Tag Archives: flybase

support_MODs

Video Tip of the Week: FlyBase TV, and a letter of support for model organism communities

This week’s video tip was prompted by a couple of things. First, it was a tweet from FlyBase, about their video channel. It’s been a while since we’d done a FlyBase Tip of the Week, so that was enough of a reason.

But it also came just after I was thinking about the importance of the model organisms, based on the campaign by the model organism databases to save their funding. Here’s a tweet from the yeast genome database (SGD) with a plea:

But this letter cites yeast, flies, WormBase, ZFIN, MGI, RGD and Gene Ontology as well.

mergeI have a soft spot for model organisms, not only because of the tremendous amount of great biology they’ve provided. I was a postdoc at The Jackson Lab, and I am acutely aware of how crucial it is to have the depth of the species specialists involved in creating and maintaining the resources that are appropriate for their organism. But it’s more than just institutional knowledge and data, of course. It’s also the importance of the community of researchers working on that organism, supporting them and having their needs met in many ways with species-specific resources.

So this week’s tip highlights some features of the FlyBase tools, as a way to remind folks of the great work that’s going on at model organism databases (MODs).

Now, if you haven’t already done so, please consider signing on to the letter of support for these databases. You can read more about the issue over at the site, but briefly:

NHGRI/NIH has recently advanced a plan in which the MODs will be integrated into a single combined database, along with a 30% reduction in funding for each MOD (see also these Nature and Science news stories). While increased integration will present many advantages, the plan will result in a loss of critical organism-specific datasets. The funding cut will also cripple core functions such as high quality literature curation and genome annotation, degrading the utility of the MODs. Given the large number of scientists that this policy change would affect and the importance of their work, this is a matter of extreme concern.

I have always shouted about the importance of high-quality curation. It’s so undervalued, but it’s only more and more crucial now that we are getting so much sequence data and we need the best existing knowledge to help guide us through it. Now is not the time to cut back on curation.

So if you have valued MOD data and community sites, please consider signing on to the letter of support.

Quick links:

FlyBase:  http://flybase.org/

Support Model Organism Databases letter: http://www.genetics-gsa.org/MODSupport/

References:

Hayden, Erica Check. “Funding for model-organism databases in trouble.” Nature News. () DOI: 10.1038/nature.2016.20134

Kaiser, Jocelyn. “Funding for key data resources in jeopardy.” Science 351.6268 (2016): 14-14. DOI: 10.1126/science.351.6268.14

Attrill, Helen, et al. “FlyBase: establishing a Gene Group resource for Drosophila melanogaster.” Nucleic acids research (2015): gkv1046. DOI: 10.1093/nar/gkv1046

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Friday SNPpets

This week’s SNPpets include stories about the FlyBase memoriam for Bill Gelbart, Phenolyzer for gene discovery from phenotypes, tissue- and tumor-PPI comparison, Beacon, shotgun metagenomics, the future decade in genomics, no-so-scary personal genome sequencing and apps for it, DNA-barcoded beer, and more.


Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


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.

 

Pointing us out at Genome.gov :)

ohonnhgripageNHGRI recently pointed out our new set of tutorials on model organism databases (funded mainly by NHGRI :) on their home page, genome.gov. Always nice to be recognized :D.

And it gives me the opportunity to again point out that we do indeed have seven publicly available tutorials and training materials (slides, exercises, etc) on model organism databases including SGD, RGD, MGI, WormBase, FlyBase and ZFIN… and a seventh on GBrowse, a generic genome browser used by some of these and other genome databases.

Check them out (and fill out the new poll to the left :D.

Tip of the Week: Converting genome coordinates

galaxylift_thumbEvery so often we get asked how to convert genomic coordinates from an earlier assembly to a later one, or even between genomes. There are several online locations to do this. In this tip of the week, I’m going to introduce you to Galaxy’s Liftover tool and point out too that UCSC Genome Browser and Flybase have similar tools (as do others I’m sure, know of any?). With this tool, you can take your coordinates and easily convert them to coordinates of a later assembly. Btw, Galaxy is a great analysis tool.

Tip of the Week: Model Organism Database tutorials

gbrowseFor the tip of the week today, we’d like to point out a number of new (free to you) tutorials on model organism database resources. These seven tutorials (include flash movie tutorial, slides for downloading, exercises and handouts) were partly funded by a NHGRI grant. We just put out a press release on this, but I thought the Tip of the Week would be a great place to introduce you to these tutorials. We have seven tutorials that are (or will soon be) publicly available (this link takes you to a list and links to all these tutorials). The first four available are on GBrowse, WormBase, RGD (Rat Genome Database) and MGI (Mouse Genome Informatics. GBrowse (the tutorial linked to here), was developed by the Generic Model Organism Database (GMOD) project and is a great tool to develop genome browsers for model and research organisms. Many model organism databases use GMOD resources in full or part, including many of the ones we have tutorials on here. Three more will be coming very soon on ZFIN (Zebrafish), FlyBase (Drosophila) and SGD (yeast). Check them out :).

Free Tutorials on Model Organism Genomic Databases Released by OpenHelix

OpenHelix today announced the free availability of tutorial suites on model organism databases and resources used extensively in research. The first tutorial suites available are GBrowse, Rat Genome Database (RGD), Mouse Genome Informatics (MGI), and WormBase. To be added in the coming weeks are Zebrafish Information Network (ZFIN), FlyBase and Saccharomyces (Yeast) Genome Database (SGD).

The tutorial suites, funded in part by a grant from the National Human Genome Research Institute of the National Institutes of Health, include a self run, narrated tutorial introducing the resource and how to use its feature and functions. Each suite also includes PowerPoint slides, handouts, and exercises that can be used for reference or for training others.

One of the first tutorials available is on GBrowse, developed by the Generic Model Organism Database (GMOD) project, a popular tool used by researchers to develop genome browsers for model organisms, species of interest, and particular topics. By learning how to use this “generic” genome browser, you can leverage that knowledge to use dozens of resources devoted to a wide range of research areas.

“The OpenHelix GBrowse user tutorial is very well done and will be an excellent resource for the many research communities that use GBrowse to visualize genomic data,” said Dave Clements of the National Evolutionary Synthesis Center who runs the GMOD help desk.

Model organisms, such as yeast, mouse, rat, flies, and many others, have long been used by researchers to expand our understanding of biology and to assess the effectiveness and safety of therapies before going to human trial. Many of the genomes of these organisms have been completely sequenced, giving the scientific community even greater insight into the organisms and their relation to human biology. The genome data is now available and searchable on publicly available online databases and resources.

You can view the Model Organism tutorials at http://www.openhelix.com/model_organisms.shtml. OpenHelix provides over 60 other tutorial suites on a number of genomic databases and resources through an individual, group, or institutional subscription. Further information can be found at www.openhelix.com.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

How to pick a genome database platform

I was reading a newsletter I get from Biotechniques, and their WebWatch often has some fun items. (You may need to get a free login to see the WebWatch.) This week they referred to the MaizeGDB database in the post Amaizing Base. Although I had been aware of MaizeGDB before, it was a nice reminder to go over and have a look to see what’s new.

When I went over there I was intrigued by the new browser they are about to launch (in mid-October). The link says “coming soon” and I went to check out the information there.

Currently that link goes to a page that describes their move to a more sequence-centric representation of their data. It was a fascinating look at their decision process to move to a new browser platform and what they decided to do. For database geeks like me, seeing their ranking of the importance of various features was very compelling.

And what they decided? GBrowse!

We have a tutorial available on GBrowse. Usually we do tutorials on specific sites, but as we kept seeing GBrowse over and over at different sites we created a tutorial for that. It helps me to understand the underlying basic browser when I visit any site that employs it. Even though the wrappings and the data types will vary at different sites, understanding how it works makes it much easier to use at any new site that uses it. HapMap, MGI, WormBase, FlyBase, TAIR, Watson’s personal genome, and a whole bunch of other sites use the GBrowse software.

Looking forward to checking out the MaizeGDB GBrowse version when it launches!

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