Generating Priorities for EchinoBase Re-design

As part of the work of upgrading Echinobase, one task is to change the interface / landing page. We are seeking feedback about the web interface. Anything that it currently used by Xenbase will be straightforward to adopt in Echinobase, but other features are also possible.

Goal: To prepare an priority list of features for the web interface for Echinobase.

Please have a look at and leave us feedback. As you do, think about specific features that you like as well as features that you do not like about the site. Also consider ways you might improve Echinobase based on design choices you find there. Your feedback could include, but should not be limited to, things such as:

  • Autofill options for gene names etc in search boxes
  • I like the layout, with links on the homepage and not in tabs on the top
  • Section for protocols/reagents on homepage
  • Blast feature with species selection on tile on main page
  • Gene expression search
  • Want to see peaks not just bars on ATAC-seq etc in Jbrowse
  • The homepage is too busy, a balance of information would be helpful
  • Currently echinobase is too urchin centric
  • There are too many choices under each of the species on the current site
  • Images/drawings/fate maps of embryos
  • etc

Please have a look and send us feedback, either through the comment form below (now closed) or by using the website contact form. We appreciate your thoughtful contributions to improving this resource!


BLAST function needs a revamp
Currently, it is very difficult to pull out your sequences.
for example, you can BLAST an mRNA from purpuratus against the L.variegatus genome, but then it is almost impossible to pull the blasted sequence result directly out, outside of trying to clunkily type the scaffold numbers into jBrowse, which is tremendously confusing at times.

Fix broken links, there are lots of dead links, or regions of text with things that should be hyperlinked and they are not

What are the RNA-seq sequences from? Gonads? embryos? specific stages?

L. variegatus and P. miniata data is really sparse and difficult to navigate

The Echinoderm community could find great value in a section present in Xenbase on Reagents and Protocols. Useful technical advances and tested reagents often take many months to be disseminated by publication, if at all, whereas Echinobase should be able to list these advances promptly. Curating is not trivial, I understand, but a link of the advancement to the investigator would make this site a priority.

The mRNA in situ hybridization, litereature, and immunohistochemistry filters for gene expression search on Xenbase would be great to have on Echinobase.