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Effective URL: https://fungidb.org/fungidb/app
Submission: On November 03 via api from US — Scanned from DE
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Release 68 7 May 2024 My Strategies Searches Tools My Workspace Data About Help Contact Us Guest Login Register My Organism Preferences (331 of 331) enabled VEuPathDB is hosting a community meeting for the FungiDB users to discuss plans for the future and answer your questions. Date & time: Tuesday, November 12, at 10 AM EST/ 3 PM UTC Register: https://upenn.zoom.us/meeting/register/tJUud-6urz8qEtzfIT-X5axAXz7fTJmhj5_A SEARCH FOR... expand all | collapse all * Genes * Organisms * Popset Isolate Sequences * Genomic Sequences * Genomic Segments * SNPs * ESTs * Metabolic Pathways * Compounds OVERVIEW OF RESOURCES AND TOOLS Take a Tour Sustainability and Future Funding Getting Started Search Strategies Genome Browser Transcriptomic Resources Phenotypic Data Downloads How to Submit Data Curation and Annotation SUSTAINABILITY AND FUTURE DIRECTIONS VEuPathDB genomic databases will continue to provide bioinformatics services under a new organizational structure. For over 25 years, VEuPathDB has delivered bioinformatics solutions to research communities worldwide. We aim to establish a sustainable FAIR Access infrastructure that supports existing omics datasets and tools, as well as develop new tools and AI-driven approaches to enhance genome data and annotation. Our vision is not only to maintain established functionalities but also to improve, streamline, and expand resources by integrating cutting-edge data and tools in collaboration with researchers worldwide. Please complete a brief anonymous survey, helping us to understand VEuPathDB usage and its impact on your work, and guide plans for the future. Take the Survey Future outlook: New tool and feature development will be driven by the needs of all research communities we serve, and will rely on additional funding. The long term sustainability of VEuPathDB will likely involve a combination of grants, donations and service contracts. We strive for transparent and open communications, especially during this period of transition. Stay tuned for more information as we make progress. And please feel free to send us your thoughts via our Contact Us link or directly at help@veupathdb.org. Read More -------------------------------------------------------------------------------- TUTORIALS AND EXERCISES Grid view APOLLO: MANUAL GENE ANNOTATION Structural and functional community curation with Apollo, a real time collaborative genome annotation and curation platform * Functional annotation * Structural annotation * Unannotated Intron Junctions FINDING OLD GENE IDS Methods for finding the current version of old or retired gene IDs * Where's my gene? GENE PAGES Explore the data and images on gene pages * Gene Pages GENETIC VARIATION SNPs and CNV based on whole genome sequencing * Genetic Variation GENOME ANNOTATION Annotate your genome against a reference using Companion, an easy and reliable parasite genome annotation resource * Companion (Part 1) * Companion (Part 2) GENOME BROWSER Basic tutorial on how to effectively explore data in the genome browser including track selection and configuration * Genome browser basics GENOME BROWSER ADVANCED Self-led exercise on investigating genes models and structural annotations with RNA-seq expression data * RNA-Seq data & gene models GO ENRICHMENT Run a GO enrichment on a set of genes from a fold change RNA-Seq search * GO Enrichment HOST RESPONSE Explore host responses by building a search strategy in HostDB * Host Response (HostDB) MAPVEU use the map to visualize, search, and analyze field-collected data including insecticide resistance (phenotypes and genotypes), population abundance, pathogen infection status, and blood meal source among others * Introduction to the new MapVeu * Legacy MapVEu (intro) * Additional features of legacy MapVEu METABOLIC PATHWAYS Learn to use metabolic pathway searches and visualization tools * Metabolic Pathways ORTHOLOGY PHYLETIC PATTERNS Leverage the transform by orthology tool, orthology tables on gene pages, OrthoMCL, and the phyletic pattern search * Orthology and Phyletic Patterns ORTHOMCL TUTORIAL Learn standard searches and ortholog group analysis within the OrthoMCL website * OrthoMCL tutorial REGULAR EXPRESSIONS & COLOCATION Use regular expressions to identify protein or DNA patters. Use the colocation tool to identify DNA segments based on their relative location on the genome * Motifs, domains and regular expressions * Regular expressions & genomic colocation SEARCH STRATEGIES (BASICS) Run basic searches, extend them into strategies, and explore search results * Search Strategies (Basics) * Search Strategies -with explanations SEARCH STRATEGIES (ADVANCED) Integrate diverse data types and leverage orthology or phylogenetic profiling * Search Strategies (Advanced) SINGLE CELL RNA SEQ Explore single cell RNA Seq data in cellxgene and compare to bulk RNA Seq data * scRNA-Seq SITE SEARCH Explore site search and learn how to filter your results or export them to a search strategy * Site Search TRANSCRIPTOMICS AND PROTEOMICS Explore searches that return genes based on expression evidence from RNA-Seq, microaray and proteomics searches * Transcriptomics searches * Proteomics searches NEW EXERCISES AND TUTORIALS WILL BE ADDED REGULARLY We continue to expand our repertoire of exercises on a regular basis. Visit this section regularly to explore new training material * -------------------------------------------------------------------------------- NEWS FUNGIDB 68 RELEASED Tue May 07 2024 We are pleased to announce the release of FungiDB 68. Release 68 Webinar Join us on Thursday May 23rd, 2024 at 10 am Eastern for our Release 68 Highlights webinar where we will demons... read more FUNGIDB 67 RELEASED Wed Feb 21 2024 We are pleased to announce the release of FungiDB 67. Release 67 Webinar Join us on Thursday Feb 29th, 2024 at 10 am Eastern for our Release 67 Highlights webinar where we will demons... read more FUNGIDB 66 RELEASED Tue Nov 28 2023 We are pleased to announce the release of FungiDB 66. Release 66 Webinar Join us on Thursday Dec 14th, 2023 at 10 am Eastern for our Release 66 Highlights webinar where we will demons... read more FUNGIDB 65 RELEASED Thu Sep 14 2023 We are pleased to announce the release of FungiDB 65. Release 65 Webinar Join us on Thursday Sept 21st, 2023 at 10 am Eastern for our Release 65 Highlights webinar where we will demon... read more FUNGIDB 64 RELEASED Wed Jul 12 2023 We are pleased to announce the release of FungiDB 64. Release 64 Webinar Join us on Thursday July 20th, 2023 at 10 am Eastern for our Release 64 Highlights webinar where we will demon... read more FUNGIDB 63 RELEASED Wed May 03 2023 We are pleased to announce the release of FungiDB 63. Release 63 Webinar Join us on Thursday May 11th, 2023 at 10 am Eastern for our Release 63 Highlights webinar where we will demons... read more FUNGIDB 62 RELEASED Thu Mar 09 2023 We are pleased to announce the release of FungiDB 62. Release 62 Webinar Join us on Thursday March 16, 2023 at 10 am Eastern for our Release 62 Highlights webinar where we will demons... read more FUNGIDB 61 RELEASED Thu Dec 15 2022 We are pleased to announce the release of FungiDB 61. Release 61 Webinar Join us on Wednesday December 21st, 2022 at 10am EST for our Release 61 Highlights webinar where we will demon... read more FUNGIDB 60 RELEASED Wed Nov 09 2022 We are pleased to announce the release of FungiDB 60. Release 60 Webinar Join us on Thursday November 17th, 2022 at 10am EST for our Release 60 Highlights webinar where we will demons... read more FUNGIDB 59 RELEASED Tue Aug 30 2022 We are pleased to announce the release of FungiDB 59. Release 59 Webinar Join us on Thursday September 15th, 2022 at 10am EDT for our Release 59 Highlights webinar where we will demon... read more FUNGIDB 58 RELEASED Thu Jun 23 2022 We are pleased to announce the release of FungiDB 58. Annual VEuPathDB Workshop (Virtual) The 15th Annual VEuPathDB workshop will be a virtual event taking place daily on September 6 - 9... read more FUNGIDB 57 RELEASED Thu Apr 21 2022 We are pleased to announce the release of FungiDB 57. Release 57 Webinar Join us on Thursday April 28th, 2022 at 10am EDT for our Release 57 Highlights webinar where we will demonstra... read more FUNGIDB 56 RELEASED Tue Feb 15 2022 We are pleased to announce the release of FungiDB 56. Release 56 Webinar Join us on Thursday February 24th, 2022 at 10am EDT for our Release 56 Highlights webinar where we will demons... read more FUNGIDB 55 RELEASED Thu Dec 02 2021 We are pleased to announce the release of FungiDB 55. Free online workshop Free 4-day virtual VEuPathDB workshop: December 13-16, 2021, 9AM-1PM US Eastern time. Preliminary schedule is... read more NEW VERSION OF VEUPATHDB GALAXY Fri Oct 08 2021 We are pleased to announce a new release of the VEuPathDB Galaxy website at https://veupathdb.globusgenomics.org. It includes an updated version of the Galaxy software, which improves the... read more FUNGIDB 54 RELEASED Wed Sep 08 2021 We are pleased to announce the release of FungiDB 54. Another way to stay in touch: The bioinformatic resource centers have established a Reddit community for free and open discussion... read more FUNGIDB 53 RELEASED Wed Jul 21 2021 We are pleased to announce the release of FungiDB 53. Another way to stay in touch: The bioinformatic resource centers have established a Reddit community for free and open discussion... read more FUNGIDB 52 RELEASED Thu May 20 2021 We are pleased to announce the release of FungiDB 52. Release 52 Webinar Join us on May 27, 2021 at 10am EDT for our Release 52 Highlights webinar where we will demonstrate and discus... read more FUNGIDB 51 RELEASED Tue Mar 16 2021 We are pleased to announce the release of FungiDB 51 . Release 51 Webinar Join us on March 31, 2021 at 10am EDT for our Release 51 Highlights webinar where we will demonstrate and dis... read more FUNGIDB 50 RELEASED Thu Dec 17 2020 We are pleased to announce the release of FungiDB 50. The URL https://FungiDB.org directs you to the newest version of our interface. The site contains all previous data plus some new tools an... read more FUNGIDB 49 RELEASED Thu Nov 05 2020 We are pleased to announce the release of FungiDB 49. The URL https://FungiDB.org directs you to the newest version of our interface. The site contains all previous data plus some new tools an... read more FUNGIDB 48 RELEASED Thu Aug 27 2020 We are pleased to announce the release of FungiDB 48. Beginning with FungiDB 48, the URL https://FungiDB.org directs you to the newest version of our interface. The site contains all previou... read more FUNGIDB 47 RELEASED Wed May 27 2020 We are pleased to announce the release of FungiDB 47. The product of 6 months of back-end infrastructure work, Release 47 includes beta.fungidb.org in addition to our legacy sites. The beta ... read more FUNGIDB 46 RELEASED Wed Nov 06 2019 We are pleased to announce the release of FungiDB 46 Release 46 Webinar Join us on December 3, 2019 at 10:00 am (EST) for our Release 46 Highlights webinar where we will di... read more FUNGIDB 45 RELEASED Thu Sep 05 2019 We are pleased to announce the release of FungiDB 45 Release 45 Webinar Join us on September 11, 2019 at 10:00 am (EST) for our Release 45 Highlights webinar where we will ... read more FUNGIDB 44 RELEASED Tue Jul 02 2019 We are pleased to announce the release of FungiDB 44 Release 44 Webinar Join us on Tuesday July 16th at 10:00 am (EST) for our Release 44 Highlights webinar where we will d... read more FUNGIDB 43 RELEASED Thu Apr 25 2019 We are pleased to announce the release of FungiDB 43 Release 43 Webinar Join us on May 15th at 10:00 am (EST) for our Release 43 Highlights webinar where we will discuss an... read more FUNGIDB 42 RELEASED Thu Mar 07 2019 We are pleased to announce the release of FungiDB 42 Release 42 Webinar Join us on March 20, 2019 10:00-11:00 AM EDT for our Release 42 Highlights webinar where we will dis... read more FUNGIDB 41 RELEASED Thu Dec 13 2018 We are pleased to announce the release of FungiDB 41 New data in FungiDB 41 Genome Sequence and Annotation: these annotated genomes appear for the fi... read more FUNGIDB 40 RELEASED Mon Oct 15 2018 We are pleased to announce the release of FungiDB 40. FungiDB 40 represents a software and features release. New features in FungiDB 40 New Sense/Antisense ... read more FUNGIDB 39 RELEASED Thu Aug 30 2018 We are pleased to announce the release of FungiDB 39 New data in FungiDB 39 Genome Sequence and Annotation: these annotated genomes appear for the fi... read more FUNGIDB 38 RELEASED Thu Jul 05 2018 We are pleased to announce the release of FungiDB 38 New data in FungiDB 38 Genome Sequence and Annotation: these annotated genomes appear for the fi... read more FUNGIDB 37 RELEASED Wed Apr 25 2018 We are pleased to announce the release of FungiDB 37 New data in FungiDB 37 Genome Sequence and Annotation: these annotated genomes ... read more FUNGIDB 36 RELEASED Mon Feb 19 2018 We are pleased to announce the release of FungiDB 36 New data in this release Genome Sequence and Annotation: these annotated genomes appear for the ... read more FUNGIDB 35 RELEASED Fri Dec 01 2017 We are pleased to announce the release of FungiDB 35 New data in this release Genome Sequence and Annotation: these annotated genomes appear for the first tim... read more FUNGIDB 34 RELEASED Thu Sep 07 2017 We are pleased to announce the release of FungiDB 34 New data in this release Genome Sequence and Annotation: these annotated genomes appear for the first tim... read more INTERPRETING RNA SEQ EXPRESSION VALUES Sun Aug 20 2017 In the transcriptomics section of gene pages, expression graphs display FPKM or RPKM values determined from uniquely aligned reads (those that align to ... read more FUNGIDB 33 RELEASED Fri Jun 30 2017 We are pleased to announce the release of FungiDB 33 New data in this release Genome Sequence and Annotation: these annotated genomes appear for the first tim... read more FUNGIDB 32 RELEASED Wed Apr 19 2017 We are pleased to announce the release of FungiDB 32 New data in this release Proteomics: Stage specific proteome [strain CEA10] &nda... read more FUNGIDB 31 RELEASED Wed Mar 08 2017 We are pleased to announce the release of FungiDB 31 New data in this release Annotated Genomes: Fusarium fujikuroi strain IMI 58289 &... read more EUPATHDB IS HIRING Tue Feb 21 2017 The Eukaryotic Pathogen Database resource (EuPathDB.org) is a large, multi-institution project that develops scientific data-mining websites ... read more FUNGIDB 30 RELEASED Fri Feb 03 2017 We are pleased to announce the release of FungiDB 30 New data in this release Genomes: The following annotated genomes appear for the first time in FungiDB. ... read more FUNGIDB 29 RELEASED Thu Oct 13 2016 We are pleased to announce the release of FungiDB 29 FungiDB 29 FungiDB 29 represents extensive efforts to improve navigation and data accessibility on reco... read more FUNGIDB 28 RELEASED Wed Mar 30 2016 We are pleased to announce the release of FungiDB 28 New data in this release The data set title below links to a full description and list of associated searches an... read more FUNGIDB 27 RELEASED Fri Feb 19 2016 We are pleased to announce the release of FungiDB 27 New data in this release The data set title below links to a full description and list of associated searches an... read more EUPATHDB OUTREACH POSITION Wed Nov 18 2015 Community Outreach Specialist The Eukaryotic Pathogen Database resource (EuPathDB.org) seeks to hire a community outreach specialist with a focus on fungal biology. The out... read more FUNGIDB 26 RELEASED Thu Oct 15 2015 We are pleased to announce the release of FungiDB 26 New data in this release The data set title below links to a full description and list of associated searches and GBrowse... read more FUNGIDB 25 RELEASED Thu Jul 23 2015 We are pleased to announce the release of FungiDB 25 New data in this release The data set title below links to a full description and list of associated searches and GBrowse... read more FUNGIDB 24 RELEASED Mon Apr 13 2015 We are pleased to announce the release of FungiDB 24 All EuPathDB release numbers have been synchronized to help us more efficiently manage our expanding n... read more FUNGIDB 3.2 RELEASED Fri Mar 06 2015 We are pleased to release FungiDB 3.2. This release include the following new data and features. New Data: Genomes ... read more LETTER TO THE EUPATHDB COMMUNITY Thu Feb 19 2015 Dear colleagues - We are writing to provide an update on the Eukaryotic Pathogen Genomics Resource (EuPathDB.org), which many hundreds of laboratories wrote to support... read more OPEN LETTER TO THE ASPERGILLUS RESEARCH COMMUNITY Wed Feb 11 2015 An open letter to the Aspergillus research community on genome database resources: As many of you may already be aware, the NIH R01 research grant that has supported devel... read more FUNGIDB 3.1 RELEASED Thu Sep 18 2014 FungiDB 3.1 is released this month. Updates 14 RNA-Seq datasets are added for a total of 22 datasets. 2 Microarray datasets are now available. Corrections SC25 of Cryptococcus gattii R265 - SC25 ... read more FUNGIDB 3.0 RELEASED Tue May 13 2014 This release of FungiDB 3.0 adds 12 new genomes for a total of 64 in the database. New species include: Aspergillus niger CBS 513.88 Aspergillus aculeatus ATCC 16872 Candida glabrat... read more FUNGIDB 2.3 RELEASED Fri May 31 2013 FungiDB 2.3 is released this month. The total genomes included in the release is now 52. New genomes included in this release include Botrytis cinerea Sclerotinia sclerotiorum Asper... read more FUNGIDB 2.1 RELEASED Mon Nov 12 2012 FungiDB 2.1 is released and includes 39 Fungal genomes from Ascomycota, Basidiomycota, and Mucormycotina (Zygomycota) and 6 genomes of Oomycetes. This release builds on the 2.0 release from Augus... read more 2.0 RELEASED Wed Aug 01 2012 The 2.0 release, with 31 genomes including 6 Oomycetes was released at fungidb.org.The release includes improved view of the lists of species, links to OrthoMCL, inclusion of Microarray and RNA-Seq... read more 2.0 ALPHA RELEASED Thu Jan 19 2012 The 2.0 alpha release, with 8 genomes, from 5 Cryptococcus, Tremella mesenterica, Neurospora crassa, and Saccharomyces cerevisiae were released at alpha.fungidb.org. This is a pre-release using new... read more ANNOTATING GENES IN FUNGIDB Tue May 03 2011 A short blog post at the Hyphal Tip is up to demonstrate how comment pages can be used to add annotation for a gene record page. This is useful way to allow community annotation, registering of gen... read more FUNGIDB 1.0 BETA Mon Mar 14 2011 We are pleased to announce the release of FungiDB 1.0 beta This release of FungiDB includes 18 genomes of 17 species of Fungi in Ascomycete, Basidiomycete, and Zygomycota The following Funga... read more See all news Warning: If our Twitter/X timeline is not displaying, you may need to log into Twitter/X or alter your browser security settings. Tweets by FungiDB Warning: If our Twitter/X timeline is not displaying, you may need to log into Twitter/X or alter your browser security settings. Tweets by VEuPathDB News and Tweets VEuPathDB makes genomic, phenotypic, and population-centric data accessible to the scientific community. FungiDB provides support for these organisms. This project is funded by the Fund for Advancement of Science and Medicine, Open Philanthropy and the Chan Zuckerberg Initiative, with additional support from the Universities of Pennsylvania and Georgia and the Wellcome Trust (Resource Grants 212929 & 218288). https://veupathdb.org https://amoebadb.org https://cryptodb.org https://fungidb.org https://giardiadb.org https://hostdb.org https://microsporidiadb.org https://piroplasmadb.org https://plasmodb.org https://toxodb.org https://trichdb.org https://tritrypdb.org https://vectorbase.org https://orthomcl.org https://clinepidb.org https://microbiomedb.org ©2024 The VEuPathDB Project Team This website requires cookies & limited processing of your personal data in order to function properly. By clicking any link on this page you are giving your consent to this as outlined in our Privacy Policy. I agree, close this banner.