Just Launched!! New tripal site

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Just Launched!! New tripal site

Sofia Robb


Check out our new tripal site. It is a companion site to a publication about embryonic development of the planarian, Schimdtea mediterranea. Embryonic origin of adult stem cells required for tissue homeostasis and regeneration

I am excited and proud of our accomplishments. I cut and paste and hacked and hobbled my way to getting this put together. Hopefully with more practice and time my work under the hood will become more sophisticated and my web design more elegant. But, by golly it works!! 

Fun features:
  • Our Glossary of Ontology Terms 
    • we created ontology terms for developmental stages and anatomy. We are in the process of getting the terms submitted to OBO to be incorporated into the composite metazoan collection of terms at uberon.
  • Term pages that display the ontology tree. See Eye
  • Expression module displays the RPKMs across developmental stages of a gene. see opsin, then go to Expression pane
  • Integration of CV terms with images
  • Gene Search page. 
    • Customized the Main lab search module materialized view to work with my search needs. Created a drupal view that searches the materialized view table to display the results 
    • Generated sparklines with the expression data
      • created a materialized view with feature_id,name,signal values
      • use javascript (jquery.sparkline) to generate plot (drupal module views_php) 
  • we also use the tripal blast ui and the tripal blast and interproscan analysis modules

I would like to create some sharable modules for some of these features, like loading of my images and associated cvterms into chado. I should explore using the chado loader. 

I looked at some of the ontology modules/APIs but I could not figure out how to use them, so i wrote code to query chado to display my ontology tables and trees.

I also need to change my gene search view download of fasta and csv to use the tripal download api. ( i think i forgot the syntax to use within the view :/ )


- Sofia





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