Comprehensive tutorials on the model organism databases ZFIN, SGD and PlantGDB and GBrowse, a model organism genome browser, enable researchers to quickly and effectively use these invaluable resources.
Seattle, WA September 15, 2008 — OpenHelix today announced the availability of new tutorial suites on several model organism resources including Zebrafish Information Network (ZFIN), Saccharomyces Genome Database (SGD) and the Plant Genome Database (PlantGDB) and also a tutorial using genome browsers with GBrowse. These four tutorials expand OpenHelix’s model organism database training which now also includes tutorials on MGI (mouse), FlyBase (drosophila), Gramene (grasses), RGD (rat), WormBase and more to come soon. Model organisms are integral to our understanding of basic biology and modern biomedical research. ZFIN is a collection of data, tools, and resources on the zebrafish (Danio rerio), a popular model organism for developmental biology and genetics research and SGD is a collection of data, tools and analyses centered around Saccharomyces cerevisiae, commonly known as bakers’ or budding yeast. PlantGDB is the primary resource for plant comparative genomics.
Additionally, OpenHelix has added a tutorial on GBrowse, a web application that allows you to explore genomic sequences together with annotated data. GBrowse is rapidly becoming the genomic browser of choice amongst model organism databases, because the browser is both universal and yet customizable.
The tutorial suites, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:
- to perform effective searches and understand the displays
- to access advanced searches enabling multifaceted queries
- to use the various databases of genes and markers, expression data, mutant genotype/phenotype details, ontologies, and more
- to investigate many related resources associated with ZFIN
- to navigate the SGD site, locate Basic and Advanced Search options, and use the site map to access additional search tools
- perform the two Basic SGD Quick and Text Search types and understand the displays
- to navigate the SGD Locus Page and access data from a variety of tools, tabs, and links
- to investigate many related resources associated with SGD
- to perform quick searches and navigate sequence pages
- to conduct BLAST searches across several plant species of your choice
- to create exon/intron gene predictions and sequence alignments
- to construct tables displaying highly varied information from many datasets
- the basic layout and search methods at GBrowse
- how to access detailed annotation data tied to genomic sequences
- how to select and customize annotations using Tracks
- how to upload and incorporate your own data or other external data sources
- take a tour of different GBrowse installations at model organism databases