Tag Archives: model organisms


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/


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

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.

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.