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1. FlyBase: a guided tour of highlighted features

   https://doi.org/10.1093/genetics/iyac035  

   Gramates, L. Sian; Agapite, Julie; Attrill, Helen; Calvi, Brian R.; Crosby, Madeline A.; dos Santos, Gilberto; Goodman, Joshua L.; Goutte-Gattat, Damien; Jenkins, Victoria K.; Kaufman, Thomas; et al (March 2022, Genetics)

   Abstract FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster. As FlyBase enters our fourth decade of service to the research community, we reflect on our unique aspects and look forward to our continued collaboration with the larger research and model organism communities. In this study, we emphasize the dedicated reports and tools we have constructed to meet the specialized needs of fly researchers but also to facilitate use by other research communities. We also highlight ways that we support the fly community, including an external resources page, help resources, and multiple avenues by which researchers can interact with FlyBase. 

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2. Exploring FlyBase Data Using QuickSearch

   https://doi.org/10.1002/cpz1.731  

   Marygold, Steven J.; the FlyBase Consortium (April 2023, Current Protocols)

   Abstract FlyBase (www.flybase.org) is the primary online database of genetic, genomic, and functional information aboutDrosophila melanogaster. The long and rich history ofDrosophilaresearch, combined with recent surges in genomic‐scale and high‐throughput technologies, means that FlyBase now houses a huge quantity of data. Researchers need to be able to query these data rapidly and intuitively, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This article describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Using the “Search FlyBase” tab of QuickSearch Basic Protocol 2: Using the “Data Class” tab of QuickSearch Basic Protocol 3: Using the “References” tab of QuickSearch Basic Protocol 4: Using the “Gene Groups” tab of QuickSearch Basic Protocol 5: Using the “Pathways” tab of QuickSearch Basic Protocol 6: Using the “GO” tab of QuickSearch Basic Protocol 7: Using the “Protein Domains” tab of QuickSearch Basic Protocol 8: Using the “Expression” tab of QuickSearch Basic Protocol 9: Using the “GAL4 etc” tab of QuickSearch Basic Protocol 10: Using the “Phenotype” tab of QuickSearch Basic Protocol 11: Using the “Human Disease” tab of QuickSearch Basic Protocol 12: Using the “Homologs” tab of QuickSearch Support Protocol 1: Managing FlyBase hit lists 

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3. Points to Consider When Establishing and Rearing Culex Mosquitoes in the Laboratory

   https://doi.org/10.1101/pdb.top107823  

   Meuti, Megan E; Siperstein, Alden; Wolkoff, Matthew (August 2023, Cold Spring Harbor Protocols)

   Culexmosquitoes transmit several pathogens to humans and animals, including viruses that cause West Nile fever and St. Louis encephalitis and filarial nematodes that cause canine heartworm and elephantiasis. Additionally, these mosquitoes have a cosmopolitan distribution and provide interesting models for understanding population genetics, overwintering dormancy, disease transmission, and other important and ecological questions. However, unlikeAedesmosquitoes that produce eggs that can be stored for weeks at a time, no obvious “stopping” point exists in the development ofCulexmosquitoes. Therefore, these mosquitoes require nearly continuous care and attention. Here, we describe some general considerations when rearing laboratory colonies ofCulexmosquitoes. We highlight different methods so that readers may choose what works best for their experimental needs and laboratory infrastructure. We hope that this information will enable additional scientists to conduct laboratory research on these important disease vectors. 

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4. Harmonizing model organism data in the Alliance of Genome Resources

   https://doi.org/10.1093/genetics/iyac022  

   Agapite, Julie; Albou, Laurent-Philippe; Aleksander, Suzanne A; Alexander, Micheal; Anagnostopoulos, Anna V; Antonazzo, Giulia; Argasinska, Joanna; Arnaboldi, Valerio; Attrill, Helen; Becerra, Andrés; et al (February 2022, Genetics)

   Wood, V (Ed.)

   Abstract The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides. 

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5. All-hazards dataset mined from the US National Incident Management System 1999–2020

   https://doi.org/10.1038/s41597-023-01955-0  

   St. Denis, Lise A.; Short, Karen C.; McConnell, Kathryn; Cook, Maxwell C.; Mietkiewicz, Nathan P.; Buckland, Mollie; Balch, Jennifer K. (December 2023, Scientific Data)

   Abstract This paper describes a dataset mined from the public archive (1999–2020) of the US National Incident Management System Incident Status Summary (ICS-209) forms (a total of 187,160 reports for 35,170 incidents, including 34,478 wildland fires). This system captures detailed daily/regular information on incident development and response, including social and economic impacts. Most (98.4%) reports are wildland fire-related, with other incident types including hurricane, hazardous materials, flood, tornado, search and rescue, civil unrest, and winter storms. The archive, although publicly available, has been difficult to use for research due to multiple record formats, inconsistent data entry, and no clean pathway from individual reports to high-level incident analysis. Here, we describe the open-source, reproducible methods used to produce a science-grade version of the data, including formal connections made to other published wildland fire data products. Among other applications, this integrated and spatially augmented dataset enables exploration of the daily progression of the most costly, damaging, and deadly environmental-hazard events in recent US history. 

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