High throughput datasets in SPELL now searchable based on topic

Data sets coming from high throughput experiments which reside in SPELL have now been updated with topics so that you can actually search by your favorite topic.  You can see the topic search options by clicking the button ‘Options for Filtering Results by Dataset Tags‘ on the SPELL home page under the search box  for Gene Name(s).

Check out the Eukaryotic Genomic Databases book!

The Eukaryotic Genomic Databases book has just been released by Springer (Editors: Kollmar, Martin) and contains detailed chapters related to the eukaryotic databases such as WormBase, FlyBase, the yeast databases, SGD and PomBase, etc. The chapters describe database contents and classic use-cases, which assist in accessing eukaryotic genomic data and encouraging comparative genomic research.

Include strain names in publications!

We urge you to explicitly state strains used in your experiments to foster reproducibility and to help WormBase biocurators get your results into WormBase.

 Historically, C. elegans researchers just stated the alleles used, based on the reasonable idea that all strains were close to Brenner’s N2.  As the years and hundreds of worm generations passed, strains diverged.  We usually don’t know the full genotype of our strains (and really won’t even with whole genome sequencing since copy number variation is often hard to detect). Including strain names will greatly help sort out any background effects that are realized later.

 We thus would like to see editors and reviewers (both anonymous and within the laboratory) help enforce the inclusion of strain names in C. elegans papers.

-Paul Sternberg