Tag Archives: drosophila

Tip of the Week: FlyBase


I have a soft spot for Flybase. My Ph.D. work used Drosophila and I’ve used Drosophila species to teach after that. Something about Dipteran  genetics fascinates me. FlyBase is also one of the older genetics and genomics databases and we’ve got a tutorial on it. Today’s tip is their 12 minute video of FlyBase for Undergrads. One of the things I always believed is that the databases and analysis tools we train on and come across in our daily work are excellent places for teaching and learning genomics for undergraduates. Lots of data and lots of analysis that would make very interesting projects and experiences that an undergraduate could do.

Today’s video starts off with a kind of silly live-action sequence :D, but fun silly, and walks through FlyBase on an introductory level. Check it out.

They have a  youtube channel with two additional (and much shorter) videos on using TermLink, a controlled vocabulary search tool, and an introduction to Fast-Track, a community paper curation tool.

 

New Online Tutorials on FlyBase, WormBase and Mouse Genome Informatics (MGI) Resources

Comprehensive tutorials on the model organism bioinformatics databases FlyBase, WormBase and MGI enable researchers to quickly and effectively use these invaluable resources.

OpenHelix today announced the availability of new tutorial suites on several model organism resources including FlyBase, WormBase and an update on the Mouse Genome Informatics (MGI) database. Model organisms are integral to our understanding of basic biology and modern biomedical research. Drosophila, C. elegans and mice are three highly researched model organisms. FlyBase and WormBase are the primary resources for molecular and genetic information on the Drosophilidae and on Caenorhabditis elegans and related species, respectively. MGI is a series of tools and databases that integrate genetics, genomics and biology for the laboratory mouse.

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 Quick Searches and navigate gene summary pages
  • browse genetic features within the context of the entire chromosome
  • construct complex queries across various sets of data stored within FlyBase, WormBase or MGI
  • perform nucleotide or amino acid sequence homology searches
  • output data in various formats, or access large data reports
  • investigate many related resources associated with MGI

To find out more about these and other tutorial suites visit OpenHelix.

Finding Flies

I finally got around to reading last month’s Nature paper on the genomic sequence of 12 Drosophila species. In addition to being genomics research (which is my field now :), it is also looking at 12 of the couple dozen species I studied for my Ph.D. (though I was only looking at the evolution of R1 & R2 retroposons in arthropods).Interesting paper, and I might go into it more in depth later (what genomics means and doesn’t mean for evolutionary studies).

But I did get to thinking, where would I go to browse and search the genomic sequence data for these 12 species ( hey, I might want to recreate my work, though the Eickbush lab already has.. and extended). Of course there are the two browsers mentioned in the paper ;-), Flybase and UCSC Genome Browser, though UCSC doesn’t include D. willistoni as I write this. I checked the other two major general genome browsers, as opposed to species or taxa specific: Ensembl and NCBI’s MapViewer. Continue reading