Argentina, Ledesma S.A. and Arauco SA for permissions and support to conduct camera trap surveys. We thank the Iran Department of Environment for permission to work within the reserves in Iran, Department of National conduct surveys in Chitwan National Park, and in Indonesia, WWF Networks, US Fish & Wildlife Service and the Hurvis Family for financially supporting the research, the Indonesian Ministry of Forestry for permission to conduct the study, and the WWF Team for their support. We also thank the Directorate for Nature Management and The Norwegian Research Council for financing camera trap surveys in Norway. ; Public domain authored by a U.S. government employee
Aim: Biodiversity loss is a major driver of ecosystem change, yet the ecological data required to detect and mitigate losses are often lacking. Recently, camera trap surveys have been suggested as a method for sampling local wildlife communities, because these observations can be collated into a global monitoring network. To demonstrate the potential of camera traps for global monitoring, we assembled data from multiple local camera trap surveys to evaluate the interchange between fine- and broad-scale processes impacting mammalian carnivore communities. Location: Argentina, Belize, Botswana, Canada, Indonesia, Iran, Madagascar, Nepal, Norway, Senegal, South Africa, and the U.S.A. Methods: We gathered camera trap data, totalling >100,000 trap nights, from across five continents. To analyse local and species-specific responses to anthropogenic and environmental variables, we fitted multispecies occurrence models to each study area. To analyse global-level responses, we then fitted a multispecies, multi-area occurrence model. Results: We recorded 4,805 detections of 96 mammalian carnivore species photographed across 1,714 camera stations located in 12 countries. At the global level, our models revealed that carnivore richness and occupancy within study areas was positively associated with prey availability. Occupancy within study areas also tended to increase with greater protection and greater distances to roads. The strength of these relationships, however, differed among countries. Main conclusions: We developed a research framework for leveraging global camera trap data to evaluate patterns of mammalian carnivore occurrence and richness across multiple spatial scales. Our research highlights the importance of intact prey populations and protected areas in conserving carnivore communities. Our research also highlights the potential of camera traps for monitoring wildlife communities and provides a case study for how this can be achieved on a global scale. We encourage greater integration and standardization among camera trap studies worldwide, which would help inform effective conservation planning for wildlife populations both locally and globally. ; Ministry of the Environment, Wildlife and Tourism; Department of Wildlife and National Parks; Botswana Predator Conservation Trust in Botswana; Ministry of Environment, Water, Forest and Tourism; Wildlife Conservation Society in Madagascar; Department of National Parks; United States Agency for International Development/Wula Nafaa Project in SenegalUnited States Agency for International Development (USAID); Cederberg Conservancy and CapeNature in South Africa; National Science FoundationNational Science Foundation (NSF) [1556248]; Pacific Southwest Region of the U.S. Forest Service; Sierra and Sequoia National Forests; Ministry of Ecology and Natural Resources of Misiones; National Parks Administration of Argentina; Fundacion Proyungas; Ledesma S.A.; ARAUCO Argentina S.A.; World Wildlife Fund Networks, U.S. Fish & Wildlife Service and the Hurvis Family; World Wildlife Fund Team; Directorate for Nature Management; Norwegian Research CouncilResearch Council of Norway ; We thank the Ministry of the Environment, Wildlife and Tourism, the Department of Wildlife and National Parks and the Botswana Predator Conservation Trust in Botswana; the Ministry of Environment, Water, Forest and Tourism and Wildlife Conservation Society in Madagascar; the Department of National Parks and United States Agency for International Development/Wula Nafaa Project in Senegal; and The Cederberg Conservancy and CapeNature in South Africa for permission and/or supporting the research in Africa. In North America, we thank Parks Canada staff for collecting data in Canada and the National Science Foundation for funding part of this project (Long Term Research In Environmental Biology Grant 1556248); the Pacific Southwest Region of the U.S. Forest Service and the Sierra and Sequoia National Forests for supporting research in the U.S. A.; and in Belize, we thank the Forest Department, Programme for Belize, Las Cuevas Research Station, Bull Run Farm, Belize Audubon Society, Wildtracks, Gallon Jug Estate and Yalbac Ranch. In South America, we thank the Ministry of Ecology and Natural Resources of Misiones, the National Parks Administration of Argentina, Fundacion Proyungas, Ledesma S.A. and ARAUCO Argentina S.A. for permissions and support to conduct camera trap surveys. In Asia, we thank the Iran Department of Environment for permission to work within the reserves in Iran, the World Wildlife Fund, the National Trust for Nature Conservation, Chitwan National Park and Department of National Parks and Wildlife Conservation for permission and support to survey in Nepal; and in Indonesia, World Wildlife Fund Networks, U.S. Fish & Wildlife Service and the Hurvis Family for financially supporting the research, the Indonesian Ministry of Forestry for permission to conduct the study, and the World Wildlife Fund Team for all their support. Lastly, in Europe we thank the Directorate for Nature Management and The Norwegian Research Council for financing the camera trap data collected in Norway. Thank you to H. S. Robinson for help during the planning stages of the manuscript. ; Public domain authored by a U.S. government employee
