VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

Autor: Jamie Long, Sheena Shah Tomko, Susanne Warrenfeltz, Kristopher Lamoureux, Mary Ann McDowell, Brett Fox, Ulrike Böhme, Mark J Hickman, Steve Fisher, David Starns, George K. Christophides, Ana Barreto, Ann Sizemore Blevins, David S. Roos, Daniel Lawson, Lin Xu, Jie Zheng, John Judkins, Kristina Davis, Ryan Doherty, Jeremy D. DeBarry, Jaroslaw Nabrzyski, Lahcen I. Campbell, Samuel S. C. Rund, Evelina Y. Basenko, Beatrice Amos, Dave Falke, Mikkel B. Christensen, Stephanie Wever Schulman, Robert Wieck, Michael J. Dunn, Gareth Maslen, Mark X. Caddick, Haiming Wang, Robert Belnap, Wei Li, Christiane Hertz-Fowler, Achchuthan Shanmugasundram, Kathryn Crouch, Sarah A. Kelly, Wojciech Bażant, Sufen Hu, Bindu Gajria, Christian J. Stoeckert, Elizabeth Harper, Jay C. Humphrey, Jessica C. Kissinger, Paul A Wilkinson, Yikun Duan, Brian P. Brunk, John Brestelli, Matthieu Barba, Robert M. MacCallum, Kallie Lies, Omar S. Harb, Vasily Sitnik, Paul Flicek, Andrew M. Jones, Disha Lodha, Gloria I. Giraldo-Calderón, John Iodice, Danielle Callan, Drew Spruill, Cristina Aurrecoechea, Connor Howington, Dae Kun Kwon
Jazyk: angličtina
Rok vydání: 2022
Předmět:
Zdroj: NUCLEIC ACIDS RESEARCH
Nucleic Acids Research
Amos, B, Aurrecoechea, C, Barba, M, Barreto, A, Basenko, E Y, Bażant, W, Belnap, R, Blevins, A S, Böhme, U, Brestelli, J, Brunk, B P, Caddick, M, Callan, D, Campbell, L, Christensen, M B, Christophides, G K, Crouch, K, Davis, K, Debarry, J, Doherty, R, Duan, Y, Dunn, M, Falke, D, Fisher, S, Flicek, P, Fox, B, Gajria, B, Giraldo-Calderón, G I, Harb, O S, Harper, E, Hertz-Fowler, C, Hickman, M J, Howington, C, Hu, S, Humphrey, J, Iodice, J, Jones, A, Judkins, J, Kelly, S A, Kissinger, J C, Kwon, D K, Lamoureux, K, Lawson, D, Li, W, Lies, K, Lodha, D, Long, J, MacCallum, R M, Maslen, G, McDowell, M A, Nabrzyski, J, Roos, D S, Rund, S S C, Schulman, S W, Shanmugasundram, A, Sitnik, V, Spruill, D, Starns, D, Stoeckert, C J, Tomko, S S, Wang, H, Warrenfeltz, S, Wieck, R, Wilkinson, P A, Xu, L & Zheng, J 2022, ' VEuPathDB : The eukaryotic pathogen, vector and host bioinformatics resource center ', Nucleic Acids Research, vol. 50, no. D1 . https://doi.org/10.1093/nar/gkab929
ISSN: 0305-1048
Popis: The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC. The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.
Databáze: OpenAIRE
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