Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases.

Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.

Update on Ebola Treatment Center Costs and Sustainability, United States, 2019.

We surveyed 56 Ebola treatment centers (ETCs) in the United States and identified costs incurred since 2014 ($1.76 million/ETC) and sustainability strategies. ETCs reported heavy reliance on federal funding. It is uncertain if, or for how long, ETCs can maintain capabilities should federal funding expire in 2020.

Cyberinfrastructure and resources to enable an integrative approach to studying forest trees.

Sequencing technologies and bioinformatic approaches are now available to resolve the challenges associated with complex and heterozygous genomes. Increased access to less expensive and more effective instrumentation will contribute to a wealth of high-quality plant genomes in the next few years. In the meantime, more than 370 tree species are associated with public projects in primary repositories that are interrogating expression profiles, identifying variants, or analyzing targeted capture without a high-quality reference genome. Genomic data from these projects generates sequences that represent intermediate assemblies for transcriptomes and genomes. These data contribute to forest tree biology, but the associated sequence remains trapped in supplemental files that are poorly integrated in plant community databases and comparative genomic platforms. Successful implementation of life science cyberinfrastructure is improving data standards, ontologies, analytic workflows, and integrated database platforms for both model and non-model plant species. Unique to forest trees with large populations that are long-lived, outcrossing, and genetically diverse, the phenotypic and environmental metrics associated with georeferenced populations are just as important as the genomic data sampled for each individual. To address questions related to forest health and productivity, cyberinfrastructure must keep pace with the magnitude of genomic and phenomic sampling of larger populations. This review examines the current landscape of cyberinfrastructure, with an emphasis on best practices and resources to align community data with the Findable, Accessible, Interoperable, and Reusable (FAIR) guidelines.

An update on US Ebola treatment center personnel management and training.

BACKGROUND: In 2014, 56 US hospitals were designated as Ebola treatment centers (ETCs). ETCs had minimum augmented capability requirements for Ebola virus disease care, including for staffing and training. We sought to identify current ETC staffing challenges and frequency of staff retraining. METHODS: In May 2019, an electronic survey was distributed to representatives of the 56 ETCs. RESULTS: Sixty-six percent (37/56) of ETCs responded. Registered nurses comprised the majority of ETC staff. All responding units required orientation training (average = 15.21 hours) and all but one required retraining. Among the top challenges that ETCs reported to maintaining high-level isolation capabilities were staff training time, staff recruitment, staff retention, and training costs. DISCUSSION: Five years after ETC designation, units face staffing challenges. Research is lacking on the effective number of hours and optimal frequency of staff training. ETCs reported smaller staffing teams compared to our 2016 assessment, but team composition remains similar. As units continue to maintain capabilities with decreasing external support and attention, the need for retraining must be balanced with logistical constraints and competing demands for staff time. CONCLUSIONS: Our study shows that US preparedness capabilities are reduced. More research, support, and funding are needed to sustain the unique knowledge and proficiency acquired by ETC teams to ensure domestic preparedness for highly hazardous communicable diseases.

Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment.

Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity.

Determining training and education needs pertaining to highly infectious disease preparedness and response: A gap analysis survey of US emergency medical services practitioners.

BACKGROUND: The Ebola virus disease outbreak highlighted the lack of consistent guidelines and training for workers outside of hospital settings. Specifically, emergency medical services (EMS) workers, who are frequently the first professionals to evaluate patients, often do not have advanced notice of patient diagnosis, and have limited time in their national curricula devoted to highly infectious disease (HID) identification and containment. All of these can place them at increased risk. To explore the depth of US EMS practitioners' HID training and education, a pilot gap analysis survey was distributed to determine where the aforementioned can be bolstered to increase occupational safety. METHODS: Electronic surveys were distributed to EMS organization members. The survey collected respondent willingness to encounter HID scenarios; current policies and procedures; and levels of knowledge, training, and available resources to address HIDs. RESULTS: A total of 2,165 surveys were initiated and collected. Eighty percent of frontline personnel were aware that their agency had an HID standard operating guideline. Almost 85% of respondents correctly marked routes of exposure for select HIDs. More than half of respondents indicated no maximum shift times in personal protective equipment. DISCUSSION: This research suggests EMS practitioners could benefit from enhanced industry-specific education, training, and planning on HID mitigation and management. CONCLUSION: Strengthening EMS preparedness in response to suspected or confirmed HID cases may not only improve patient outcomes, but also worker and community safety.

Growing and cultivating the forest genomics database, TreeGenes.

Forest trees are valued sources of pulp, timber and biofuels, and serve a role in carbon sequestration, biodiversity maintenance and watershed stability. Examining the relationships among genetic, phenotypic and environmental factors for these species provides insight on the areas of concern for breeders and researchers alike. The TreeGenes database is a web-based repository that is home to 1790 tree species and over 1500 registered users. The database provides a curated archive for high-throughput genomics, including reference genomes, transcriptomes, genetic maps and variant data. These resources are paired with extensive phenotypic information and environmental layers. TreeGenes recently migrated to Tripal, an integrated and open-source database schema and content management system. This migration enabled developments focused on data exchange, data transfer and improved analytical capacity, as well as providing TreeGenes the opportunity to communicate with the following partner databases: Hardwood Genomics Web, Genome Database for Rosaceae, and the Citrus Genome Database. Recent development in TreeGenes has focused on coordinating information for georeferenced accessions, including metadata acquisition and ontological frameworks, to improve integration across studies combining genetic, phenotypic and environmental data. This focus was paired with the development of tools to enable comparative genomics and data visualization. By combining advanced data importers, relevant metadata standards and integrated analytical frameworks, TreeGenes provides a platform for researchers to store, submit and analyze forest tree data.